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Wang W, Liu F, Ugalde MV, Pyle AM. A compact regulatory RNA element in mouse Hsp70 mRNA. NAR MOLECULAR MEDICINE 2024; 1:ugae002. [PMID: 38318492 PMCID: PMC10840451 DOI: 10.1093/narmme/ugae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/08/2024] [Accepted: 01/24/2024] [Indexed: 02/07/2024]
Abstract
Hsp70 (70 kDa heat shock protein) performs molecular chaperone functions by assisting the folding of newly synthesized and misfolded proteins, thereby counteracting various cell stresses and preventing multiple diseases, including neurodegenerative disorders and cancers. It is well established that, immediately after heat shock, Hsp70 gene expression is mediated by a canonical mechanism of cap-dependent translation. However, the molecular mechanism of Hsp70 expression during heat shock remains elusive. Intriguingly, the 5' end of Hsp70 messenger RNA (mRNA) appears to form a compact structure with the potential to regulate protein expression in a cap-independent manner. Here, we determined the minimal length of the mHsp70 5'-terminal mRNA sequence that is required for RNA folding into a highly compact structure. This span of this RNA element was mapped and the secondary structure characterized by chemical probing, resulting in a secondary structural model that includes multiple stable stems, including one containing the canonical start codon. All of these components, including a short stretch of the 5' open reading frame (ORF), were shown to be vital for RNA folding. This work provides a structural basis for future investigations on the role of translational regulatory structures in the 5' untranslated region and ORF sequences of Hsp70 during heat shock.
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Affiliation(s)
- Wenshuai Wang
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Fei Liu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Maria Vera Ugalde
- Department of Biochemistry. McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Anna Marie Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
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2
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Wang W, Liu F, Ugalde MV, Pyle AM. A compact regulatory RNA element in mouse Hsp70 mRNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.22.529618. [PMID: 36865185 PMCID: PMC9980084 DOI: 10.1101/2023.02.22.529618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Hsp70 performs molecular chaperone functions by assisting in folding newly synthesized or misfolded proteins, thereby counteracting various cell stresses and preventing multiple diseases including neurodegenerative disorders and cancer. It is well established that Hsp70 upregulation during post-heat shock stimulus is mediated by cap-dependent translation. However, the molecular mechanisms of Hsp70 expression during heat shock stimulus remains elusive, even though the 5' end of Hsp70 mRNA may form a compact structure to positively regulate protein expression in the mode of cap-independent translation. The minimal truncation which can fold to a compact structure was mapped and its secondary structure was characterized by chemical probing. The predicted model revealed a highly compact structure with multiple stems. Including the stem where the canonical start codon is located, several stems were identified to be vital for RNA folding, thereby providing solid structural basis for future investigations on the function of this RNA structure on Hsp70 translation during heat shock.
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3
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Chen N, Wu M, Tang GP, Wang HJ, Huang CX, Wu XJ, He Y, Zhang B, Huang CH, Liu H, Wang WM, Wang HL. Effects of Acute Hypoxia and Reoxygenation on Physiological and Immune Responses and Redox Balance of Wuchang Bream ( Megalobrama amblycephala Yih, 1955). Front Physiol 2017. [PMID: 28642716 PMCID: PMC5462904 DOI: 10.3389/fphys.2017.00375] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
To study Megalobrama amblycephala adaption to water hypoxia, the changes in physiological levels, innate immune responses, redox balance of M.amblycephala during hypoxia were investigated in the present study. When M. amblycephala were exposed to different dissolved oxygen (DO) including control (DO: 5.5 mg/L) and acute hypoxia (DO: 3.5 and 1.0 mg/L, respectively), hemoglobin (Hb), methemoglobin (MetHb), glucose, Na+, succinatedehydrogenase (SDH), lactate, interferon alpha (IFNα), and lysozyme (LYZ), except hepatic glycogen and albumin gradually increased with the decrease of DO level. When M. amblycephala were exposed to different hypoxia time including 0.5 and 6 h (DO: 3.5 mg/L), and then reoxygenation for 24 h after 6 h hypoxia, Hb, MetHb, glucose, lactate, and IFNα, except Na+, SDH, hepatic glycogen, albumin, and LYZ increased with the extension of hypoxia time, while the above investigated indexes (except albumin, IFNα, and LYZ) decreased after reoxygenation. On the other hand, the liver SOD, CAT, hydrogen peroxide (H2O2), and total ROS were all remained at lower levels under hypoxia stress. Finally, Hif-1α protein in the liver, spleen, and gill were increased with the decrease of oxygen concentration and prolongation of hypoxia time. Interestingly, one Hsp70 isoforms mediated by internal ribozyme entry site (IRES) named junior Hsp70 was only detected in liver, spleen and gill. Taken together, these results suggest that hypoxia affects M. amblycephala physiology and reduces liver oxidative stress. Hypoxia-reoxygenation stimulates M. amblycephala immune parameter expressions, while Hsp70 response to hypoxia is tissue-specific.
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Affiliation(s)
- Nan Chen
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural UniversityWuhan, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei ProvinceWuhan, China
| | - Meng Wu
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural UniversityWuhan, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei ProvinceWuhan, China
| | - Guo-Pan Tang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural UniversityWuhan, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei ProvinceWuhan, China.,Laboratory of Freshwater Animal Breeding, College of Animal Science and Technology, Henan University of Animal Husbandry and EconomyZhengzhou, China
| | - Hui-Juan Wang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural UniversityWuhan, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei ProvinceWuhan, China
| | - Chun-Xiao Huang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural UniversityWuhan, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei ProvinceWuhan, China
| | - Xin-Jie Wu
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural UniversityWuhan, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei ProvinceWuhan, China
| | - Yan He
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural UniversityWuhan, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei ProvinceWuhan, China
| | - Bao Zhang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural UniversityWuhan, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei ProvinceWuhan, China
| | - Cui-Hong Huang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural UniversityWuhan, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei ProvinceWuhan, China
| | - Hong Liu
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural UniversityWuhan, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei ProvinceWuhan, China
| | - Wei-Min Wang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural UniversityWuhan, China
| | - Huan-Ling Wang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural UniversityWuhan, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei ProvinceWuhan, China
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Sajjanar B, Deb R, Raina SK, Pawar S, Brahmane MP, Nirmale AV, Kurade NP, Manjunathareddy GB, Bal SK, Singh NP. Untranslated regions (UTRs) orchestrate translation reprogramming in cellular stress responses. J Therm Biol 2017; 65:69-75. [DOI: 10.1016/j.jtherbio.2017.02.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 11/29/2022]
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5
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Carnicelli D, Arfilli V, Onofrillo C, Alfieri RR, Petronini PG, Montanaro L, Brigotti M. Cap-independent protein synthesis is enhanced by betaine under hypertonic conditions. Biochem Biophys Res Commun 2017; 483:936-940. [PMID: 28082201 DOI: 10.1016/j.bbrc.2017.01.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 01/09/2017] [Indexed: 01/15/2023]
Abstract
Protein synthesis is one of the main cellular functions inhibited during hypertonic challenge. The subsequent accumulation of the compatible osmolyte betaine during the later adaptive response allows not only recovery of translation but also its stimulation. In this paper, we show that betaine modulates translation by enhancing the formation of cap-independent 48 S pre-initiation complexes, leaving cap-dependent 48 S pre-initiation complexes basically unchanged. In the presence of betaine, CrPV IRES- and sodium-dependent neutral amino acid transporter-2 (SNAT2) 5'-UTR-driven translation is 2- and 1.5-fold stimulated in MCF7 cells, respectively. Thus, betaine could provide an advantage in translation of messengers coding for proteins implicated in the response of cells to different stressors, which are often recognized by ribosomal 40 S subunit through simplified cap-independent mechanisms.
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Affiliation(s)
- Domenica Carnicelli
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale, Università di Bologna, Bologna, Italy
| | - Valentina Arfilli
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale, Università di Bologna, Bologna, Italy
| | - Carmine Onofrillo
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale, Università di Bologna, Bologna, Italy
| | - Roberta R Alfieri
- Dipartimento di Medicina Clinica e Sperimentale, Università di Parma, Parma, Italy
| | | | - Lorenzo Montanaro
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale, Università di Bologna, Bologna, Italy
| | - Maurizio Brigotti
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale, Università di Bologna, Bologna, Italy.
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Penzo M, Carnicelli D, Montanaro L, Brigotti M. A reconstituted cell-free assay for the evaluation of the intrinsic activity of purified human ribosomes. Nat Protoc 2016; 11:1309-25. [PMID: 27336708 DOI: 10.1038/nprot.2016.072] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We describe a cell-free translation system for evaluating the activity of ribosomes stringently purified from human cells. This system is based on in vitro reconstitution of the cellular translation machinery, in which a ribosome-free rabbit reticulocyte lysate (RRL) is reassembled with human ribosomes and in vitro-transcribed reporter mRNAs. The protocol describes the preparation of the RRL-derived fractions, purification of ribosomes devoid of detectable nonribosomal-associated factors, and assembly of the reactions to evaluate ribosomal translational efficiency and fidelity using appropriate reporter transcripts. The whole procedure can be completed in ∼2.5 d (plus 2 weeks for RRL preparation and cell expansion time). This protocol can be applied to study intrinsic functional properties (cis-acting element-mediated translation initiation or translational fidelity) of ribosome populations from different sources (including nonhuman origin). It is therefore useful for the characterization of ribosomal function in ribosomopathies and cancer, and it will be applicable in the emerging fields of ribosome diversity and specialized ribosomes.
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Affiliation(s)
- Marianna Penzo
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Domenica Carnicelli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Lorenzo Montanaro
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Maurizio Brigotti
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
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7
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Wang R, Ferraris JD, Izumi Y, Dmitrieva N, Ramkissoon K, Wang G, Gucek M, Burg MB. Global discovery of high-NaCl-induced changes of protein phosphorylation. Am J Physiol Cell Physiol 2014; 307:C442-54. [PMID: 24965592 DOI: 10.1152/ajpcell.00379.2013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
High extracellular NaCl, such as in the renal medulla, can perturb and even kill cells, but cells mount protective responses that enable them to survive and function. Many high-NaCl-induced perturbations and protective responses are known, but the signaling pathways involved are less clear. Change in protein phosphorylation is a common mode of cell signaling, but there was no unbiased survey of protein phosphorylation in response to high NaCl. We used stable isotopic labeling of amino acids in cell culture coupled to mass spectrometry to identify changes in protein phosphorylation in human embryonic kidney (HEK 293) cells exposed to high NaCl. We reproducibly identify >8,000 unique phosphopeptides in 4 biological replicate samples with a 1% false discovery rate. High NaCl significantly changed phosphorylation of 253 proteins. Western analysis and targeted ion selection mass spectrometry confirm a representative sample of the phosphorylation events. We analyze the affected proteins by functional category to infer how altered protein phosphorylation might signal cellular responses to high NaCl, including alteration of cell cycle, cyto/nucleoskeletal organization, DNA double-strand breaks, transcription, proteostasis, metabolism of mRNA, and cell death.
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Affiliation(s)
- Rong Wang
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Joan D Ferraris
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Yuichiro Izumi
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Natalia Dmitrieva
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Kevin Ramkissoon
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Guanghui Wang
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Marjan Gucek
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Maurice B Burg
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
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Jones CI, Grima DP, Waldron JA, Jones S, Parker HN, Newbury SF. The 5'-3' exoribonuclease Pacman (Xrn1) regulates expression of the heat shock protein Hsp67Bc and the microRNA miR-277-3p in Drosophila wing imaginal discs. RNA Biol 2013; 10:1345-55. [PMID: 23792537 PMCID: PMC3817156 DOI: 10.4161/rna.25354] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Pacman/Xrn1 is a highly conserved exoribonuclease known to play a critical role in gene regulatory events such as control of mRNA stability, RNA interference and regulation via miRNAs. Although Pacman has been well studied in Drosophila tissue culture cells, the biologically relevant cellular pathways controlled by Pacman in natural tissues are unknown. This study shows that a hypomorphic mutation in pacman (pcm5) results in smaller wing imaginal discs. These tissues, found in the larva, are known to grow and differentiate to form wing and thorax structures in the adult fly. Using microarray analysis, followed by quantitative RT-PCR, we show that eight mRNAs were increased in level by > 2-fold in the pcm5 mutant wing discs compared with the control. The levels of pre-mRNAs were tested for five of these mRNAs; four did not increase in the pcm5 mutant, showing that they are regulated at the post-transcriptional level and, therefore, could be directly affected by Pacman. These transcripts include one that encodes the heat shock protein Hsp67Bc, which is upregulated 11.9-fold at the post-transcriptional level and 2.3-fold at the protein level. One miRNA, miR-277-3p, is 5.6-fold downregulated at the post-transcriptional level in mutant discs, suggesting that Pacman affects its processing in this tissue. Together, these data show that a relatively small number of mRNAs and miRNAs substantially change in abundance in pacman mutant wing imaginal discs. Since Hsp67Bc is known to regulate autophagy and protein synthesis, it is possible that Pacman may control the growth of wing imaginal discs by regulating these processes.
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Affiliation(s)
- Christopher I Jones
- Brighton and Sussex Medical School; Medical Research Building; University of Sussex; Falmer, Brighton, UK
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