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Litberg TJ, Horowitz S. Roles of Nucleic Acids in Protein Folding, Aggregation, and Disease. ACS Chem Biol 2024; 19:809-823. [PMID: 38477936 PMCID: PMC11149768 DOI: 10.1021/acschembio.3c00695] [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] [Indexed: 03/14/2024]
Abstract
The role of nucleic acids in protein folding and aggregation is an area of continued research, with relevance to understanding both basic biological processes and disease. In this review, we provide an overview of the trajectory of research on both nucleic acids as chaperones and their roles in several protein misfolding diseases. We highlight key questions that remain on the biophysical and biochemical specifics of how nucleic acids have large effects on multiple proteins' folding and aggregation behavior and how this pertains to multiple protein misfolding diseases.
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Affiliation(s)
- Theodore J. Litberg
- Department of Chemistry & Biochemistry and The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, 80208, USA
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Scott Horowitz
- Department of Chemistry & Biochemistry and The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, 80208, USA
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2
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Pathak BK, Banerjee S, Mondal S, Chakraborty B, Sengupta J, Barat C. Unfolded protein exhibits antiassociation activity toward the 50S subunit facilitating 70S ribosome dissociation. FEBS J 2017; 284:3915-3930. [DOI: 10.1111/febs.14282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 09/05/2017] [Accepted: 09/26/2017] [Indexed: 01/24/2023]
Affiliation(s)
- Bani K. Pathak
- Department of Biotechnology St Xavier's College KolkataIndia
- Structural Biology and Bio‐Informatics Division Indian Institute of Chemical Biology (Council of Scientific and Industrial Research) Kolkata India
| | | | - Surojit Mondal
- Department of Biotechnology St Xavier's College KolkataIndia
| | - Biprashekhar Chakraborty
- Structural Biology and Bio‐Informatics Division Indian Institute of Chemical Biology (Council of Scientific and Industrial Research) Kolkata India
| | - Jayati Sengupta
- Structural Biology and Bio‐Informatics Division Indian Institute of Chemical Biology (Council of Scientific and Industrial Research) Kolkata India
| | - Chandana Barat
- Department of Biotechnology St Xavier's College KolkataIndia
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3
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Sequestration of Ribosome during Protein Aggregate Formation: Contribution of ribosomal RNA. Sci Rep 2017; 7:42017. [PMID: 28169307 PMCID: PMC5294636 DOI: 10.1038/srep42017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 01/06/2017] [Indexed: 12/21/2022] Open
Abstract
An understanding of the mechanisms underlying protein aggregation and cytotoxicity of the protein aggregates is crucial in the prevention of several diseases in humans. Ribosome, the cellular protein synthesis machine is capable of acting as a protein folding modulator. The peptidyltransferase center residing in the domain V of large ribosomal subunit 23S rRNA is the centre for the protein folding ability of the ribosome and is also the cellular target of several antiprion compounds. Our in vitro studies unexpectedly reveal that the partial unfolding or aggregation of lysozyme under reducing conditions in presence of the ribosome can induce aggregation of ribosomal components. Electrostatic interactions complemented by specific rRNA-protein interaction drive the ribosome-protein aggregation process. Under similar conditions the rRNA, especially the large subunit rRNA and in vitro transcribed RNA corresponding to domain V of 23S rRNA (bDV RNA) stimulates lysozyme aggregation leading to RNA-protein aggregate formation. Protein aggregation during the refolding of non-disulfide containing protein BCAII at high concentrations also induces ribosome aggregation. BCAII aggregation was also stimulated in presence of the large subunit rRNA. Our observations imply that the specific sequestration of the translation machine by aggregating proteins might contribute to their cytotoxicity.
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Das D, Samanta D, Bhattacharya A, Basu A, Das A, Ghosh J, Chakrabarti A, Das Gupta C. A Possible Role of the Full-Length Nascent Protein in Post-Translational Ribosome Recycling. PLoS One 2017; 12:e0170333. [PMID: 28099529 PMCID: PMC5242463 DOI: 10.1371/journal.pone.0170333] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 01/03/2017] [Indexed: 11/30/2022] Open
Abstract
Each cycle of translation initiation in bacterial cell requires free 50S and 30S ribosomal subunits originating from the post-translational dissociation of 70S ribosome from the previous cycle. Literature shows stable dissociation of 70S from model post-termination complexes by the concerted action of Ribosome Recycling Factor (RRF) and Elongation Factor G (EF-G) that interact with the rRNA bridge B2a/B2b joining 50S to 30S. In such experimental models, the role of full-length nascent protein was never considered seriously. We observed relatively slow release of full-length nascent protein from 50Sof post translation ribosome, and in that process, its toe prints on the rRNA in vivo and in in vitro translation with E.coli S30 extract. We reported earlier that a number of chemically unfolded proteins like bovine carbonic anhydrase (BCA), lactate dehydrogenase (LDH), malate dehydrogenase (MDH), lysozyme, ovalbumin etc., when added to free 70Sin lieu of the full length nascent proteins, also interact with identical RNA regions of the 23S rRNA. Interestingly the rRNA nucleotides that slow down release of the C-terminus of full-length unfolded protein were found in close proximity to the B2a/B2b bridge. It indicated a potentially important chemical reaction conserved throughout the evolution. Here we set out to probe that conserved role of unfolded protein conformation in splitting the free or post-termination 70S. How both the RRF-EFG dependent and the plausible nascent protein–EFG dependent ribosome recycling pathways might be relevant in bacteria is discussed here.
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Affiliation(s)
- Debasis Das
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata, India
| | - Dibyendu Samanta
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata, India
| | - Arpita Bhattacharya
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata, India
| | - Arunima Basu
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata, India
- Department of Microbiology, Raidighi College, Raidighi, 24 Parganas (S), West Bengal, India
| | - Anindita Das
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata, India
| | - Jaydip Ghosh
- Department of Microbiology, St. Xavier’s College, Kolkata, India
| | - Abhijit Chakrabarti
- Crystallography & Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, Kolkata, India
| | - Chanchal Das Gupta
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata, India
- Department of Life Sciences and Biotechnology, Jadavpur University, Kolkata, India
- * E-mail:
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5
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Mondal S, Pathak BK, Ray S, Barat C. Impact of P-Site tRNA and antibiotics on ribosome mediated protein folding: studies using the Escherichia coli ribosome. PLoS One 2014; 9:e101293. [PMID: 25000563 PMCID: PMC4085065 DOI: 10.1371/journal.pone.0101293] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 06/04/2014] [Indexed: 12/22/2022] Open
Abstract
Background The ribosome, which acts as a platform for mRNA encoded polypeptide synthesis, is also capable of assisting in folding of polypeptide chains. The peptidyl transferase center (PTC) that catalyzes peptide bond formation resides in the domain V of the 23S rRNA of the bacterial ribosome. Proper positioning of the 3′ –CCA ends of the A- and P-site tRNAs via specific interactions with the nucleotides of the PTC are crucial for peptidyl transferase activity. This RNA domain is also the center for ribosomal chaperoning activity. The unfolded polypeptide chains interact with the specific nucleotides of the PTC and are released in a folding competent form. In vitro transcribed RNA corresponding to this domain (bDV RNA) also displays chaperoning activity. Results The present study explores the effects of tRNAs, antibiotics that are A- and P-site PTC substrate analogs (puromycin and blasticidin) and macrolide antibiotics (erythromycin and josamycin) on the chaperoning ability of the E. coli ribosome and bDV RNA. Our studies using mRNA programmed ribosomes show that a tRNA positioned at the P-site effectively inhibits the ribosome's chaperoning function. We also show that the antibiotic blasticidin (that mimics the interaction between 3′–CCA end of P/P-site tRNA with the PTC) is more effective in inhibiting ribosome and bDV RNA chaperoning ability than either puromycin or the macrolide antibiotics. Mutational studies of the bDV RNA could identify the nucleotides U2585 and G2252 (both of which interact with P-site tRNA) to be important for its chaperoning ability. Conclusion Both protein synthesis and their proper folding are crucial for maintenance of a functional cellular proteome. The PTC of the ribosome is attributed with both these abilities. The silencing of the chaperoning ability of the ribosome in the presence of P-site bound tRNA might be a way to segregate these two important functions.
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Affiliation(s)
- Surojit Mondal
- Department of Biotechnology, St. Xavier's College, Kolkata, West Bengal, India
| | - Bani Kumar Pathak
- Department of Biotechnology, St. Xavier's College, Kolkata, West Bengal, India
| | - Sutapa Ray
- Dr. B.C Guha Centre for Genetic Engineering and Department of Biotechnology, Calcutta University, Kolkata, West Bengal, India
| | - Chandana Barat
- Department of Biotechnology, St. Xavier's College, Kolkata, West Bengal, India
- * E-mail:
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Pathak BK, Mondal S, Ghosh AN, Barat C. The ribosome can prevent aggregation of partially folded protein intermediates: studies using the Escherichia coli ribosome. PLoS One 2014; 9:e96425. [PMID: 24805251 PMCID: PMC4013144 DOI: 10.1371/journal.pone.0096425] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 04/07/2014] [Indexed: 11/19/2022] Open
Abstract
Background Molecular chaperones that support de novo folding of proteins under non stress condition are classified as chaperone ‘foldases’ that are distinct from chaperone’ holdases’ that provide high affinity binding platform for unfolded proteins and prevent their aggregation specifically under stress conditions. Ribosome, the cellular protein synthesis machine can act as a foldase chaperone that can bind unfolded proteins and release them in folding competent state. The peptidyl transferase center (PTC) located in the domain V of the 23S rRNA of Escherichia coli ribosome (bDV RNA) is the chaperoning center of the ribosome. It has been proposed that via specific interactions between the RNA and refolding proteins, the chaperone provides information for the correct folding of unfolded polypeptide chains. Results We demonstrate using Escherichia coli ribosome and variants of its domain V RNA that the ribosome can bind to partially folded intermediates of bovine carbonic anhydrase II (BCAII) and lysozyme and suppress aggregation during their refolding. Using mutants of domain V RNA we demonstrate that the time for which the chaperone retains the bound protein is an important factor in determining its ability to suppress aggregation and/or support reactivation of protein. Conclusion The ribosome can behave like a ‘holdase’ chaperone and has the ability to bind and hold back partially folded intermediate states of proteins from participating in the aggregation process. Since the ribosome is an essential organelle that is present in large numbers in all living cells, this ability of the ribosome provides an energetically inexpensive way to suppress cellular aggregation. Further, this ability of the ribosome might also be crucial in the context that the ribosome is one of the first chaperones to be encountered by a large nascent polypeptide chains that have a tendency to form partially folded intermediates immediately following their synthesis.
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Affiliation(s)
- Bani Kumar Pathak
- Department of Biotechnology, St. Xavier’s College, Kolkata, West Bengal, India
| | - Surojit Mondal
- Department of Biotechnology, St. Xavier’s College, Kolkata, West Bengal, India
| | - Amar Nath Ghosh
- National Institute of Cholera and Enteric Diseases P-33, Scheme XM, Beleghata, India
| | - Chandana Barat
- Department of Biotechnology, St. Xavier’s College, Kolkata, West Bengal, India
- * E-mail:
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Pang Y, Kurella S, Voisset C, Samanta D, Banerjee D, Schabe A, Das Gupta C, Galons H, Blondel M, Sanyal S. The antiprion compound 6-aminophenanthridine inhibits the protein folding activity of the ribosome by direct competition. J Biol Chem 2013; 288:19081-9. [PMID: 23673663 DOI: 10.1074/jbc.m113.466748] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Domain V of the 23S/25S/28S rRNA of the large ribosomal subunit constitutes the active center for the protein folding activity of the ribosome (PFAR). Using in vitro transcribed domain V rRNAs from Escherichia coli and Saccharomyces cerevisiae as the folding modulators and human carbonic anhydrase as a model protein, we demonstrate that PFAR is conserved from prokaryotes to eukaryotes. It was shown previously that 6-aminophenanthridine (6AP), an antiprion compound, inhibits PFAR. Here, using UV cross-linking followed by primer extension, we show that the protein substrates and 6AP interact with a common set of nucleotides on domain V of 23S rRNA. Mutations at the interaction sites decreased PFAR and resulted in loss or change of the binding pattern for both the protein substrates and 6AP. Moreover, kinetic analysis of human carbonic anhydrase refolding showed that 6AP decreased the yield of the refolded protein but did not affect the rate of refolding. Thus, we conclude that 6AP competitively occludes the protein substrates from binding to rRNA and thereby inhibits PFAR. Finally, we propose a scheme clarifying the mechanism by which 6AP inhibits PFAR.
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Affiliation(s)
- Yanhong Pang
- Department of Cell and Molecular Biology, Uppsala University, 75124 Uppsala, Sweden
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Das A, Ghosh J, Bhattacharya A, Samanta D, Das D, Das Gupta C. Involvement of mitochondrial ribosomal proteins in ribosomal RNA-mediated protein folding. J Biol Chem 2011; 286:43771-43781. [PMID: 22020935 DOI: 10.1074/jbc.m111.263574] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The peptidyl transferase center of the domain V of large ribosomal RNA in the prokaryotic and eukaryotic cytosolic ribosomes acts as general protein folding modulator. We showed earlier that one part of the domain V (RNA1 containing the peptidyl transferase loop) binds unfolded protein and directs it to a folding competent state (FCS) that is released by the other part (RNA2) to attain the folded native state by itself. Here we show that the peptidyl transferase loop of the mitochondrial ribosome releases unfolded proteins in FCS extremely slowly despite its lack of the rRNA segment analogous to RNA2. The release of FCS can be hastened by the equivalent activity of RNA2 or the large subunit proteins of the mitochondrial ribosome. The RNA2 or large subunit proteins probably introduce some allosteric change in the peptidyl transferase loop to enable it to release proteins in FCS.
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Affiliation(s)
- Anindita Das
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata 700009, India; Department of Biological Sciences, Indian Institute of Science Education and Research, Mohanpur, Nadia 741252, India
| | - Jaydip Ghosh
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata 700009, India; Department of Microbiology, St. Xavier's College, Kolkata 700016, India
| | - Arpita Bhattacharya
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata 700009, India
| | - Dibyendu Samanta
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata 700009, India
| | - Debasis Das
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata 700009, India
| | - Chanchal Das Gupta
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata 700009, India; Department of Biological Sciences, Indian Institute of Science Education and Research, Mohanpur, Nadia 741252, India.
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9
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Reis SD, Pang Y, Vishnu N, Voisset C, Galons H, Blondel M, Sanyal S. Mode of action of the antiprion drugs 6AP and GA on ribosome assisted protein folding. Biochimie 2011; 93:1047-54. [PMID: 21396977 DOI: 10.1016/j.biochi.2011.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 03/01/2011] [Indexed: 01/25/2023]
Abstract
The ribosome, the protein synthesis machinery of the cell, has also been implicated in protein folding. This activity resides within the domain V of the main RNA component of the large subunit of the ribosome. It has been shown that two antiprion drugs 6-aminophenanthridine (6AP) and Guanabenz (GA) bind to the ribosomal RNA and inhibit specifically the protein folding activity of the ribosome. Here, we have characterized with biochemical experiments, the mode of inhibition of these two drugs using ribosomes or ribosomal components active in protein folding (referred to as 'ribosomal folding modulators' or RFMs) from both bacteria Escherichia coli and yeast Saccharomyces cerevisiae, and human carbonic anhydrase (HCA) as a sample protein. Our results indicate that 6AP and GA inhibit the protein folding activity of the ribosome by competition with the unfolded protein for binding to the ribosome. As a result, the yield of the refolded protein decreases, but the rate of its refolding remains unaffected. Further, 6AP- and GA mediated inhibition of RFM mediated refolding can be reversed by the addition of RFMs in excess. We also demonstrate with delayed addition of the ribosome and the antiprion drugs that there is a short time-span in the range of seconds within which the ribosome interacts with the unfolded protein. Thus we conclude that the protein folding activity of the ribosome is conserved from bacteria to eukaryotes and most likely the substrate for RFMs is an early refolding state of the target protein.
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Affiliation(s)
- Suzana Dos Reis
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124 Uppsala, Sweden
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Bekesi A, Pukancsik M, Haasz P, Felfoldi L, Leveles I, Muha V, Hunyadi-Gulyas E, Erdei A, Medzihradszky KF, Vertessy BG. Association of RNA with the uracil-DNA-degrading factor has major conformational effects and is potentially involved in protein folding. FEBS J 2010; 278:295-315. [PMID: 21134127 DOI: 10.1111/j.1742-4658.2010.07951.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recently, a novel uracil-DNA-degrading factor protein (UDE) was identified in Drosophila melanogaster, with homologues only in pupating insects. Its unique uracil-DNA-degrading activity and a potential domain organization pattern have been described. UDE seems to be the first representative of a new protein family with unique enzyme activity that has a putative role in insect development. In addition, UDE may also serve as potential tool in molecular biological applications. Owing to lack of homology with other proteins with known structure and/or function, de novo data are required for a detailed characterization of UDE structure and function. Here, experimental evidence is provided that recombinant protein is present in two distinct conformers. One of these contains a significant amount of RNA strongly bound to the protein, influencing its conformation. Detailed biophysical characterization of the two distinct conformational states (termed UDE and RNA-UDE) revealed essential differences. UDE cannot be converted into RNA-UDE by addition of the same RNA, implying putatively joint processes of RNA binding and protein folding in this conformational species. By real-time PCR and sequencing after random cloning, the bound RNA pool was shown to consist of UDE mRNA and the two ribosomal RNAs, also suggesting cotranslational RNA-assisted folding. This finding, on the one hand, might open a way to obtain a conformationally homogeneous UDE preparation, promoting successful crystallization; on the other hand, it might imply a further molecular function of the protein. In fact, RNA-dependent complexation of UDE was also demonstrated in a fruit fly pupal extract, suggesting physiological relevance of RNA binding of this DNA-processing enzyme.
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Affiliation(s)
- Angela Bekesi
- Institute of Enzymology, Biological Research Centre, Hungarian Academy of Sciences, Budapest, Hungary.
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Psaila R, Ponti D, Ponzi M, Gigliani F, Battaglia PA. A small sequence in domain v of the mitochondrial large ribosomal RNA restores Drosophila melanogaster pole cell determination in uv-irradiated embryos. Cell Mol Biol Lett 2010; 15:365-76. [PMID: 20386994 PMCID: PMC6275646 DOI: 10.2478/s11658-010-0013-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Accepted: 03/24/2010] [Indexed: 11/20/2022] Open
Abstract
The mechanism by which the mitochondrial large rRNA is involved in the restoration of the pole cell-forming ability in Drosophila embryos is still unknown. We identified a 15-ribonucleotide sequence which is conserved from the protobacterium Wolbachia to the higher eukaryotes in domain V of the mitochondrial large rRNA. This short sequence is sufficient to restore pole cell determination in UV-irradiated Drosophila embryos. Here, we provide evidence that the conserved 15-base sequence is sufficient to restore luciferase activity in vitro. Moreover, we show that the internal GAGA sequence is involved in protein binding and that mutations in this tetranucleotide affect the sequence's ability to restore luciferase activity. The obtained results lead us to propose that mtlrRNA may be involved either in damaged protein reactivation or in protein biosynthesis during pole cell determination.
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Affiliation(s)
- Rossana Psaila
- Dipartimento di Biologia Cellulare e Neuroscienze, Istituto Superiore di Sanità Viale Regina Elena 299, 00161 Roma, Italy
| | - Donatella Ponti
- Dipartimento di Biotecnologie Cellulari ed Ematologia, Universita degliStudi di Roma “Sapienza”, Viale Regina Elena 324, 00161 Roma, Italy
- Dipartimento di Patologia Molecolare, Universita’ degli Studi di Roma “Sapienza”, Corso della Repubblica 79, 04100 Latina, Italy
| | - Marta Ponzi
- Dipartimento di Biologia Cellulare e Neuroscienze, Istituto Superiore di Sanità Viale Regina Elena 299, 00161 Roma, Italy
| | - Franca Gigliani
- Dipartimento di Biotecnologie Cellulari ed Ematologia, Universita degliStudi di Roma “Sapienza”, Viale Regina Elena 324, 00161 Roma, Italy
| | - Piero Augusto Battaglia
- Dipartimento di Biologia Cellulare e Neuroscienze, Istituto Superiore di Sanità Viale Regina Elena 299, 00161 Roma, Italy
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Das D, Samanta D, Das A, Ghosh J, Bhattacharya A, Basu A, Chakrabarti A, Das Gupta C. Ribosome: The Structure-Function Relation and a New Paradigm to the Protein Folding Problem. Isr J Chem 2010. [DOI: 10.1002/ijch.201000004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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13
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Kong Q, Stockinger MP, Chang Y, Tashiro H, Lin CLG. The presence of rRNA sequences in polyadenylated RNA and its potential functions. Biotechnol J 2008; 3:1041-6. [PMID: 18683164 DOI: 10.1002/biot.200800122] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Accumulating evidence has shown that various lengths of ribosomal RNA (rRNA) sequences are widely present in polyadenylated RNA. This review article will discuss these polyadenylated rRNA containing transcripts (PART). PART are highly abundant and widely expressed in various tissues. It appears that there may be two types of PART. One type, type I, contains the rRNA segments (from approximately 10 nucleotides up to several hundred nucleotides) located within the transcripts. It has been demonstrated that short rRNA sequences within type I PART may function as cis-regulatory elements that regulate translational efficiency. The other type, type II, contains large portions or almost entire sequences of rRNA with a cap at the 5' end and poly(A) at 3' end. Recent work has shown that some type II PART have functional significance for some neurodegenerative disease processes and may play an important role in the pathogenesis of diseases. Further investigation in this area is critical to understanding the basic biology of PART and the potential role of PART in diseases.
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Affiliation(s)
- Qiongman Kong
- Department of Neuroscience, The Ohio State University, Columbus, OH, USA
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14
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Das D, Das A, Samanta D, Ghosh J, Dasgupta S, Bhattacharya A, Basu A, Sanyal S, Das Gupta C. Role of the ribosome in protein folding. Biotechnol J 2008; 3:999-1009. [PMID: 18702035 DOI: 10.1002/biot.200800098] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In all organisms, the ribosome synthesizes and folds full length polypeptide chains into active three-dimensional conformations. The nascent protein goes through two major interactions, first with the ribosome which synthesizes the polypeptide chain and holds it for a considerable length of time, and then with the chaperones. Some of the chaperones are found in solution as well as associated to the ribosome. A number of in vitro and in vivo experiments revealed that the nascent protein folds through specific interactions of some amino acids with the nucleotides in the peptidyl transferase center (PTC) in the large ribosomal subunit. The mechanism of this folding differs from self-folding. In this article, we highlight the folding of nascent proteins on the ribosome and the influence of chaperones etc. on protein folding.
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Affiliation(s)
- Debasis Das
- Department of Biophysics, Molecular Biology and Genetics, University College of Science, Kolkata, India
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15
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Protein folding by domain V of Escherichia coli 23S rRNA: specificity of RNA-protein interactions. J Bacteriol 2008; 190:3344-52. [PMID: 18310328 DOI: 10.1128/jb.01800-07] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The peptidyl transferase center, present in domain V of 23S rRNA of eubacteria and large rRNA of plants and animals, can act as a general protein folding modulator. Here we show that a few specific nucleotides in Escherichia coli domain V RNA bind to unfolded proteins and, as shown previously, bring the trapped proteins to a folding-competent state before releasing them. These nucleotides are the same for the proteins studied so far: bovine carbonic anhydrase, lactate dehydrogenase, malate dehydrogenase, and chicken egg white lysozyme. The amino acids that interact with these nucleotides are also found to be specific in the two cases tested: bovine carbonic anhydrase and lysozyme. They are either neutral or positively charged and are present in random coils on the surface of the crystal structure of both the proteins. In fact, two of these amino acid-nucleotide pairs are identical in the two cases. How these features might help the process of protein folding is discussed.
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16
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Basu A, Samanta D, Bhattacharya A, Das A, Das D, DasGupta C. Protein folding following synthesis in vitro and in vivo: Association of newly synthesized protein with 50S subunit of E. coli ribosome. Biochem Biophys Res Commun 2008; 366:592-7. [DOI: 10.1016/j.bbrc.2007.11.142] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Accepted: 11/29/2007] [Indexed: 10/22/2022]
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In vitro protein folding by E. coli ribosome: unfolded protein splitting 70S to interact with 50S subunit. Biochem Biophys Res Commun 2007; 366:598-603. [PMID: 18068121 DOI: 10.1016/j.bbrc.2007.11.143] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Accepted: 11/29/2007] [Indexed: 11/20/2022]
Abstract
Folding of unfolded protein on Escherichia coli 70S ribosome is accompanied by rapid dissociation of the ribosome into 50S and 30S subunits. The dissociation rate of 70S ribosome with unfolded protein is much faster than that caused by combined effect of translation and polypeptide release factors known to be involved in the dissociation of ribosome into subunits. The protein then reaches a "folding competent" state on 50S and is released to take up native conformation by itself. Release before attaining the folding competent state or prevention of release by cross-linking it with ribosome, would not allow the protein to get back to its native conformation.
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18
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HYPK, a Huntingtin interacting protein, reduces aggregates and apoptosis induced by N-terminal Huntingtin with 40 glutamines in Neuro2a cells and exhibits chaperone-like activity. Hum Mol Genet 2007; 17:240-55. [DOI: 10.1093/hmg/ddm301] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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19
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Abstract
The ribosome is responsible for protein synthesis, the translation of the genetic code, in all living organisms. Ribosomes are composed of RNA (ribosomal RNA) and protein (ribosomal protein). Soluble protein factors bind to the ribosome and facilitate different phases of translation. Genetic approaches have proved useful for the identification and characterization of the structural and functional roles of specific nucleotides in ribosomal RNA and of specific amino acids in ribosomal proteins and in ribosomal factors. This chapter summarizes examples of mutations identified in ribosomal RNA, ribosomal proteins, and ribosomal factors.
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MESH Headings
- Animals
- Base Sequence
- DNA Mutational Analysis
- Humans
- Mutation
- Nucleic Acid Conformation
- Peptide Elongation Factors/genetics
- Peptide Initiation Factors/genetics
- Peptide Termination Factors/genetics
- Protein Subunits/genetics
- RNA, Ribosomal, 16S/analysis
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/physiology
- RNA, Ribosomal, 23S/analysis
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/physiology
- Ribosomal Proteins/genetics
- Ribosomes/genetics
- Sequence Analysis, RNA
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Affiliation(s)
- Kathleen L Triman
- Department of Biology, Franklin and Marshall College, Lancaster, PA 17604, USA
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Ghosh J, Basu A, Pal S, Chowdhuri S, Bhattacharya A, Pal D, Chattoraj DK, DasGupta C. Ribosome-DnaK interactions in relation to protein folding. Mol Microbiol 2003; 48:1679-92. [PMID: 12791147 DOI: 10.1046/j.1365-2958.2003.03538.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bacterial ribosomes or their 50S subunit can refold many unfolded proteins. The folding activity resides in domain V of 23S RNA of the 50S subunit. Here we show that ribosomes can also refold a denatured chaperone, DnaK, in vitro, and the activity may apply in the folding of nascent DnaK polypeptides in vivo. The chaperone was unusual as the native protein associated with the 50S subunit stably with a 1:1 stoichiometry in vitro. The binding site of the native protein appears to be different from the domain V of 23S RNA, the region with which denatured proteins interact. The DnaK binding influenced the protein folding activity of domain V modestly. Conversely, denatured protein binding to domain V led to dissociation of the native chaperone from the 50S subunit. DnaK thus appears to depend on ribosomes for its own folding, and upon folding, can rebind to ribosome to modulate its general protein folding activity.
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Affiliation(s)
- Jaydip Ghosh
- Department of Biophysics, Molecular Biology and Genetics, University of Calcutta, 92 A. P. C. Road, India
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