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Gayen A, Mukherjee A, Kumar K, Majumder S, Chakrabarti S, Mukherjee C. The mRNA-capping enzyme localizes to stress granules in the cytoplasm and maintains cap homeostasis of target mRNAs. J Cell Sci 2024; 137:jcs261578. [PMID: 38841902 DOI: 10.1242/jcs.261578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 04/08/2024] [Indexed: 06/07/2024] Open
Abstract
The model of RNA stability has undergone a transformative shift with the revelation of a cytoplasmic capping activity that means a subset of transcripts are recapped autonomously of their nuclear counterparts. The present study demonstrates nucleo-cytoplasmic shuttling of the mRNA-capping enzyme (CE, also known as RNA guanylyltransferase and 5'-phosphatase; RNGTT), traditionally acknowledged for its nuclear localization and functions, elucidating its contribution to cytoplasmic capping activities. A unique nuclear export sequence in CE mediates XPO1-dependent nuclear export of CE. Notably, during sodium arsenite-induced oxidative stress, cytoplasmic CE (cCE) congregates within stress granules (SGs). Through an integrated approach involving molecular docking and subsequent co-immunoprecipitation, we identify eIF3b, a constituent of SGs, as an interactive associate of CE, implying that it has a potential role in guiding cCE to SGs. We measured the cap status of specific mRNA transcripts from U2OS cells that were non-stressed, stressed and recovered from stress, which indicated that cCE-target transcripts lost their caps during stress but remarkably regained cap stability during the recovery phase. This comprehensive study thus uncovers a novel facet of cytoplasmic CE, which facilitates cellular recovery from stress by maintaining cap homeostasis of target mRNAs.
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Affiliation(s)
- Anakshi Gayen
- RNABio Lab, Institute of Health Sciences, Presidency University, Kolkata, West Bengal 700156, India
- CellBio Lab, Institute of Health Sciences, Presidency University, Kolkata, West Bengal 700156, India
| | - Avik Mukherjee
- RNABio Lab, Institute of Health Sciences, Presidency University, Kolkata, West Bengal 700156, India
| | - Krishna Kumar
- Structural Biology and Bioinformatics Division, Council for Scientific and Industrial Research (CSIR) - Indian Institute of Chemical Biology (IICB), Kolkata, West Bengal 700091, India
| | - Shubhra Majumder
- CellBio Lab, Institute of Health Sciences, Presidency University, Kolkata, West Bengal 700156, India
| | - Saikat Chakrabarti
- Structural Biology and Bioinformatics Division, Council for Scientific and Industrial Research (CSIR) - Indian Institute of Chemical Biology (IICB), Kolkata, West Bengal 700091, India
| | - Chandrama Mukherjee
- RNABio Lab, Institute of Health Sciences, Presidency University, Kolkata, West Bengal 700156, India
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Haqqani AS, Mianoor Z, Star AT, Detcheverry FE, Delaney CE, Stanimirovic DB, Hamel E, Badhwar A. Proteome Profiling of Brain Vessels in a Mouse Model of Cerebrovascular Pathology. BIOLOGY 2023; 12:1500. [PMID: 38132326 PMCID: PMC10740654 DOI: 10.3390/biology12121500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023]
Abstract
Cerebrovascular pathology that involves altered protein levels (or signaling) of the transforming growth factor beta (TGFβ) family has been associated with various forms of age-related dementias, including Alzheimer disease (AD) and vascular cognitive impairment and dementia (VCID). Transgenic mice overexpressing TGFβ1 in the brain (TGF mice) recapitulate VCID-associated cerebrovascular pathology and develop cognitive deficits in old age or when submitted to comorbid cardiovascular risk factors for dementia. We characterized the cerebrovascular proteome of TGF mice using mass spectrometry (MS)-based quantitative proteomics. Cerebral arteries were surgically removed from 6-month-old-TGF and wild-type mice, and proteins were extracted and analyzed by gel-free nanoLC-MS/MS. We identified 3602 proteins in brain vessels, with 20 demonstrating significantly altered levels in TGF mice. For total and/or differentially expressed proteins (p ≤ 0.01, ≥ 2-fold change), using multiple databases, we (a) performed protein characterization, (b) demonstrated the presence of their RNA transcripts in both mouse and human cerebrovascular cells, and (c) demonstrated that several of these proteins were present in human extracellular vesicles (EVs) circulating in blood. Finally, using human plasma, we demonstrated the presence of several of these proteins in plasma and plasma EVs. Dysregulated proteins point to perturbed brain vessel vasomotricity, remodeling, and inflammation. Given that blood-isolated EVs are novel, attractive, and a minimally invasive biomarker discovery platform for age-related dementias, several proteins identified in this study can potentially serve as VCID markers in humans.
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Affiliation(s)
- Arsalan S. Haqqani
- Human Health Therapeutics Research Centre, National Research Council Canada, 1200 Montreal Road, Ottawa, ON K1A 0R6, Canada; (A.S.H.); (A.T.S.); (C.E.D.); (D.B.S.)
| | - Zainab Mianoor
- Multiomics Investigation of Neurodegenerative Diseases (MIND) Laboratory, 4545 Chemin Queen Mary, Montreal, QC H3W 1W4, Canada; (Z.M.); (F.E.D.)
- Département de Pharmacologie et Physiologie, Institut de Génie Biomédical, Université de Montréal, 2900 Boulevard Édouard-Montpetit, Montreal, QC H3T 1J4, Canada
- Centre de Recherche de l’Institut Universitaire de Gériatrie (CRIUGM), 4545 Chemin Queen Mary, Montreal, QC H3W 1W4, Canada
| | - Alexandra T. Star
- Human Health Therapeutics Research Centre, National Research Council Canada, 1200 Montreal Road, Ottawa, ON K1A 0R6, Canada; (A.S.H.); (A.T.S.); (C.E.D.); (D.B.S.)
| | - Flavie E. Detcheverry
- Multiomics Investigation of Neurodegenerative Diseases (MIND) Laboratory, 4545 Chemin Queen Mary, Montreal, QC H3W 1W4, Canada; (Z.M.); (F.E.D.)
- Département de Pharmacologie et Physiologie, Institut de Génie Biomédical, Université de Montréal, 2900 Boulevard Édouard-Montpetit, Montreal, QC H3T 1J4, Canada
- Centre de Recherche de l’Institut Universitaire de Gériatrie (CRIUGM), 4545 Chemin Queen Mary, Montreal, QC H3W 1W4, Canada
| | - Christie E. Delaney
- Human Health Therapeutics Research Centre, National Research Council Canada, 1200 Montreal Road, Ottawa, ON K1A 0R6, Canada; (A.S.H.); (A.T.S.); (C.E.D.); (D.B.S.)
| | - Danica B. Stanimirovic
- Human Health Therapeutics Research Centre, National Research Council Canada, 1200 Montreal Road, Ottawa, ON K1A 0R6, Canada; (A.S.H.); (A.T.S.); (C.E.D.); (D.B.S.)
| | - Edith Hamel
- Laboratory of Cerebrovascular Research, Montreal Neurological Institute, McGill University, 3801 Rue University, Montreal, QC H3A 2B4, Canada;
| | - AmanPreet Badhwar
- Human Health Therapeutics Research Centre, National Research Council Canada, 1200 Montreal Road, Ottawa, ON K1A 0R6, Canada; (A.S.H.); (A.T.S.); (C.E.D.); (D.B.S.)
- Multiomics Investigation of Neurodegenerative Diseases (MIND) Laboratory, 4545 Chemin Queen Mary, Montreal, QC H3W 1W4, Canada; (Z.M.); (F.E.D.)
- Département de Pharmacologie et Physiologie, Institut de Génie Biomédical, Université de Montréal, 2900 Boulevard Édouard-Montpetit, Montreal, QC H3T 1J4, Canada
- Centre de Recherche de l’Institut Universitaire de Gériatrie (CRIUGM), 4545 Chemin Queen Mary, Montreal, QC H3W 1W4, Canada
- Laboratory of Cerebrovascular Research, Montreal Neurological Institute, McGill University, 3801 Rue University, Montreal, QC H3A 2B4, Canada;
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Del Valle-Morales D, Romano G, Le P, Saviana M, Brown R, Micalo L, Li H, Ferlita AL, Nigita G, Nana-Sinkam P, Acunzo M. METTL3 alters capping enzyme expression and its activity on ribosomal proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.22.568301. [PMID: 38045284 PMCID: PMC10690260 DOI: 10.1101/2023.11.22.568301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The 5' cap, catalyzed by RNA guanylyltransferase and 5'-phosphatase (RNGTT), is a vital mRNA modification for the functionality of mRNAs. mRNA capping occurs in the nucleus for the maturation of the functional mRNA and in the cytoplasm for fine-tuning gene expression. Given the fundamental importance of RNGTT in mRNA maturation and expression there is a need to further investigate the regulation of RNGTT. N6-methyladenosine (m 6 A) is one of the most abundant RNA modifications involved in the regulation of protein translation, mRNA stability, splicing, and export. We sought to investigate whether m 6 A could regulate the expression and activity of RNGTT. A motif for the m 6 A writer methyltransferase 3 (METTL3) in the 3'UTR of RNGTT mRNA was identified. Knockdown of METTL3 resulted in destabilizing RNGTT mRNA, and reduced protein expression. Sequencing of capped mRNAs identified an underrepresentation of ribosomal protein mRNA overlapping with 5' terminal oligopyrimidine (TOP) mRNAs and genes are dysregulated when cytoplasmic capping is inhibited. Pathway analysis identified disruptions in the mTOR and p70S6K pathways. A reduction in RPS6 mRNA capping, protein expression, and phosphorylation was detected with METTL3 knockdown.
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Ma J, Yang Z, Huang Z, Li L, Huang J, Chen J, Ni R, Luo L, He J. Rngtt governs biliary-derived liver regeneration initiation by transcriptional regulation of mTORC1 and Dnmt1 in zebrafish. Hepatology 2023; 78:167-178. [PMID: 36724876 DOI: 10.1097/hep.0000000000000186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/23/2022] [Indexed: 02/03/2023]
Abstract
In cases of end-stage liver diseases, the proliferation of existing hepatocytes is compromised, a feature of human chronic liver disease, in which most hepatocytes are dysfunctional. So far, liver transplantation represents the only curative therapeutic solution for advanced liver diseases, and the shortage of donor organs leads to high morbidity and mortality worldwide. The promising treatment is to prompt the biliary epithelial cells (BECs) transdifferentiation. However, the critical factors governing the initiation of BEC-derived liver regeneration are largely unknown. The zebrafish has advantages in large-scale genetic screens to identify the critical factors involved in liver regeneration. Here, we combined N-ethyl-N-nitrosourea screen, positional cloning, transgenic lines, antibody staining, and in situ hybridization methods and identified a liver regeneration defect mutant ( lrd ) using the zebrafish extensive liver injury model. Through positional cloning and genomic sequencing, we mapped the mutation site to rngtt . Loss of rngtt leads to the defects of BEC dedifferentiation, bipotential progenitor cell activation, and cell proliferation in the initiation stage of liver regeneration. The transdifferentiation from BECs to hepatocytes did not occur even at the late stage of liver regeneration. Mechanically, Rngtt transcriptionally regulates the attachment of mRNA cap to mTOR complex 1 (mTORC1) components and dnmt1 to maintain the activation of mTORC1 and DNA methylation in BECs after severe liver injury and prompt BEC to hepatocyte conversion. Furthermore, rptor and dnmt1 mutants displayed the same liver regeneration defects as rngtt mutation. In conclusion, our results suggest Rngtt is a new factor that initiates BEC-derived liver regeneration.
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Affiliation(s)
- Jianlong Ma
- Institute of Developmental Biology and Regenerative Medicine, Southwest University, Beibei, Chongqing, China
| | - Zhuolin Yang
- Institute of Developmental Biology and Regenerative Medicine, Southwest University, Beibei, Chongqing, China
| | - Zhuofu Huang
- Institute of Developmental Biology and Regenerative Medicine, Southwest University, Beibei, Chongqing, China
| | - Linke Li
- Institute of Developmental Biology and Regenerative Medicine, Southwest University, Beibei, Chongqing, China
| | - Jingliang Huang
- Institute of Developmental Biology and Regenerative Medicine, Southwest University, Beibei, Chongqing, China
| | - Jingying Chen
- Institute of Developmental Biology and Regenerative Medicine, Southwest University, Beibei, Chongqing, China
- University of Chinese Academy of Sciences (Chongqing), Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Beibei, Chongqing, China
| | - Rui Ni
- Institute of Developmental Biology and Regenerative Medicine, Southwest University, Beibei, Chongqing, China
| | - Lingfei Luo
- Institute of Developmental Biology and Regenerative Medicine, Southwest University, Beibei, Chongqing, China
| | - Jianbo He
- Institute of Developmental Biology and Regenerative Medicine, Southwest University, Beibei, Chongqing, China
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5
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Mukherjee A, Islam S, Kieser RE, Kiss DL, Mukherjee C. Long noncoding RNAs are substrates for cytoplasmic capping enzyme. FEBS Lett 2023; 597:947-961. [PMID: 36856012 PMCID: PMC11119571 DOI: 10.1002/1873-3468.14603] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 02/04/2023] [Accepted: 02/08/2023] [Indexed: 03/02/2023]
Abstract
Cytoplasmic capping returns a cap to specific mRNAs, thus protecting uncapped RNAs from decay. Prior to the identification of cytoplasmic capping, uncapped mRNAs were thought to be degraded. Here, we test whether long noncoding RNAs (lncRNAs) are substrates of the cytoplasmic capping enzyme (cCE). The subcellular localisation of 14 lncRNAs associated with sarcomas were examined in U2OS osteosarcoma cells. We used 5' rapid amplification of cDNA ends (RACE) to assay uncapped forms of these lncRNAs. Inhibiting cytoplasmic capping elevated uncapped forms of selected lncRNAs indicating a plausible role of cCE in targeting them. Analysis of published cap analysis of gene expression (CAGE) data shows increased prevalence of certain 5'-RACE cloned sequences, suggesting that these uncapped lncRNAs are targets of cytoplasmic capping.
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Affiliation(s)
- Avik Mukherjee
- Institute of Health Sciences, Presidency University, Kolkata, India
| | - Safirul Islam
- Institute of Health Sciences, Presidency University, Kolkata, India
| | - Rachel E Kieser
- Center for RNA Therapeutics, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
| | - Daniel L Kiss
- Center for RNA Therapeutics, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
- Weill Cornell Medical College, New York, NY, USA
- Houston Methodist Cancer Center, Houston, TX, USA
- Houston Methodist Academic Institute, Houston, TX, USA
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Ostalé CM, Esteban N, López-Varea A, de Celis JF. Functional requirements of protein kinases and phosphatases in the development of the Drosophila melanogaster wing. G3-GENES GENOMES GENETICS 2021; 11:6380433. [PMID: 34599799 PMCID: PMC8664455 DOI: 10.1093/g3journal/jkab348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/06/2021] [Indexed: 11/14/2022]
Abstract
Protein kinases and phosphatases constitute a large family of conserved enzymes that control a variety of biological processes by regulating the phosphorylation state of target proteins. They play fundamental regulatory roles during cell cycle progression and signaling, among other key aspects of multicellular development. The complement of protein kinases and phosphatases includes approximately 326 members in Drosophila, and they have been the subject of several functional screens searching for novel components of signaling pathways and regulators of cell division and survival. These approaches have been carried out mostly in cell cultures using RNA interference to evaluate the contribution of each protein in different functional assays, and have contributed significantly to assign specific roles to the corresponding genes. In this work we describe the results of an evaluation of the Drosophila complement of kinases and phosphatases using the wing as a system to identify their functional requirements in vivo. We also describe the results of several modifying screens aiming to identify among the set of protein kinases and phosphatases additional components or regulators of the activities of the Epidermal Growth Factor and Insulin receptors signaling pathways.
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Affiliation(s)
- Cristina M Ostalé
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Nuria Esteban
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Ana López-Varea
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Jose F de Celis
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
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7
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Interplay of mRNA capping and transcription machineries. Biosci Rep 2021; 40:221784. [PMID: 31904821 PMCID: PMC6981093 DOI: 10.1042/bsr20192825] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/02/2020] [Accepted: 01/06/2020] [Indexed: 12/31/2022] Open
Abstract
Early stages of transcription from eukaryotic promoters include two principal events: the capping of newly synthesized mRNA and the transition of RNA polymerase II from the preinitiation complex to the productive elongation state. The capping checkpoint model implies that these events are tightly coupled, which is necessary for ensuring the proper capping of newly synthesized mRNA. Recent findings also show that the capping machinery has a wider effect on transcription and the entire gene expression process. The molecular basis of these phenomena is discussed.
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8
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Lu X, Luan S, Dai P, Luo K, Chen B, Cao B, Sun L, Yan Y, Kong J. Insights into the molecular basis of immunosuppression and increasing pathogen infection severity of ammonia toxicity by transcriptome analysis in pacific white shrimp Litopenaeus vannamei. FISH & SHELLFISH IMMUNOLOGY 2019; 88:528-539. [PMID: 30885745 DOI: 10.1016/j.fsi.2019.03.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 03/09/2019] [Accepted: 03/12/2019] [Indexed: 06/09/2023]
Abstract
The high concentration of ammonia resulting from intensive culture system and environmental pollution could cause disease occurrence in shrimp, but little information is available on its molecular mechanisms. In this study, we performed comparative transcriptome analysis among WSSV-infected shrimp under ammonia stress (LAV), WSSV-infected shrimp under normal water (LV), and normal shrimp under ammonia stress (LA) groups to identify the key genes and pathways involved in immunosuppression and increasing pathogen infection severity caused by ammonia toxicity in Litopenaeus vannamei. Totally, 526 significantly differential expressed genes (DEGs) were identified in LAV group compared to LV and LA groups, among which 270 genes were lost expressed and 67 genes uniquely expressed in the LAV group. According to the public functional reports for the annotated DEGs, they potentially involved in the following functions: (1) accelerating pathogen adhesion, invasion and multiplication; (2) reducing the ability for pathogen defense and immune response; (3) inhibiting positive regulation of apoptotic and antioxidant defense for host homeostasis; (4) inhibiting transcription and protein transport; (5) and increasing protein methylation and ubiquitination, etc. A total of 13 pathways were obtained mainly involving in this process, which mainly led to the following changes: (1) increasing the immunosuppression, anemia, endocrine dysfunction, neurotoxic effect and neuroinvasion, atherosclerosis and thrombogenesis, blood-brain barrier penetration, thyroid disorder, necrosis, inflammation, and circadian disturbance; (2) reducing the ability of vascular remodeling, angiogenesis, cell survival, migration, apoptosis, and lymph transferred to blood stream; (3) leading to cell hypertrophy, cellular shape changes, and mesangial matrix expansion. The present results firstly supplied molecular mechanisms for the ammonia toxicity inhibiting the immune system and increasing pathogen infection severity in shrimp, which is a prerequisite for better understanding the pathogenesis caused by ammonia toxicity.
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Affiliation(s)
- Xia Lu
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Sheng Luan
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Ping Dai
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Kun Luo
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Baolong Chen
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Baoxiang Cao
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Li Sun
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Yunjun Yan
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Jie Kong
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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9
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Networks of mRNA Processing and Alternative Splicing Regulation in Health and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1157:1-27. [PMID: 31342435 DOI: 10.1007/978-3-030-19966-1_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
mRNA processing events introduce an intricate layer of complexity into gene expression processes, supporting a tremendous level of diversification of the genome's coding and regulatory potential, particularly in vertebrate species. The recent development of massive parallel sequencing methods and their adaptation to the identification and quantification of different RNA species and the dynamics of mRNA metabolism and processing has generated an unprecedented view over the regulatory networks that are established at this level, which contribute to sustain developmental, tissue specific or disease specific gene expression programs. In this chapter, we provide an overview of the recent evolution of transcriptome profiling methods and the surprising insights that have emerged in recent years regarding distinct mRNA processing events - from the 5' end to the 3' end of the molecule.
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Trotman JB, Schoenberg *DR. A recap of RNA recapping. WILEY INTERDISCIPLINARY REVIEWS. RNA 2019; 10:e1504. [PMID: 30252202 PMCID: PMC6294674 DOI: 10.1002/wrna.1504] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/13/2018] [Accepted: 08/01/2018] [Indexed: 12/12/2022]
Abstract
The N7-methylguanosine cap is a hallmark of the 5' end of eukaryotic mRNAs and is required for gene expression. Loss of the cap was believed to lead irreversibly to decay. However, nearly a decade ago, it was discovered that mammalian cells contain enzymes in the cytoplasm that are capable of restoring caps onto uncapped RNAs. In this review, we summarize recent advances in our understanding of cytoplasmic RNA recapping and discuss the biochemistry of this process and its impact on regulating and diversifying the transcriptome. Although most studies focus on mammalian RNA recapping, we also highlight new observations for recapping in disparate eukaryotic organisms, with the trypanosome recapping system appearing to be a fascinating example of convergent evolution. We conclude with emerging insights into the biological significance of RNA recapping and prospects for the future of this evolving area of study. This article is categorized under: RNA Processing > RNA Editing and Modification Translation > Translation Regulation RNA Processing > Capping and 5' End Modifications RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Jackson B. Trotman
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, The Ohio State University, Columbus, OH 43210,
| | - *Daniel R. Schoenberg
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, schoenberg,
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Trotman JB, Agana BA, Giltmier AJ, Wysocki VH, Schoenberg DR. RNA-binding proteins and heat-shock protein 90 are constituents of the cytoplasmic capping enzyme interactome. J Biol Chem 2018; 293:16596-16607. [PMID: 30166341 PMCID: PMC6204893 DOI: 10.1074/jbc.ra118.004973] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/22/2018] [Indexed: 01/20/2023] Open
Abstract
The N7-methylguanosine cap is added in the nucleus early in gene transcription and is a defining feature of eukaryotic mRNAs. Mammalian cells also possess cytoplasmic machinery for restoring the cap at uncapped or partially degraded RNA 5' ends. Central to both pathways is capping enzyme (CE) (RNA guanylyltransferase and 5'-phosphatase (RNGTT)), a bifunctional, nuclear and cytoplasmic enzyme. CE is recruited to the cytoplasmic capping complex by binding of a C-terminal proline-rich sequence to the third Src homology 3 (SH3) domain of NCK adapter protein 1 (NCK1). To gain broader insight into the cellular context of cytoplasmic recapping, here we identified the protein interactome of cytoplasmic CE in human U2OS cells through two complementary approaches: chemical cross-linking and recovery with cytoplasmic CE and protein screening with proximity-dependent biotin identification (BioID). This strategy unexpectedly identified 66 proteins, 52 of which are RNA-binding proteins. We found that CE interacts with several of these proteins independently of RNA, mediated by sequences within its N-terminal triphosphatase domain, and we present a model describing how CE-binding proteins may function in defining recapping targets. This analysis also revealed that CE is a client protein of heat shock protein 90 (HSP90). Nuclear and cytoplasmic CEs were exquisitely sensitive to inhibition of HSP90, with both forms declining significantly following treatment with each of several HSP90 inhibitors. Importantly, steady-state levels of capped mRNAs decreased in cells treated with the HSP90 inhibitor geldanamycin, raising the possibility that the cytotoxic effect of these drugs may partially be due to a general reduction in translatable mRNAs.
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Affiliation(s)
- Jackson B Trotman
- From the Center for RNA Biology
- Ohio State Biochemistry Program
- Department of Biological Chemistry and Pharmacology, and
| | - Bernice A Agana
- From the Center for RNA Biology
- Ohio State Biochemistry Program
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210
| | - Andrew J Giltmier
- From the Center for RNA Biology
- Department of Biological Chemistry and Pharmacology, and
| | - Vicki H Wysocki
- From the Center for RNA Biology
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210
| | - Daniel R Schoenberg
- From the Center for RNA Biology,
- Department of Biological Chemistry and Pharmacology, and
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12
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Ohta S, Schoenwolf GC. Dorsoventral differences in cAMP levels and correlated changes in the subcellular distribution of the PKA catalytic domain, provide further evidence that PKA signaling coordinates dorsoventral patterning of the otocyst. Dev Growth Differ 2018; 60:431-441. [PMID: 29920660 DOI: 10.1111/dgd.12543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/09/2018] [Accepted: 05/10/2018] [Indexed: 01/22/2023]
Abstract
Dorsoventral (DV) patterning of the otocyst gives rise to formation of the morphologically and functionally complex membranous labyrinth composed of unique dorsal and ventral sensory organs. DV patterning results from extracellular signaling by secreted growth factors, which presumably form reciprocal concentration gradients across the DV axis of the otocyst. Previous work suggested a model in which two important growth factors, bone morphogenetic protein (BMP) and SHH, undergo crosstalk through an intersecting pathway to coordinate DV patterning. cAMP-dependent protein kinase A (PKA) lies at the heart of this pathway. Here, we provide further evidence that PKA signaling coordinates DV patterning, showing that both BMPs and SHH regulate cAMP levels, with BMPs increasing levels in the dorsal otocyst and SHH decreasing levels in the ventral otocyst. This, in turn, results in regional changes in the subcellular distribution of the catalytic domain of PKA, as well as DV regulation of PKA activity, increasing it dorsally and decreasing it ventrally. These new results fill an important gap in our previous understanding of how ligand signaling acts intracellularly during otocyst DV patterning and early morphogenesis, thereby initiating the series of events leading to formation of the inner ear sensory organs that function in balance and hearing.
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Affiliation(s)
- Sho Ohta
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, Utah
| | - Gary C Schoenwolf
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, Utah
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