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Kassab MA, Chen Y, Wang X, He B, Brown EJ, Yu X. RNA 2'-O-methylation promotes persistent R-loop formation and AID-mediated IgH class switch recombination. BMC Biol 2024; 22:151. [PMID: 38977974 PMCID: PMC11232215 DOI: 10.1186/s12915-024-01947-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/26/2024] [Indexed: 07/10/2024] Open
Abstract
BACKGROUND RNA-DNA hybrids or R-loops are associated with deleterious genomic instability and protective immunoglobulin class switch recombination (CSR). However, the underlying phenomenon regulating the two contrasting functions of R-loops is unknown. Notably, the underlying mechanism that protects R-loops from classic RNase H-mediated digestion thereby promoting persistence of CSR-associated R-loops during CSR remains elusive. RESULTS Here, we report that during CSR, R-loops formed at the immunoglobulin heavy (IgH) chain are modified by ribose 2'-O-methylation (2'-OMe). Moreover, we find that 2'-O-methyltransferase fibrillarin (FBL) interacts with activation-induced cytidine deaminase (AID) associated snoRNA aSNORD1C to facilitate the 2'-OMe. Moreover, deleting AID C-terminal tail impairs its association with aSNORD1C and FBL. Disrupting FBL, AID or aSNORD1C expression severely impairs 2'-OMe, R-loop stability and CSR. Surprisingly, FBL, AID's interaction partner and aSNORD1C promoted AID targeting to the IgH locus. CONCLUSION Taken together, our results suggest that 2'-OMe stabilizes IgH-associated R-loops to enable productive CSR. These results would shed light on AID-mediated CSR and explain the mechanism of R-loop-associated genomic instability.
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Affiliation(s)
- Muzaffer Ahmad Kassab
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA.
- Present address: Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Yibin Chen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
- Present address: Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Xin Wang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
- Present address: Westlake University, Hangzhou, Zhejiang, P. R. China
| | - Bo He
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
- Present address: Division of Cellular and Developmental Biology, Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94705, USA
| | - Eric J Brown
- Present address: Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Xiaochun Yu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA.
- Present address: Westlake University, Hangzhou, Zhejiang, P. R. China.
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2
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Liu Y, Zhou J, Li X, Zhang X, Shi J, Wang X, Li H, Miao S, Chen H, He X, Dong L, Lee GR, Zheng J, Liu RJ, Su B, Ye Y, Flavell RA, Yi C, Wu Y, Li HB. tRNA-m 1A modification promotes T cell expansion via efficient MYC protein synthesis. Nat Immunol 2022; 23:1433-1444. [PMID: 36138184 DOI: 10.1038/s41590-022-01301-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 08/04/2022] [Indexed: 02/04/2023]
Abstract
Naive T cells undergo radical changes during the transition from dormant to hyperactive states upon activation, which necessitates de novo protein production via transcription and translation. However, the mechanism whereby T cells globally promote translation remains largely unknown. Here, we show that on exit from quiescence, T cells upregulate transfer RNA (tRNA) m1A58 'writer' proteins TRMT61A and TRMT6, which confer m1A58 RNA modification on a specific subset of early expressed tRNAs. These m1A-modified early tRNAs enhance translation efficiency, enabling rapid and necessary synthesis of MYC and of a specific group of key functional proteins. The MYC protein then guides the exit of naive T cells from a quiescent state into a proliferative state and promotes rapid T cell expansion after activation. Conditional deletion of the Trmt61a gene in mouse CD4+ T cells causes MYC protein deficiency and cell cycle arrest, disrupts T cell expansion upon cognate antigen stimulation and alleviates colitis in a mouse adoptive transfer colitis model. Our study elucidates for the first time, to our knowledge, the in vivo physiological roles of tRNA-m1A58 modification in T cell-mediated pathogenesis and reveals a new mechanism of tRNA-m1A58-controlled T cell homeostasis and signal-dependent translational control of specific key proteins.
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Affiliation(s)
- Yongbo Liu
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Zhou
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Xiaoyu Li
- Department of Biochemistry and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoting Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Jintong Shi
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xuefei Wang
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hao Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Shan Miao
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huifang Chen
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Chongqing International Institute for Immunology, Chongqing, China
| | - Xiaoxiao He
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liting Dong
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Gap Ryol Lee
- Department of Life Science, Sogang University, Seoul, Republic of Korea
| | - Junke Zheng
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ru-Juan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Bing Su
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Youqiong Ye
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA. .,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA.
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China. .,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China. .,Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
| | - Yuzhang Wu
- Chongqing International Institute for Immunology, Chongqing, China.
| | - Hua-Bing Li
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,Chongqing International Institute for Immunology, Chongqing, China. .,Department of Geriatrics, Medical Center on Aging of Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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3
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Huang T, He WJ, Li C, Zhang JB, Liao YC, Song B, Yang P. Transcriptome-wide analyses of RNA m6A methylation in hexaploid wheat reveal its roles in mRNA translation regulation. FRONTIERS IN PLANT SCIENCE 2022; 13:917335. [PMID: 36092414 PMCID: PMC9453602 DOI: 10.3389/fpls.2022.917335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
N6-methyladenosine (m6A) is the most abundant RNA modification in eukaryotic messenger RNAs. m6A was discovered in wheat about 40 years ago; however, its potential roles in wheat remain unknown. In this study, we profiled m6As in spikelets transcriptome at the flowering stage of hexaploid wheat and found that m6As are evenly distributed across the A, B, and D subgenomes but their extents and locations vary across homeologous genes. m6As are enriched in homeologous genes with close expression levels and the m6A methylated genes are more conserved. The extent of m6A methylation is negatively correlated with mRNA expression levels and its presence on mRNAs has profound impacts on mRNA translation in a location-dependent manner. Specifically, m6As within coding sequences and 3'UTRs repress the translation of mRNAs while the m6As within 5'UTRs and start codons could promote it. The m6A-containing mRNAs are significantly enriched in processes and pathways of "translation" and "RNA transport," suggesting the potential role of m6As in regulating the translation of genes involved in translation regulation. Our data also show a stronger translation inhibition by small RNAs (miRNA and phasiRNA) than by m6A methylation, and no synergistical effect between the two was observed. We propose a secondary amplification machinery of translation regulation triggered by the changes in m6A methylation status. Taken together, our results suggest translation regulation as a key role played by m6As in hexaploid wheat.
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Affiliation(s)
- Tao Huang
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wei-Jie He
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Cheng Li
- College of Agriculture, Shihezi University, Shihezi, China
| | - Jing-Bo Zhang
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yu-Cai Liao
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Bo Song
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Peng Yang
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Jiangsu Ruihua Agricultural Science and Technology Co., Ltd., Suqian, China
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4
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Beauregard AP, Hannay B, Gharib E, Crapoulet N, Finn N, Guerrette R, Ouellet A, Robichaud GA. Pax-5 Protein Expression Is Regulated by Transcriptional 3'UTR Editing. Cells 2021; 11:cells11010076. [PMID: 35011638 PMCID: PMC8750734 DOI: 10.3390/cells11010076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/16/2021] [Accepted: 12/21/2021] [Indexed: 02/07/2023] Open
Abstract
The Pax-5 gene encodes a transcription factor that is essential for B-cell commitment and maturation. However, Pax-5 deregulation is associated with various cancer lesions, notably hematopoietic cancers. Mechanistically, studies have characterized genetic alterations within the Pax-5 locus that result in either dominant oncogenic function or haploinsufficiency-inducing mutations leading to oncogenesis. Apart from these mutations, some examples of aberrant Pax-5 expression cannot be associated with genetic alterations. In the present study, we set out to elucidate potential alterations in post-transcriptional regulation of Pax-5 expression and establish that Pax-5 transcript editing represents an important means to aberrant expression. Upon the profiling of Pax-5 mRNA in leukemic cells, we found that the 3′end of the Pax-5 transcript is submitted to alternative polyadenylation (APA) and alternative splicing events. Using rapid amplification of cDNA ends (3′RACE) from polysomal fractions, we found that Pax-5 3′ untranslated region (UTR) shortening correlates with increased ribosomal occupancy for translation. These observations were also validated using reporter gene assays with truncated 3′UTR regions cloned downstream of a luciferase gene. We also showed that Pax-5 3′UTR editing has direct repercussions on regulatory elements such as miRNAs, which in turn impact Pax-5 protein expression. More importantly, we found that advanced staging of various hematopoietic cancer lesions relates to shorter Pax-5 3′UTRs. Altogether, our findings identify novel molecular mechanisms that account for aberrant expression and function of the Pax-5 oncogene in cancer cells. These findings also present new avenues for strategic intervention in Pax-5-mediated cancers.
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Affiliation(s)
- Annie-Pier Beauregard
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB E1A 3E9, Canada; (A.-P.B.); (B.H.); (E.G.); (N.C.); (R.G.); (A.O.)
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada
| | - Brandon Hannay
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB E1A 3E9, Canada; (A.-P.B.); (B.H.); (E.G.); (N.C.); (R.G.); (A.O.)
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada
| | - Ehsan Gharib
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB E1A 3E9, Canada; (A.-P.B.); (B.H.); (E.G.); (N.C.); (R.G.); (A.O.)
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada
| | - Nicolas Crapoulet
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB E1A 3E9, Canada; (A.-P.B.); (B.H.); (E.G.); (N.C.); (R.G.); (A.O.)
- Dr. Georges-L-Dumont University Hospital Centre, Moncton, NB E1C 8X3, Canada;
| | - Nicholas Finn
- Dr. Georges-L-Dumont University Hospital Centre, Moncton, NB E1C 8X3, Canada;
| | - Roxann Guerrette
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB E1A 3E9, Canada; (A.-P.B.); (B.H.); (E.G.); (N.C.); (R.G.); (A.O.)
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada
| | - Amélie Ouellet
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB E1A 3E9, Canada; (A.-P.B.); (B.H.); (E.G.); (N.C.); (R.G.); (A.O.)
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada
| | - Gilles A. Robichaud
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB E1A 3E9, Canada; (A.-P.B.); (B.H.); (E.G.); (N.C.); (R.G.); (A.O.)
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada
- Correspondence: ; Tel.: +1-(506)-858-4320
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5
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Zheng D, Cho H, Wang W, Rambout X, Tian B, Maquat LE. 3'READS + RIP defines differential Staufen1 binding to alternative 3'UTR isoforms and reveals structures and sequence motifs influencing binding and polysome association. RNA (NEW YORK, N.Y.) 2020; 26:1621-1636. [PMID: 32796083 PMCID: PMC7566578 DOI: 10.1261/rna.076133.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/15/2020] [Indexed: 06/11/2023]
Abstract
Staufen1 (STAU1) is an RNA-binding protein (RBP) that interacts with double-stranded RNA structures and has been implicated in regulating different aspects of mRNA metabolism. Previous studies have indicated that STAU1 interacts extensively with RNA structures in coding regions (CDSs) and 3'-untranslated regions (3'UTRs). In particular, duplex structures formed within 3'UTRs by inverted-repeat Alu elements (IRAlus) interact with STAU1 through its double-stranded RNA-binding domains (dsRBDs). Using 3' region extraction and deep sequencing coupled to ribonucleoprotein immunoprecipitation (3'READS + RIP), together with reanalyzing previous STAU1 binding and RNA structure data, we delineate STAU1 interactions transcriptome-wide, including binding differences between alternative polyadenylation (APA) isoforms. Consistent with previous reports, RNA structures are dominant features for STAU1 binding to CDSs and 3'UTRs. Overall, relative to short 3'UTR counterparts, longer 3'UTR isoforms of genes have stronger STAU1 binding, most likely due to a higher frequency of RNA structures, including specific IRAlus sequences. Nevertheless, a sizable fraction of genes express transcripts showing the opposite trend, attributable to AU-rich sequences in their alternative 3'UTRs that may recruit antagonistic RBPs and/or destabilize RNA structures. Using STAU1-knockout cells, we show that strong STAU1 binding to mRNA 3'UTRs generally enhances polysome association. However, IRAlus generally have little impact on STAU1-mediated polysome association despite having strong interactions with the protein. Taken together, our work reveals complex interactions of STAU1 with its cognate RNA substrates. Our data also shed light on distinct post-transcriptional fates for the widespread APA isoforms in mammalian cells.
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Affiliation(s)
- Dinghai Zheng
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Hana Cho
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Wei Wang
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Xavier Rambout
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Bin Tian
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
- Program in Gene Expression and Regulation, and Center for Systems and Computational Biology, Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
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6
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Liu L, Wu Y, Li Q, Liang J, He Q, Zhao L, Chen J, Cheng M, Huang Z, Ren H, Chen J, Peng L, Gao F, Chen D, Wang A. METTL3 Promotes Tumorigenesis and Metastasis through BMI1 m 6A Methylation in Oral Squamous Cell Carcinoma. Mol Ther 2020; 28:2177-2190. [PMID: 32621798 PMCID: PMC7544972 DOI: 10.1016/j.ymthe.2020.06.024] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 05/16/2020] [Accepted: 06/18/2020] [Indexed: 01/04/2023] Open
Abstract
RNA modification plays an essential function in regulating gene expression and diverse biological processes. RNA modification enzyme methyltransferase-like 3 (METTL3) affects tumor progression by regulating the N6-methyladenosine (m6A) modification in the mRNAs of critical oncogenes or tumor suppressors, but its effect in oral squamous cell carcinoma (OSCC) remains unknown. In this study, we revealed that METTL3 was consistently upregulated in two OSCC cohorts, and high METTL3 expression was associated with poor prognosis. Functionally, cell proliferation, self-renewal, migration, and invasion ability in vitro and tumor growth and metastasis in vivo were decreased after METTL3 knockdown in OSCC cells. In contrast, the opposite results were obtained after METTL3 overexpression. In addition, the results obtained with the Mettl3 genetically modified mouse model validated the essential role of Mettl3 in chemical-induced oral carcinogenesis. In mechanism, methylated RNA immunoprecipitation sequencing (MeRIP-seq), MeRIP-quantitative real-time PCR, and luciferase reporter and mutagenesis assays identified that METTL3 mediates the m6A modification in the 3′ UTR of BMI1 mRNA. METTL3 promotes BMI1 translation in OSCC under the cooperation with m6A reader IGF2BP1. Our findings revealed that METTL3 promotes OSCC proliferation and metastasis through BMI1 m6A methylation, suggesting that the METTL3-m6A-BMI1 axis may serve as a prognostic biomarker or therapeutic target in patients with OSCC.
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Affiliation(s)
- Lin Liu
- Department of Oral and Maxillofacial Surgery, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Yu Wu
- Department of Oral and Maxillofacial Surgery, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Qiuli Li
- Department of Head and Neck Surgery, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Jianfeng Liang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-Sen University, Guangzhou 510080, China
| | - Qianting He
- Department of Oral and Maxillofacial Surgery, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Luodan Zhao
- Department of Stomatology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Jianwen Chen
- Department of Otolaryngology, Center for Translational Medicine, Precision Medicine Institute, First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Maosheng Cheng
- Department of Genetics, School of Life Science, Anhui Medical University, Anhui 230031, China
| | - Zhexun Huang
- Department of Oral and Maxillofacial Surgery, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Hui Ren
- Department of Oral and Maxillofacial Surgery, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Jie Chen
- Department of Oral and Maxillofacial Surgery, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Liang Peng
- Department of Oncology, Chinese PLA General Hospital, Beijing 100853, China
| | - Fengxin Gao
- Guangzhou Epibiotek Co., Ltd, Guangzhou 510700, China
| | - Demeng Chen
- Department of Otolaryngology, Center for Translational Medicine, Precision Medicine Institute, First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China.
| | - Anxun Wang
- Department of Oral and Maxillofacial Surgery, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China.
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7
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Manganese-induced cellular disturbance in the baker's yeast, Saccharomyces cerevisiae with putative implications in neuronal dysfunction. Sci Rep 2019; 9:6563. [PMID: 31024033 PMCID: PMC6484083 DOI: 10.1038/s41598-019-42907-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 04/09/2019] [Indexed: 12/24/2022] Open
Abstract
Manganese (Mn) is an essential element, but in humans, chronic and/or acute exposure to this metal can lead to neurotoxicity and neurodegenerative disorders including Parkinsonism and Parkinson’s Disease by unclear mechanisms. To better understand the effects that exposure to Mn2+ exert on eukaryotic cell biology, we exposed a non-essential deletion library of the yeast Saccharomyces cerevisiae to a sub-inhibitory concentration of Mn2+ followed by targeted functional analyses of the positive hits. This screen produced a set of 43 sensitive deletion mutants that were enriched for genes associated with protein biosynthesis. Our follow-up investigations demonstrated that Mn reduced total rRNA levels in a dose-dependent manner and decreased expression of a β-galactosidase reporter gene. This was subsequently supported by analysis of ribosome profiles that suggested Mn-induced toxicity was associated with a reduction in formation of active ribosomes on the mRNAs. Altogether, these findings contribute to the current understanding of the mechanism of Mn-triggered cytotoxicity. Lastly, using the Comparative Toxicogenomic Database, we revealed that Mn shared certain similarities in toxicological mechanisms with neurodegenerative disorders including amyotrophic lateral sclerosis, Alzheimer’s, Parkinson’s and Huntington’s diseases.
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8
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Ma H, Wang X, Cai J, Dai Q, Natchiar SK, Lv R, Chen K, Lu Z, Chen H, Shi YG, Lan F, Fan J, Klaholz BP, Pan T, Shi Y, He C. N 6-Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation. Nat Chem Biol 2018; 15:88-94. [PMID: 30531910 DOI: 10.1038/s41589-018-0184-3] [Citation(s) in RCA: 247] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/30/2018] [Indexed: 01/09/2023]
Abstract
N6-Methyladenosine (m6A) RNA modification is present in messenger RNAs (mRNA), ribosomal RNAs (rRNA), and spliceosomal RNAs (snRNA) in humans. Although mRNA m6A modifications have been extensively studied and shown to play critical roles in many cellular processes, the identity of m6A methyltransferases for rRNAs and the function of rRNA m6A modifications are unknown. Here we report a new m6A methyltransferase, ZCCHC4, which primarily methylates human 28S rRNA and also interacts with a subset of mRNAs. ZCCHC4 knockout eliminates m6A4220 modification in 28S rRNA, reduces global translation, and inhibits cell proliferation. We also find that ZCCHC4 protein is overexpressed in hepatocellular carcinoma tumors, and ZCCHC4 knockout significantly reduces tumor size in a xenograft mouse model. Our results highlight the functional significance of an rRNA m6A modification in translation and in tumor biology.
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Affiliation(s)
- Honghui Ma
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Institute of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Xiaoyun Wang
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Jiabin Cai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, China
| | - Qing Dai
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - S Kundhavai Natchiar
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), CNRS, Inserm, Université de Strasbourg, Illkirch, France
| | - Ruitu Lv
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Kai Chen
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Zhike Lu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Hao Chen
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yujiang Geno Shi
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Institute of Biomedical Sciences, Fudan University, Shanghai, China.,Endocrinology Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Fei Lan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, China
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), CNRS, Inserm, Université de Strasbourg, Illkirch, France
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
| | - Yang Shi
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Institute of Biomedical Sciences, Fudan University, Shanghai, China. .,Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA. .,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA. .,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
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9
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Heavy metal sensitivities of gene deletion strains for ITT1 and RPS1A connect their activities to the expression of URE2, a key gene involved in metal detoxification in yeast. PLoS One 2018; 13:e0198704. [PMID: 30231023 PMCID: PMC6145592 DOI: 10.1371/journal.pone.0198704] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 08/28/2018] [Indexed: 11/19/2022] Open
Abstract
Heavy metal and metalloid contaminations are among the most concerning types of pollutant in the environment. Consequently, it is important to investigate the molecular mechanisms of cellular responses and detoxification pathways for these compounds in living organisms. To date, a number of genes have been linked to the detoxification process. The expression of these genes can be controlled at both transcriptional and translational levels. In baker’s yeast, Saccharomyces cerevisiae, resistance to a wide range of toxic metals is regulated by glutathione S-transferases. Yeast URE2 encodes for a protein that has glutathione peroxidase activity and is homologous to mammalian glutathione S-transferases. The URE2 expression is critical to cell survival under heavy metal stress. Here, we report on the finding of two genes, ITT1, an inhibitor of translation termination, and RPS1A, a small ribosomal protein, that when deleted yeast cells exhibit similar metal sensitivity phenotypes to gene deletion strain for URE2. Neither of these genes were previously linked to metal toxicity. Our gene expression analysis illustrates that these two genes affect URE2 mRNA expression at the level of translation.
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10
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A Screen for Candidate Targets of Lysine Polyphosphorylation Uncovers a Conserved Network Implicated in Ribosome Biogenesis. Cell Rep 2018; 22:3427-3439. [DOI: 10.1016/j.celrep.2018.02.104] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 01/12/2018] [Accepted: 02/27/2018] [Indexed: 11/22/2022] Open
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11
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Demonstration of translation elongation factor 3 activity from a non-fungal species, Phytophthora infestans. PLoS One 2018; 13:e0190524. [PMID: 29300771 PMCID: PMC5754060 DOI: 10.1371/journal.pone.0190524] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 12/15/2017] [Indexed: 01/20/2023] Open
Abstract
In most eukaryotic organisms, translation elongation requires two highly conserved elongation factors eEF1A and eEF2. Fungal systems are unique in requiring a third factor, the eukaryotic Elongation Factor 3 (eEF3). For decades, eEF3, a ribosome-dependent ATPase, was considered "fungal-specific", however, recent bioinformatics analysis indicates it may be more widely distributed among other unicellular eukaryotes. In order to determine whether divergent eEF3-like proteins from other eukaryotic organisms can provide the essential functions of eEF3 in budding yeast, the eEF3-like proteins from Schizosaccharomyes pombe and an oomycete, Phytophthora infestans, were cloned and expressed in Saccharomyces cerevisiae. Plasmid shuffling experiments showed that both S. pombe and P. infestans eEF3 can support the growth of S. cerevisiae in the absence of endogenous budding yeast eEF3. Consistent with its ability to provide the essential functions of eEF3, P. infestans eEF3 possessed ribosome-dependent ATPase activity. Yeast cells expressing P. infestans eEF3 displayed reduced protein synthesis due to defects in translation elongation/termination. Identification of eEF3 in divergent species will advance understanding of its function and the ribosome specific determinants that lead to its requirement as well as contribute to the identification of functional domains of eEF3 for potential drug discovery.
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12
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Dadura K, Płocińska R, Rumijowska-Galewicz A, Płociński P, Żaczek A, Dziadek B, Zaborowski A, Dziadek J. PdtaS Deficiency Affects Resistance of Mycobacteria to Ribosome Targeting Antibiotics. Front Microbiol 2017; 8:2145. [PMID: 29163430 PMCID: PMC5676007 DOI: 10.3389/fmicb.2017.02145] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/19/2017] [Indexed: 11/13/2022] Open
Abstract
Two-component regulatory systems (TCSSs) are key regulatory elements responsible for the adaptation of bacteria to environmental stresses. A classical TCSS is typically comprised of a sensory histidine kinase and a corresponding response regulator. Here, we used homologous recombination to construct a Mycobacterium smegmatis mutant defective in the synthesis of cytosolic histidine kinase PdtaS (Msmeg_1918). The resulting ΔpdtaS mutant strain was tested in the Phenotype Microarray screening system, which allowed us to identify aminoglycoside antibiotic sensitivity, tetracyclines antibiotic resistance as well as membrane transport and respiration, as the main processes affected by removal of pdtaS. The antibiotic sensitivity profiles were confirmed by survival assessment and complementation studies. To gain insight into the molecular mechanisms responsible for the observed phenotype, we compared ribosomal RNA and protein profiles of the mutant and wild-type strains. We carried out Northern blotting and qRT-PCR to compare rRNA levels and analyzed ribosome sedimentation patterns of the wild-type and mutant strains on sucrose gradients. Isolated ribosomes were further used to estimate relative abundance of individual proteins in the ribosomal subunits using label free mass spectrometry analysis. Additionally, the ΔpdtaS mutant revealed lower activity of the respiratory chain as measured by the rate of TTC (triphenyltetrazolium chloride) reduction, while at the same time showing only insignificant changes in the uptake of aminoglycosides. We postulate that deficiency of PdtaS affects the oxidative respiration rates and ribosomal composition causing relevant changes to intrinsic resistance or susceptibility to antibiotics targeting ribosomes, which are commonly used to treat mycobacterial infections.
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Affiliation(s)
- Karolina Dadura
- Institute for Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Renata Płocińska
- Institute for Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | | | | | - Anna Żaczek
- Department of Biochemistry and Cell Biology, University of Rzeszów, Rzeszów, Poland
| | - Bożena Dziadek
- Department of Immunoparasitology, University of Łódź, Łódź, Poland
| | | | - Jarosław Dziadek
- Institute for Medical Biology, Polish Academy of Sciences, Łódź, Poland
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13
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Mencke R, Harms G, Moser J, van Meurs M, Diepstra A, Leuvenink HG, Hillebrands JL. Human alternative Klotho mRNA is a nonsense-mediated mRNA decay target inefficiently spliced in renal disease. JCI Insight 2017; 2:94375. [PMID: 29046474 DOI: 10.1172/jci.insight.94375] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 09/14/2017] [Indexed: 12/11/2022] Open
Abstract
Klotho is a renal protein involved in phosphate homeostasis, which is downregulated in renal disease. It has long been considered an antiaging factor. Two Klotho gene transcripts are thought to encode membrane-bound and secreted Klotho. Indeed, soluble Klotho is detectable in bodily fluids, but the relative contributions of Klotho secretion and of membrane-bound Klotho shedding are unknown. Recent advances in RNA surveillance reveal that premature termination codons, as present in alternative Klotho mRNA (for secreted Klotho), prime mRNAs for degradation by nonsense-mediated mRNA decay (NMD). Disruption of NMD led to accumulation of alternative Klotho mRNA, indicative of normally continuous degradation. RNA IP for NMD core factor UPF1 resulted in enrichment for alternative Klotho mRNA, which was also not associated with polysomes, indicating no active protein translation. Alternative Klotho mRNA transcripts colocalized with some P bodies, where NMD transcripts are degraded. Moreover, we could not detect secreted Klotho in vitro. These results suggest that soluble Klotho is likely cleaved membrane-bound Klotho only. Furthermore, we found that, especially in acute kidney injury, splicing of the 2 mRNA transcripts is dysregulated, which was recapitulated by various noxious stimuli in vitro. This likely constitutes a novel mechanism resulting in the downregulation of membrane-bound Klotho.
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Affiliation(s)
- Rik Mencke
- Department of Pathology and Medical Biology (Division of Pathology), University of Groningen, University Medical Center Groningen (UMCG), Groningen, The Netherlands.,The NIGRAM consortium detailed in the Supplemental Acknowledgments
| | - Geert Harms
- Department of Pathology and Medical Biology (Division of Pathology), University of Groningen, University Medical Center Groningen (UMCG), Groningen, The Netherlands.,The NIGRAM consortium detailed in the Supplemental Acknowledgments
| | - Jill Moser
- Department of Intensive Care Medicine.,Department of Pathology and Medical Biology (Division of Medical Biology), and
| | - Matijs van Meurs
- Department of Intensive Care Medicine.,Department of Pathology and Medical Biology (Division of Medical Biology), and
| | - Arjan Diepstra
- Department of Pathology and Medical Biology (Division of Pathology), University of Groningen, University Medical Center Groningen (UMCG), Groningen, The Netherlands
| | - Henri G Leuvenink
- Department of Surgery (Division of Experimental Surgery), University of Groningen, UMCG, Groningen, The Netherlands
| | - Jan-Luuk Hillebrands
- Department of Pathology and Medical Biology (Division of Pathology), University of Groningen, University Medical Center Groningen (UMCG), Groningen, The Netherlands.,The NIGRAM consortium detailed in the Supplemental Acknowledgments
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14
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Namjoshi SV, Raab-Graham KF. Screening the Molecular Framework Underlying Local Dendritic mRNA Translation. Front Mol Neurosci 2017; 10:45. [PMID: 28286470 PMCID: PMC5323403 DOI: 10.3389/fnmol.2017.00045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 02/10/2017] [Indexed: 12/13/2022] Open
Abstract
In the last decade, bioinformatic analyses of high-throughput proteomics and transcriptomics data have enabled researchers to gain insight into the molecular networks that may underlie lasting changes in synaptic efficacy. Development and utilization of these techniques have advanced the field of learning and memory significantly. It is now possible to move from the study of activity-dependent changes of a single protein to modeling entire network changes that require local protein synthesis. This data revolution has necessitated the development of alternative computational and statistical techniques to analyze and understand the patterns contained within. Thus, the focus of this review is to provide a synopsis of the journey and evolution toward big data techniques to address still unanswered questions regarding how synapses are modified to strengthen neuronal circuits. We first review the seminal studies that demonstrated the pivotal role played by local mRNA translation as the mechanism underlying the enhancement of enduring synaptic activity. In the interest of those who are new to the field, we provide a brief overview of molecular biology and biochemical techniques utilized for sample preparation to identify locally translated proteins using RNA sequencing and proteomics, as well as the computational approaches used to analyze these data. While many mRNAs have been identified, few have been shown to be locally synthesized. To this end, we review techniques currently being utilized to visualize new protein synthesis, a task that has proven to be the most difficult aspect of the field. Finally, we provide examples of future applications to test the physiological relevance of locally synthesized proteins identified by big data approaches.
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Affiliation(s)
- Sanjeev V Namjoshi
- Center for Learning and Memory, The University of Texas at Austin, AustinTX, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, AustinTX, USA
| | - Kimberly F Raab-Graham
- Center for Learning and Memory, The University of Texas at Austin, AustinTX, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, AustinTX, USA; Department of Physiology and Pharmacology, Wake Forest Health Sciences, Medical Center Boulevard, Winston-SalemNC, USA
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15
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Abstract
Ribosome profiling provides a genome-wide view of translation with unprecedented resolution. Application of this approach to fission and budding yeast revealed widespread regulation of translational efficiency, translation of short open reading frames on unannotated transcripts, and frequent translation of open reading frames in 5' leader sequences. We present here a detailed protocol for the application of ribosome profiling to meiotic fission yeast cells, although the approach should be easily adapted to budding yeast.
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Affiliation(s)
- Caia Duncan
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge, CB2 1QW, UK
| | - Juan Mata
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge, CB2 1QW, UK.
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16
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Hendrick HM, Welter BH, Hapstack MA, Sykes SE, Sullivan WJ, Temesvari LA. Phosphorylation of Eukaryotic Initiation Factor-2α during Stress and Encystation in Entamoeba Species. PLoS Pathog 2016; 12:e1006085. [PMID: 27930733 PMCID: PMC5179133 DOI: 10.1371/journal.ppat.1006085] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 12/22/2016] [Accepted: 11/23/2016] [Indexed: 12/21/2022] Open
Abstract
Entamoeba histolytica is an enteric pathogen responsible for amoebic dysentery and liver abscess. It alternates between the host-restricted trophozoite form and the infective environmentally-stable cyst stage. Throughout its lifecycle E. histolytica experiences stress, in part, from host immune pressure. Conversion to cysts is presumed to be a stress-response. In other systems, stress induces phosphorylation of a serine residue on eukaryotic translation initiation factor-2α (eIF2α). This inhibits eIF2α activity resulting in a general decline in protein synthesis. Genomic data reveal that E. histolytica possesses eIF2α (EheIF2α) with a conserved phosphorylatable serine at position 59 (Ser59). Thus, this pathogen may have the machinery for stress-induced translational control. To test this, we exposed cells to different stress conditions and measured the level of total and phospho-EheIF2α. Long-term serum starvation, long-term heat shock, and oxidative stress induced an increase in the level of phospho-EheIF2α, while short-term serum starvation, short-term heat shock, or glucose deprivation did not. Long-term serum starvation also caused a decrease in polyribosome abundance, which is in accordance with the observation that this condition induces phosphorylation of EheIF2α. We generated transgenic cells that overexpress wildtype EheIF2α, a non-phosphorylatable variant of eIF2α in which Ser59 was mutated to alanine (EheIF2α-S59A), or a phosphomimetic variant of eIF2α in which Ser59 was mutated to aspartic acid (EheIF2α-S59D). Consistent with the known functions of eIF2α, cells expressing wildtype or EheIF2α-S59D exhibited increased or decreased translation, respectively. Surprisingly, cells expressing EheIF2α-S59A also exhibited reduced translation. Cells expressing EheIF2α-S59D were more resistant to long-term serum starvation underscoring the significance of EheIF2α phosphorylation in managing stress. Finally, phospho-eIF2α accumulated during encystation in E. invadens, a model encystation system. Together, these data demonstrate that the eIF2α-dependent stress response system is operational in Entamoeba species. Entamoeba histolytica is the causative agent of amoebic dysentery and liver abscess and is prevalent in underdeveloped countries that lack proper sanitation. Infection is acquired by ingestion of the cyst form in contaminated food or water. During infection, the parasite experiences stress including demanding growth conditions and host immune pressure. Conversion to the infective cyst may be induced by such stress. In other organisms, stress causes a decrease in protein biosynthesis by inducing phosphorylation of eIF2α, which participates in translation initiation. We exposed E. histolytica to six different stress conditions and observed that some of these conditions (long-term serum starvation, long-term heat shock, and oxidative stress) induced an increase in the level of phospho-eIF2α. Long-term serum starvation was also accompanied by a decrease in mRNA translation. A cell line expressing a mutant version of eIF2α that behaves as a phosphomimetic exhibited decreased translation and increased survival during long-term serum starvation. Finally, phospho-eIF2α accumulated in cysts of E. invadens, a reptilian pathogen that readily encysts in vitro. Together, these data demonstrate that the eIF2α-dependent stress response system is operational in Entamoeba and may regulate encystation.
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Affiliation(s)
- Holland M. Hendrick
- Department of Biological Sciences, Clemson University Clemson, South Carolina, United States of America
- Eukaryotic Pathogens Innovation Center (EPIC) Clemson University Clemson, South Carolina, United States of America
| | - Brenda H. Welter
- Department of Biological Sciences, Clemson University Clemson, South Carolina, United States of America
- Eukaryotic Pathogens Innovation Center (EPIC) Clemson University Clemson, South Carolina, United States of America
| | - Matthew A. Hapstack
- Department of Biological Sciences, Clemson University Clemson, South Carolina, United States of America
- Eukaryotic Pathogens Innovation Center (EPIC) Clemson University Clemson, South Carolina, United States of America
| | - Steven E. Sykes
- Department of Biological Sciences, Clemson University Clemson, South Carolina, United States of America
- Eukaryotic Pathogens Innovation Center (EPIC) Clemson University Clemson, South Carolina, United States of America
| | - William J. Sullivan
- Department of Pharmacology and Toxicology Indiana University School of Medicine Indianaplois, IN United States of America
- Department of Microbiology and Immunology Indiana University School of Medicine Indianapolis, IN United States of America
| | - Lesly A. Temesvari
- Department of Biological Sciences, Clemson University Clemson, South Carolina, United States of America
- Eukaryotic Pathogens Innovation Center (EPIC) Clemson University Clemson, South Carolina, United States of America
- * E-mail:
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17
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Hansji H, Leung EY, Baguley BC, Finlay GJ, Cameron-Smith D, Figueiredo VC, Askarian-Amiri ME. ZFAS1: a long noncoding RNA associated with ribosomes in breast cancer cells. Biol Direct 2016; 11:62. [PMID: 27871336 PMCID: PMC5117590 DOI: 10.1186/s13062-016-0165-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 11/11/2016] [Indexed: 12/20/2022] Open
Abstract
Background Most of the eukaryotic genome is transcribed, yielding a complex network of transcripts including thousands of lncRNAs that generally lack protein coding potential. However, only a small percentage of these molecules has been functionally characterised, and discoveries of specific functions demonstrate layers of complexity. A large percentage of lncRNAs is located in the cytoplasm, associated with ribosomes but the function of the majority of these transcripts is unclear. The current study analyses putative mechanisms of action of the lncRNA species member ZFAS1 that was initially discovered by microarray analysis of murine tissues undergoing mammary gland development. As developmental genes are often deregulated in cancer, here we have studied its function in breast cancer cell lines. Results Using human breast cancer cell lines, ZFAS1 was found to be expressed in all cell lines tested, albeit at different levels of abundance. Following subcellular fractionation, human ZFAS1 was found in both nucleus and cytoplasm (as is the mouse orthologue) in an isoform-independent manner. Sucrose gradients based on velocity sedimentation were utilised to separate the different components of total cell lysate, and surprisingly ZFAS1 was primarily co-localised with light polysomes. Further investigation into ribosome association through subunit dissociation studies showed that ZFAS1 was predominantly associated with the 40S small ribosomal subunit. The expression levels of ZFAS1 and of mRNAs encoding several ribosomal proteins that have roles in ribosome assembly, production and maturation were tightly correlated. ZFAS1 knockdown significantly reduced RPS6 phosphorylation. Conclusion A large number of lncRNAs associate with ribosomes but the function of the majority of these lncRNAs has not been elucidated. The association of the lncRNA ZFAS1 with a subpopulation of ribosomes and the correlation with expression of mRNAs for ribosomal proteins suggest a ribosome-interacting mechanism pertaining to their assembly or biosynthetic activity. ZFAS1 may represent a new class of lncRNAs which associates with ribosomes to regulate their function. Reviewers This article was reviewed by Christine Vande Velde, Nicola Aceto and Haruhiko Siomi. Electronic supplementary material The online version of this article (doi:10.1186/s13062-016-0165-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Herah Hansji
- Auckland Cancer Society Research Centre, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand.,Department of Molecular Medicine and Pathology, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand
| | - Euphemia Y Leung
- Auckland Cancer Society Research Centre, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand.,Department of Molecular Medicine and Pathology, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand
| | - Bruce C Baguley
- Auckland Cancer Society Research Centre, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand
| | - Graeme J Finlay
- Auckland Cancer Society Research Centre, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand.,Department of Molecular Medicine and Pathology, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand
| | - David Cameron-Smith
- The Liggins Institute, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand
| | - Vandre C Figueiredo
- The Liggins Institute, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand
| | - Marjan E Askarian-Amiri
- Auckland Cancer Society Research Centre, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand. .,Department of Molecular Medicine and Pathology, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand.
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18
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Machinaga A, Ishihara S, Shirai A, Takase-Yoden S. Splicing of Friend Murine Leukemia Virus env-mRNA Enhances Its Ability to Form Polysomes. Front Microbiol 2016; 7:160. [PMID: 26909075 PMCID: PMC4754430 DOI: 10.3389/fmicb.2016.00160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 01/29/2016] [Indexed: 12/12/2022] Open
Abstract
Friend murine leukemia virus (MLV) belongs to the gamma retroviruses of the Retroviridae family. The positive-sense RNA of its genome contains a 5' long terminal repeat (LTR), 5' leader sequence, gag, pol, env, and 3' LTR. Transcription from proviral DNA begins from the R region of the 5' LTR and ends at the polyadenylation signal located at the R region of the other end of the 3' LTR. There is a 5' splice site in the 5' leader sequence and a 3' splice site at the 3' end of the pol region. Both full-length unspliced mRNAs and a singly spliced mRNA (env-mRNA) are produced in MLV-infected cells. The MLV Env protein plays important roles both in viral adsorption to host cells and in neuropathogenic disease in MLV-infected mice and rats. Understanding the regulatory mechanisms controlling Env expression is important for determining the functions of the Env protein. We have previously shown that splicing increases env-mRNA stability and translation efficiency. Generally, mRNA polysome formation correlates with translation efficiency. Therefore, here we investigated the effects of env-mRNA splicing on polysome formation to identify mechanisms for Env up-regulation due to splicing. We performed polysome profile analyses using Env-expression plasmids producing spliced or unspliced env-mRNA and showed that the former formed polysomes more efficiently than the latter. Thus, splicing of env-mRNA facilitated polysome formation, suggesting that this contributes to up-regulation of Env expression. We replaced the env region of the expression plasmids with a luciferase (luc) gene, and found that in this case both unspliced and spliced luc-mRNA formed polysomes to a similar extent. Thus, we conclude that whether mRNA polysome formation is affected by splicing depends on the structure of gene in question.
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Affiliation(s)
- Akihito Machinaga
- Department of Bioinformatics, Graduate School of Engineering, Soka University Tokyo, Japan
| | - Syuhei Ishihara
- Department of Bioinformatics, Graduate School of Engineering, Soka University Tokyo, Japan
| | - Akiko Shirai
- Department of Bioinformatics, Graduate School of Engineering, Soka University Tokyo, Japan
| | - Sayaka Takase-Yoden
- Department of Bioinformatics, Graduate School of Engineering, Soka UniversityTokyo, Japan; Department of Science and Engineering for Sustainable Innovation, Faculty of Science and Engineering, Soka UniversityTokyo, Japan
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19
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Xu S, Zhou R, Ren Z, Zhou B, Lin Z, Hou G, Deng Y, Zi J, Lin L, Wang Q, Liu X, Xu X, Wen B, Liu S. Appraisal of the Missing Proteins Based on the mRNAs Bound to Ribosomes. J Proteome Res 2015; 14:4976-84. [PMID: 26500078 DOI: 10.1021/acs.jproteome.5b00476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Considering the technical limitations of mass spectrometry in protein identification, the mRNAs bound to ribosomes (RNC-mRNA) are assumed to reflect the mRNAs participating in the translational process. The RNC-mRNA data are reasoned to be useful for appraising the missing proteins. A set of the multiomics data including free-mRNAs, RNC-mRNAs, and proteomes was acquired from three liver cancer cell lines. On the basis of the missing proteins in neXtProt (release 2014-09-19), the bioinformatics analysis was carried out in three phases: (1) finding how many neXtProt missing proteins have or do not have RNA-seq and/or MS/MS evidence, (2) analyzing specific physicochemical and biological properties of the missing proteins that lack both RNA-seq and MS/MS evidence, and (3) analyzing the combined properties of these missing proteins. Total of 1501 missing proteins were found by neither RNC-mRNA nor MS/MS in the three liver cancer cell lines. For these missing proteins, some are expected higher hydrophobicity, unsuitable detection, or sensory functions as properties at the protein level, while some are predicted to have nonexpressing chromatin structures on the corresponding gene level. With further integrated analysis, we could attribute 93% of them (1391/1501) to these causal factors, which result in the expression products scarcely detected by RNA-seq or MS/MS.
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Affiliation(s)
- Shaohang Xu
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Ruo Zhou
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Zhe Ren
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Baojin Zhou
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Zhilong Lin
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Guixue Hou
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , BeiChen West Road, Beijing 100101, China
| | - Yamei Deng
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , BeiChen West Road, Beijing 100101, China
| | - Jin Zi
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Liang Lin
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Quanhui Wang
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , BeiChen West Road, Beijing 100101, China
| | - Xin Liu
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Xun Xu
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Bo Wen
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Siqi Liu
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , BeiChen West Road, Beijing 100101, China
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20
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Yang SX, Guo C, Zhang YK, Sun JT, Hong XY. Expression level and immunolocalization of de novo methyltransferase 3 protein (TuDNMT3) in adult females and males of the two-spotted spider mite, Tetranychus urticae. EXPERIMENTAL & APPLIED ACAROLOGY 2015; 67:381-392. [PMID: 26246190 DOI: 10.1007/s10493-015-9957-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 07/22/2015] [Indexed: 06/04/2023]
Abstract
DNA methylation is an epigenetic mechanism for regulating developmental and other important processes in eukaryotes. Several essential components of the DNA methylation machinery have been identified, such as DNA methyltransferases. In the two-spotted spider mite, Tetranychus urticae Koch, we have identified one DNA methyltransferase 3 gene (Tudnmt3) and tentatively investigated its potential role in adult females and males. Here, to better elucidate the functional role of Tudnmt3, its protein structure, expression and localization were subjected to more detailed analyses. Bioinformatic analyses clearly showed that the structure of TuDNMT3 was highly conserved, with several vital amino acid residues for the activation and stabilization of its confirmation. Western blot analyses revealed that this protein was expressed in both genders, with higher expression in adult females, which was inconsistent with the gene expression, suggesting translational regulation of Tudnmt3. Subsequent immunodetection provided supportive evidence for higher expression of the TuDNMT3 protein in adult females and indicated that this protein was generally localized in the cytoplasm and that its expression was predominantly confined to the genital region of spider mites, strengthening the hypothesis that de novo methylation mediated by Tudnmt3 in gonad development or gametogenesis has a different mechanism from maintenance methyltransferase.
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Affiliation(s)
- Si-Xia Yang
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Chao Guo
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yan-Kai Zhang
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jing-Tao Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China.
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21
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Tholen M, Wolanski J, Stolze B, Chiabudini M, Gajda M, Bronsert P, Stickeler E, Rospert S, Reinheckel T. Stress-resistant Translation of Cathepsin L mRNA in Breast Cancer Progression. J Biol Chem 2015; 290:15758-15769. [PMID: 25957406 DOI: 10.1074/jbc.m114.624353] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Indexed: 11/06/2022] Open
Abstract
The cysteine protease cathepsin L (CTSL) is often thought to act as a tumor promoter by enhancing tumor progression and metastasis. This goes along with increased CTSL activity in various tumor entities; however, the mechanisms leading to high CTSL levels are incompletely understood. With the help of the polyoma middle T oncogene driven breast cancer mouse model expressing a human CTSL genomic transgene, we show that CTSL indeed promotes breast cancer metastasis to the lung. During tumor formation and progression high expression levels of CTSL are maintained by enduring translation of CTSL mRNA. Interestingly, human breast cancer specimens expressed the same pattern of 5' untranslated region (UTR) splice variants as the transgenic mice and the human cancer cell line MDA-MB 321. By polyribosome profiling of tumor tissues and human breast cancer cells, we observe an intrinsic resistance of CTSL to stress-induced shutdown of translation. This ability can be attributed to all 5' UTR variants of CTSL and is not dependent on a previously described internal ribosomal entry site motif. In conclusion, we provide in vivo functional evidence for overexpressed CTSL as a promoter of lung metastasis, whereas high CTSL levels are maintained during tumor progression due to stress-resistant mRNA translation.
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Affiliation(s)
- Martina Tholen
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Julia Wolanski
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Britta Stolze
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Marco Chiabudini
- Institute of Biochemistry and Molecular Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, 79104 Freiburg
| | - Mieczyslaw Gajda
- Institute of Pathology, Friedrich-Schiller University, 07743 Jena, Germany
| | - Peter Bronsert
- Institute of Pathology, University Medical Center Freiburg, 79106 Freiburg; Comprehensive Cancer Center/German Cancer Consortium (DKTK), 79106 Freiburg
| | - Elmar Stickeler
- Comprehensive Cancer Center/German Cancer Consortium (DKTK), 79106 Freiburg; Clinic for Gynecology, University Medical Center Freiburg, 79106 Freiburg, Germany
| | - Sabine Rospert
- Institute of Biochemistry and Molecular Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, 79104 Freiburg
| | - Thomas Reinheckel
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, 79104 Freiburg; Comprehensive Cancer Center/German Cancer Consortium (DKTK), 79106 Freiburg.
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22
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Edwalds-Gilbert G. Location is everything: an educational primer for use with "genetic analysis of the ribosome biogenesis factor Ltv1 of Saccharomyces cerevisiae". Genetics 2015; 199:307-13. [PMID: 25657348 PMCID: PMC4317645 DOI: 10.1534/genetics.114.173641] [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] [Indexed: 11/18/2022] Open
Abstract
The article by Merwin et al. in the November 2014 issue of GENETICS provides insight into ribosome biogenesis, an essential multistep process that involves myriad factors and three cellular compartments. The specific protein of interest in this study is low-temperature viability protein (Ltv1), which functions as a small ribosomal subunit maturation factor. The authors investigated its possible additional function in small-subunit nuclear export. This Primer provides information for students to help them analyze the paper by Merwin et al. (2014), including an overview of the authors' research question and methods.
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Affiliation(s)
- Gretchen Edwalds-Gilbert
- W.M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711
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23
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Methylation of ribosomal RNA by NSUN5 is a conserved mechanism modulating organismal lifespan. Nat Commun 2015; 6:6158. [PMID: 25635753 PMCID: PMC4317494 DOI: 10.1038/ncomms7158] [Citation(s) in RCA: 198] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 12/11/2014] [Indexed: 01/01/2023] Open
Abstract
Several pathways modulating longevity and stress resistance converge on translation by targeting ribosomal proteins or initiation factors, but whether this involves modifications of ribosomal RNA is unclear. Here, we show that reduced levels of the conserved RNA methyltransferase NSUN5 increase the lifespan and stress resistance in yeast, worms and flies. Rcm1, the yeast homologue of NSUN5, methylates C2278 within a conserved region of 25S rRNA. Loss of Rcm1 alters the structural conformation of the ribosome in close proximity to C2278, as well as translational fidelity, and favours recruitment of a distinct subset of oxidative stress-responsive mRNAs into polysomes. Thus, rather than merely being a static molecular machine executing translation, the ribosome exhibits functional diversity by modification of just a single rRNA nucleotide, resulting in an alteration of organismal physiological behaviour, and linking rRNA-mediated translational regulation to modulation of lifespan, and differential stress response. Cellular pathways modulating longevity and stress resistance are known to affect protein translation. Here the authors show that the RNA methyltransferase, Nsun5, or its yeast homologue Rcm1, regulates lifespan of three different model organisms by modifying ribosomal RNA at a specific cytosine residue.
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24
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Gamm M, Peviani A, Honsel A, Snel B, Smeekens S, Hanson J. Increased sucrose levels mediate selective mRNA translation in Arabidopsis. BMC PLANT BIOLOGY 2014; 14:306. [PMID: 25403240 PMCID: PMC4252027 DOI: 10.1186/s12870-014-0306-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 10/27/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND Protein synthesis is a highly energy demanding process and is regulated according to cellular energy levels. Light and sugar availability affect mRNA translation in plant cells but the specific roles of these factors remain unclear. In this study, sucrose was applied to Arabidopsis seedlings kept in the light or in the dark, in order to distinguish sucrose and light effects on transcription and translation. These were studied using microarray analysis of steady-state mRNA and mRNA bound to translating ribosomes. RESULTS Steady-state mRNA levels were affected differently by sucrose in the light and in the dark but general translation increased to a similar extent in both conditions. For a majority of the transcripts changes of the transcript levels were followed by changes in polysomal mRNA levels. However, for 243 mRNAs, a change in polysomal occupancy (defined as polysomal levels related to steady-state levels of the mRNA) was observed after sucrose treatment in the light, but not in the dark condition. Many of these mRNAs are annotated as encoding ribosomal proteins, supporting specific translational regulation of this group of transcripts. Unexpectedly, the numbers of ribosomes bound to each mRNA decreased for mRNAs with increased polysomal occupancy. CONCLUSIONS Our results suggest that sucrose regulate translation of these 243 mRNAs specifically in the light, through a novel regulatory mechanism. Our data shows that increased polysomal occupancy is not necessarily leading to more ribosomes per transcript, suggesting a mechanism of translational induction not solely dependent on increased translation initiation rates.
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Affiliation(s)
- Magdalena Gamm
- />Molecular Plant Physiology, Institute of Environmental
Biology, Utrecht University, Utrecht, The Netherlands
| | - Alessia Peviani
- />Theoretical Biology and Bioinformatics, Department of Biology, Faculty
of Science, Utrecht University, Utrecht, The Netherlands
| | - Anne Honsel
- />Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-90187 Umeå, Sweden
| | - Berend Snel
- />Theoretical Biology and Bioinformatics, Department of Biology, Faculty
of Science, Utrecht University, Utrecht, The Netherlands
| | - Sjef Smeekens
- />Molecular Plant Physiology, Institute of Environmental
Biology, Utrecht University, Utrecht, The Netherlands
| | - Johannes Hanson
- />Molecular Plant Physiology, Institute of Environmental
Biology, Utrecht University, Utrecht, The Netherlands
- />Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-90187 Umeå, Sweden
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25
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Zhang Q, Zhou X, Wu R, Mosley A, Zeng SX, Xing Z, Lu H. The role of IMP dehydrogenase 2 in Inauhzin-induced ribosomal stress. eLife 2014; 3. [PMID: 25347121 PMCID: PMC4209374 DOI: 10.7554/elife.03077] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Accepted: 10/06/2014] [Indexed: 11/13/2022] Open
Abstract
The 'ribosomal stress (RS)-p53 pathway' is triggered by any stressor or genetic alteration that disrupts ribosomal biogenesis, and mediated by several ribosomal proteins (RPs), such as RPL11 and RPL5, which inhibit MDM2 and activate p53. Inosine monophosphate (IMP) dehydrogenase 2 (IMPDH2) is a rate-limiting enzyme in de novo guanine nucleotide biosynthesis and crucial for maintaining cellular guanine deoxy- and ribonucleotide pools needed for DNA and RNA synthesis. It is highly expressed in many malignancies. We previously showed that inhibition of IMPDH2 leads to p53 activation by causing RS. Surprisingly, our current study reveals that Inauzhin (INZ), a novel non-genotoxic p53 activator by inhibiting SIRT1, can also inhibit cellular IMPDH2 activity, and reduce the levels of cellular GTP and GTP-binding nucleostemin that is essential for rRNA processing. Consequently, INZ induces RS and the RPL11/RPL5-MDM2 interaction, activating p53. These results support the new notion that INZ suppresses cancer cell growth by dually targeting SIRT1 and IMPDH2.
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Affiliation(s)
- Qi Zhang
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, United States
| | - Xiang Zhou
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, United States
| | - RuiZhi Wu
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, United States
| | - Amber Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, United States
| | - Shelya X Zeng
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, United States
| | - Zhen Xing
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, United States
| | - Hua Lu
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, United States
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26
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Temporally defined neocortical translation and polysome assembly are determined by the RNA-binding protein Hu antigen R. Proc Natl Acad Sci U S A 2014; 111:E3815-24. [PMID: 25157170 DOI: 10.1073/pnas.1408305111] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Precise spatiotemporal control of mRNA translation machinery is essential to the development of highly complex systems like the neocortex. However, spatiotemporal regulation of translation machinery in the developing neocortex remains poorly understood. Here, we show that an RNA-binding protein, Hu antigen R (HuR), regulates both neocorticogenesis and specificity of neocortical translation machinery in a developmental stage-dependent manner in mice. Neocortical absence of HuR alters the phosphorylation states of initiation and elongation factors in the core translation machinery. In addition, HuR regulates the temporally specific positioning of functionally related mRNAs into the active translation sites, the polysomes. HuR also determines the specificity of neocortical polysomes by defining their combinatorial composition of ribosomal proteins and initiation and elongation factors. For some HuR-dependent proteins, the association with polysomes likewise depends on the eukaryotic initiation factor 2 alpha kinase 4, which associates with HuR in prenatal developing neocortices. Finally, we found that deletion of HuR before embryonic day 10 disrupts both neocortical lamination and formation of the main neocortical commissure, the corpus callosum. Our study identifies a crucial role for HuR in neocortical development as a translational gatekeeper for functionally related mRNA subgroups and polysomal protein specificity.
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27
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CERKL, a retinal disease gene, encodes an mRNA-binding protein that localizes in compact and untranslated mRNPs associated with microtubules. PLoS One 2014; 9:e87898. [PMID: 24498393 PMCID: PMC3912138 DOI: 10.1371/journal.pone.0087898] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 12/30/2013] [Indexed: 11/25/2022] Open
Abstract
The function of CERKL (CERamide Kinase Like), a causative gene of retinitis pigmentosa and cone-rod dystrophy, still awaits characterization. To approach its cellular role we have investigated the subcellular localization and interaction partners of the full length CERKL isoform, CERKLa of 532 amino acids, in different cell lines, including a photoreceptor-derived cell line. We demonstrate that CERKLa is a main component of compact and untranslated mRNPs and that associates with other RNP complexes such as stress granules, P-bodies and polysomes. CERKLa is a protein that binds through its N-terminus to mRNAs and interacts with other mRNA-binding proteins like eIF3B, PABP, HSP70 and RPS3. Except for eIF3B, these interactions depend on the integrity of mRNAs but not of ribosomes. Interestingly, the C125W CERKLa pathological mutant does not interact with eIF3B and is absent from these complexes. Compact mRNPs containing CERKLa also associate with microtubules and are found in neurites of neural differentiated cells. These localizations had not been reported previously for any member of the retinal disorders gene family and should be considered when investigating the pathogenic mechanisms and therapeutical approaches in these diseases.
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28
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Sasikumar AN, Kinzy TG. Mutations in the chromodomain-like insertion of translation elongation factor 3 compromise protein synthesis through reduced ATPase activity. J Biol Chem 2013; 289:4853-60. [PMID: 24379402 DOI: 10.1074/jbc.m113.536201] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Translation elongation is mediated by ribosomes and multiple soluble factors, many of which are conserved across bacteria and eukaryotes. During elongation, eukaryotic elongation factor 1A (eEF1A; EF-Tu in bacteria) delivers aminoacylated-tRNA to the A-site of the ribosome, whereas eEF2 (EF-G in bacteria) translocates the ribosome along the mRNA. Fungal translation elongation is striking in its absolute requirement for a third factor, the ATPase eEF3. eEF3 binds close to the E-site of the ribosome and has been proposed to facilitate the removal of deacylated tRNA from the E-site. eEF3 has two ATP binding cassette (ABC) domains, the second of which carries a unique chromodomain-like insertion hypothesized to play a significant role in its binding to the ribosome. This model was tested in the current study using a mutational analysis of the Sac7d region of the chromodomain-like insertion. Specific mutations in this domain result in reduced growth rate as well as slower translation elongation. In vitro analysis demonstrates that these mutations do not affect the ability of eEF3 to interact with the ribosome. Kinetic analysis revealed a larger turnover number for ribosomes in comparison to eEF3, indicating that the partial reactions involving the ribosome are significantly faster than that of eEF3. Mutations in the chromodomain-like insertion severely compromise the ribosome stimulated ATPase of eEF3, strongly suggesting that it exerts an allosteric effect on the hydrolytic activity of eEF3. The chromodomain-like insertion is, therefore, vital to eEF3 function and may be targeted for developing novel antifungal drugs.
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Affiliation(s)
- Arjun N Sasikumar
- From the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854-5635
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29
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Akizu N, Cantagrel V, Schroth J, Cai N, Vaux K, McCloskey D, Naviaux RK, Van Vleet J, Fenstermaker AG, Silhavy JL, Scheliga JS, Toyama K, Morisaki H, Sonmez FM, Celep F, Oraby A, Zaki MS, Al-Baradie R, Faqeih EA, Saleh MAM, Spencer E, Rosti RO, Scott E, Nickerson E, Gabriel S, Morisaki T, Holmes EW, Gleeson JG. AMPD2 regulates GTP synthesis and is mutated in a potentially treatable neurodegenerative brainstem disorder. Cell 2013; 154:505-17. [PMID: 23911318 DOI: 10.1016/j.cell.2013.07.005] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 05/10/2013] [Accepted: 07/01/2013] [Indexed: 01/03/2023]
Abstract
Purine biosynthesis and metabolism, conserved in all living organisms, is essential for cellular energy homeostasis and nucleic acid synthesis. The de novo synthesis of purine precursors is under tight negative feedback regulation mediated by adenosine and guanine nucleotides. We describe a distinct early-onset neurodegenerative condition resulting from mutations in the adenosine monophosphate deaminase 2 gene (AMPD2). Patients have characteristic brain imaging features of pontocerebellar hypoplasia (PCH) due to loss of brainstem and cerebellar parenchyma. We found that AMPD2 plays an evolutionary conserved role in the maintenance of cellular guanine nucleotide pools by regulating the feedback inhibition of adenosine derivatives on de novo purine synthesis. AMPD2 deficiency results in defective GTP-dependent initiation of protein translation, which can be rescued by administration of purine precursors. These data suggest AMPD2-related PCH as a potentially treatable early-onset neurodegenerative disease.
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Affiliation(s)
- Naiara Akizu
- Neurogenetics Laboratory, Institute for Genomic Medicine, Rady Children's Hospital, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA
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30
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Orlowska KP, Klosowska K, Szczesny RJ, Cysewski D, Krawczyk PS, Dziembowski A. A new strategy for gene targeting and functional proteomics using the DT40 cell line. Nucleic Acids Res 2013; 41:e167. [PMID: 23892402 PMCID: PMC3783193 DOI: 10.1093/nar/gkt650] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
DT40 cells derived from chicken B lymphocytes exhibit exceptionally high homologous recombination rates. Therefore, they can be used as a convenient tool and model for gene targeting experiments. However, lack of efficient cloning strategies, protein purification protocols and a well annotated protein database limits the utility of these cells for proteomic studies. Here we describe a fast and inexpensive experimental pipeline for protein localization, quantification and mass spectrometry-based interaction studies using DT40 cells. Our newly designed set of pQuant vectors and a sequence- and ligation-independent cloning (SLIC) strategy allow for simple and efficient generation of gene targeting constructs, facilitating homologous-recombination-based protein tagging on a multi-gene scale. We also report proof of principle results using the key proteins involved in RNA decay, namely EXOSC8, EXOSC9, CNOT7 and UPF1.
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Affiliation(s)
- Kinga P Orlowska
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland and Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
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31
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Mateyak MK, Kinzy TG. ADP-ribosylation of translation elongation factor 2 by diphtheria toxin in yeast inhibits translation and cell separation. J Biol Chem 2013; 288:24647-55. [PMID: 23853096 DOI: 10.1074/jbc.m113.488783] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Eukaryotic translation elongation factor 2 (eEF2) facilitates the movement of the peptidyl tRNA-mRNA complex from the A site of the ribosome to the P site during protein synthesis. ADP-ribosylation (ADP(R)) of eEF2 by bacterial toxins on a unique diphthamide residue inhibits its translocation activity, but the mechanism is unclear. We have employed a hormone-inducible diphtheria toxin (DT) expression system in Saccharomyces cerevisiae which allows for the rapid induction of ADP(R)-eEF2 to examine the effects of DT in vivo. ADP(R) of eEF2 resulted in a decrease in total protein synthesis consistent with a defect in translation elongation. Association of eEF2 with polyribosomes, however, was unchanged upon expression of DT. Upon prolonged exposure to DT, cells with an abnormal morphology and increased DNA content accumulated. This observation was specific to DT expression and was not observed when translation elongation was inhibited by other methods. Examination of these cells by electron microscopy indicated a defect in cell separation following mitosis. These results suggest that expression of proteins late in the cell cycle is particularly sensitive to inhibition by ADP(R)-eEF2.
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Affiliation(s)
- Maria K Mateyak
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
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32
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Wang T, Cui Y, Jin J, Guo J, Wang G, Yin X, He QY, Zhang G. Translating mRNAs strongly correlate to proteins in a multivariate manner and their translation ratios are phenotype specific. Nucleic Acids Res 2013; 41:4743-54. [PMID: 23519614 PMCID: PMC3643591 DOI: 10.1093/nar/gkt178] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
As a well-known phenomenon, total mRNAs poorly correlate to proteins in their abundances as reported. Recent findings calculated with bivariate models suggested even poorer such correlation, whereas focusing on the translating mRNAs (ribosome nascent-chain complex-bound mRNAs, RNC-mRNAs) subset. In this study, we analysed the relative abundances of mRNAs, RNC-mRNAs and proteins on genome-wide scale, comparing human lung cancer A549 and H1299 cells with normal human bronchial epithelial (HBE) cells, respectively. As discovered, a strong correlation between RNC-mRNAs and proteins in their relative abundances could be established through a multivariate linear model by integrating the mRNA length as a key factor. The R2 reached 0.94 and 0.97 in A549 versus HBE and H1299 versus HBE comparisons, respectively. This correlation highlighted that the mRNA length significantly contributes to the translational modulation, especially to the translational initiation, favoured by its correlation with the mRNA translation ratio (TR) as observed. We found TR is highly phenotype specific, which was substantiated by both pathway analysis and biased TRs of the splice variants of BDP1 gene, which is a key transcription factor of transfer RNAs. These findings revealed, for the first time, the intrinsic and genome-wide translation modulations at translatomic level in human cells at steady-state, which are tightly correlated to the protein abundance and functionally relevant to cellular phenotypes.
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Affiliation(s)
- Tong Wang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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33
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Esposito AM, Kinzy TG. The eukaryotic translation elongation Factor 1Bgamma has a non-guanine nucleotide exchange factor role in protein metabolism. J Biol Chem 2010; 285:37995-8004. [PMID: 20926387 DOI: 10.1074/jbc.m110.160887] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The turnover of damaged proteins is critical to cell survival during stressful conditions such as heat shock or oxidative stress. The accumulation of misfolded proteins in the endoplasmic reticulum (ER) is toxic to cells. Therefore these proteins must be efficiently exported from the ER and degraded by the proteasome or the vacuole. Previously it was shown that the loss of eukaryotic elongation factor 1Bγ (eEF1Bγ) from the yeast Saccharomyces cerevisiae results in resistance to oxidative stress. Strains lacking eEF1Bγ show severe defects in protein turnover during conditions of oxidative stress. Furthermore, these strains accumulate a greater amount of oxidized proteins, which correlates with changes in heat shock chaperones. These strains show severe defects in vacuole morphology and defects related to the maturation of carboxypeptidase Y that is not dependent on the catalytic subunit of the eEF1B complex as a guanine nucleotide exchange factor. Finally, eEF1Bγ co-immunoprecipitates with an essential component of ER-Golgi transport vesicles. Taken together, these results support a broader protein metabolism role for eEF1Bγ.
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Affiliation(s)
- Anthony M Esposito
- Department of Molecular Genetics, Microbiology and Immunology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854-5635, USA
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