1
|
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.
Collapse
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
| |
Collapse
|
2
|
Ham S, Lee C. Exploring the impact of nucleic acids on protein stability in bacterial cell lysate. Biochim Biophys Acta Gen Subj 2023; 1867:130445. [PMID: 37591417 DOI: 10.1016/j.bbagen.2023.130445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/02/2023] [Accepted: 08/14/2023] [Indexed: 08/19/2023]
Abstract
- Addition of salt enhanced thermal stability of model substrate proteins by reducing electrostatic repulsion between protein molecules. - However, the opposite effect was observed with bacterial cell lysate, indicating that certain molecules within the lysate could enhance protein stability via electrostatic interactions. - Such molecules present in cell lysate were found to be nucleic acids known to have a potent anti-aggregation activity toward proteins involving electrostatic interactions. - Nucleic acids showed chaperone activity in physiological salt concentration within cells and in buffer or medium commonly used in experiments. - The chaperone activity of nucleic acids should be taken into account when performing various in vitro assays using cell lysate or samples containing nucleic acids.
Collapse
Affiliation(s)
- Soojeong Ham
- Department of Biological Sciences, Ajou University, Suwon, South Korea
| | - Changhan Lee
- Department of Biological Sciences, Ajou University, Suwon, South Korea.
| |
Collapse
|
3
|
Kofman C, Watkins AM, Kim D, Willi JA, Wooldredge A, Karim A, Das R, Jewett MC. Computationally-guided design and selection of high performing ribosomal active site mutants. Nucleic Acids Res 2022; 50:13143-13154. [PMID: 36484094 PMCID: PMC9825160 DOI: 10.1093/nar/gkac1036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/13/2022] [Accepted: 10/22/2022] [Indexed: 12/14/2022] Open
Abstract
Understanding how modifications to the ribosome affect function has implications for studying ribosome biogenesis, building minimal cells, and repurposing ribosomes for synthetic biology. However, efforts to design sequence-modified ribosomes have been limited because point mutations in the ribosomal RNA (rRNA), especially in the catalytic active site (peptidyl transferase center; PTC), are often functionally detrimental. Moreover, methods for directed evolution of rRNA are constrained by practical considerations (e.g. library size). Here, to address these limitations, we developed a computational rRNA design approach for screening guided libraries of mutant ribosomes. Our method includes in silico library design and selection using a Rosetta stepwise Monte Carlo method (SWM), library construction and in vitro testing of combined ribosomal assembly and translation activity, and functional characterization in vivo. As a model, we apply our method to making modified ribosomes with mutant PTCs. We engineer ribosomes with as many as 30 mutations in their PTCs, highlighting previously unidentified epistatic interactions, and show that SWM helps identify sequences with beneficial phenotypes as compared to random library sequences. We further demonstrate that some variants improve cell growth in vivo, relative to wild type ribosomes. We anticipate that SWM design and selection may serve as a powerful tool for rRNA engineering.
Collapse
Affiliation(s)
- Camila Kofman
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Andrew M Watkins
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
- Prescient Design, Genentech, South San Francisco, CA 94080, USA
| | - Do Soon Kim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Inceptive Nucleics, Inc., Palo Alto, CA 94304, USA
| | - Jessica A Willi
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Alexandra C Wooldredge
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
- Department of Physics, Stanford University, Stanford, CA 94305, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Robert H. Lurie Comprehensive Cancer Center and Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA
| |
Collapse
|
4
|
Modulating co-translational protein folding by rational design and ribosome engineering. Nat Commun 2022; 13:4243. [PMID: 35869078 PMCID: PMC9307626 DOI: 10.1038/s41467-022-31906-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 07/08/2022] [Indexed: 12/23/2022] Open
Abstract
Co-translational folding is a fundamental process for the efficient biosynthesis of nascent polypeptides that emerge through the ribosome exit tunnel. To understand how this process is modulated by the shape and surface of the narrow tunnel, we have rationally engineered three exit tunnel protein loops (uL22, uL23 and uL24) of the 70S ribosome by CRISPR/Cas9 gene editing, and studied the co-translational folding of an immunoglobulin-like filamin domain (FLN5). Our thermodynamics measurements employing 19F/15N/methyl-TROSY NMR spectroscopy together with cryo-EM and molecular dynamics simulations reveal how the variations in the lengths of the loops present across species exert their distinct effects on the free energy of FLN5 folding. A concerted interplay of the uL23 and uL24 loops is sufficient to alter co-translational folding energetics, which we highlight by the opposite folding outcomes resulting from their extensions. These subtle modulations occur through a combination of the steric effects relating to the shape of the tunnel, the dynamic interactions between the ribosome surface and the unfolded nascent chain, and its altered exit pathway within the vestibule. These results illustrate the role of the exit tunnel structure in co-translational folding, and provide principles for how to remodel it to elicit a desired folding outcome. The narrow exit tunnel of the ribosome is important for cotranslational protein folding. Here, authors show that their rationally designed and engineered exit tunnel protein loops modulate the free energy of nascent chain dynamics and folding.
Collapse
|
5
|
Pang Y, Kovachev P, Sanyal S. Ribosomal RNA Modulates Aggregation of the Podospora Prion Protein HET-s. Int J Mol Sci 2020; 21:ijms21176340. [PMID: 32882892 PMCID: PMC7504336 DOI: 10.3390/ijms21176340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 08/28/2020] [Indexed: 01/19/2023] Open
Abstract
The role of the nucleic acids in prion aggregation/disaggregation is becoming more and more evident. Here, using HET-s prion from fungi Podospora anserina (P. anserina) as a model system, we studied the role of RNA, particularly of different domains of the ribosomal RNA (rRNA), in its aggregation process. Our results using Rayleigh light scattering, Thioflavin T (ThT) binding, transmission electron microscopy (TEM) and cross-seeding assay show that rRNA, in particular the domain V of the major rRNA from the large subunit of the ribosome, substantially prevents insoluble amyloid and amorphous aggregation of the HET-s prion in a concentration-dependent manner. Instead, it facilitates the formation of the soluble oligomeric “seeds”, which are capable of promoting de novo HET-s aggregation. The sites of interactions of the HET-s prion protein on domain V rRNA were identified by primer extension analysis followed by UV-crosslinking, which overlap with the sites previously identified for the protein-folding activity of the ribosome (PFAR). This study clarifies a missing link between the rRNA-based PFAR and the mode of propagation of the fungal prions.
Collapse
|
6
|
Abstract
As a mental framework for the transition of self-replicating biological forms, the RNA world concept stipulates a dual function of RNAs as genetic substance and catalyst. The chaperoning function is found intrinsic to ribozymes involved in protein synthesis and tRNA maturation, enriching the primordial RNA world with proteins of biological relevance. The ribozyme-resident protein folding activity, even before the advent of protein-based molecular chaperone, must have expedited the transition of the RNA world into the present protein theatre.
Collapse
Affiliation(s)
- Ahyun Son
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver , Denver, CO, USA
| | - Scott Horowitz
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver , Denver, CO, USA
| | - Baik L Seong
- Department of Biotechnology, College of Bioscience and Biotechnology, Yonsei University , Seoul, Korea.,Vaccine Innovation Technology Alliance (VITAL)-Korea, Yonsei University , Seoul, Korea
| |
Collapse
|
7
|
Addabbo RM, Dalphin MD, Mecha MF, Liu Y, Staikos A, Guzman-Luna V, Cavagnero S. Complementary Role of Co- and Post-Translational Events in De Novo Protein Biogenesis. J Phys Chem B 2020; 124:6488-6507. [DOI: 10.1021/acs.jpcb.0c03039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Rayna M. Addabbo
- Biophysics Graduate Degree Program, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Matthew D. Dalphin
- Biophysics Graduate Degree Program, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Miranda F. Mecha
- Biophysics Graduate Degree Program, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Yue Liu
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Alexios Staikos
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Valeria Guzman-Luna
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Silvia Cavagnero
- Biophysics Graduate Degree Program, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| |
Collapse
|
8
|
Kovachev PS, Gomes MPB, Cordeiro Y, Ferreira NC, Valadão LPF, Ascari LM, Rangel LP, Silva JL, Sanyal S. RNA modulates aggregation of the recombinant mammalian prion protein by direct interaction. Sci Rep 2019; 9:12406. [PMID: 31455808 PMCID: PMC6712051 DOI: 10.1038/s41598-019-48883-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 08/12/2019] [Indexed: 12/22/2022] Open
Abstract
Recent studies have proposed that nucleic acids act as potential cofactors for protein aggregation and prionogenesis. By means of sedimentation, transmission electron microscopy, circular dichroism, static and dynamic light scattering, we have studied how RNA can influence the aggregation of the murine recombinant prion protein (rPrP). We find that RNA, independent of its sequence, source and size, modulates rPrP aggregation in a bimodal fashion, affecting both the extent and the rate of rPrP aggregation in a concentration dependent manner. Analogous to RNA-induced liquid-liquid phase transitions observed for other proteins implicated in neurodegenerative diseases, high protein to RNA ratios stimulate rPrP aggregation, while low ratios suppress it. However, the latter scenario also promotes formation of soluble oligomeric aggregates capable of seeding de novo rPrP aggregation. Furthermore, RNA co-aggregates with rPrP and thereby gains partial protection from RNase digestion. Our results also indicate that rPrP interacts with the RNAs with its N-terminus. In summary, this study elucidates the proposed adjuvant role of RNA in prion protein aggregation and propagation, and thus advocates an auxiliary role of the nucleic acids in protein aggregation in general.
Collapse
Affiliation(s)
- Petar Stefanov Kovachev
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Box-596, 75124, Sweden
| | - Mariana P B Gomes
- Instituto de Tecnologia em Imunobiológicos, Bio-Manguinhos, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Yraima Cordeiro
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Natália C Ferreira
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil.,Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States of America
| | - Leticia P Felix Valadão
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Lucas M Ascari
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Luciana P Rangel
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Jerson L Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Ciência Tecnologia de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil.
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Box-596, 75124, Sweden.
| |
Collapse
|
9
|
Wallis CP, Richman TR, Filipovska A, Rackham O. Tighter Ligand Binding Can Compensate for Impaired Stability of an RNA-Binding Protein. ACS Chem Biol 2018; 13:1499-1505. [PMID: 29808990 DOI: 10.1021/acschembio.8b00424] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
It has been widely shown that ligand-binding residues, by virtue of their orientation, charge, and solvent exposure, often have a net destabilizing effect on proteins that is offset by stability conferring residues elsewhere in the protein. This structure-function trade-off can constrain possible adaptive evolutionary changes of function and may hamper protein engineering efforts to design proteins with new functions. Here, we present evidence from a large randomized mutant library screen that, in the case of PUF RNA-binding proteins, this structural relationship may be inverted and that active-site mutations that increase protein activity are also able to compensate for impaired stability. We show that certain mutations in RNA-protein binding residues are not necessarily destabilizing and that increased ligand-binding can rescue an insoluble, unstable PUF protein. We hypothesize that these mutations restabilize the protein via thermodynamic coupling of protein folding and RNA binding.
Collapse
Affiliation(s)
- Christopher P. Wallis
- Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands 6009, Australia
| | - Tara R. Richman
- Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands 6009, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands 6009, Australia
- School of Molecular Sciences, The University of Western Australia, Crawley 6009, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands 6009, Australia
- School of Molecular Sciences, The University of Western Australia, Crawley 6009, Australia
| |
Collapse
|
10
|
Voisset C, Blondel M, Jones GW, Friocourt G, Stahl G, Chédin S, Béringue V, Gillet R. The double life of the ribosome: When its protein folding activity supports prion propagation. Prion 2017; 11:89-97. [PMID: 28362551 DOI: 10.1080/19336896.2017.1303587] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
It is no longer necessary to demonstrate that ribosome is the central machinery of protein synthesis. But it is less known that it is also key player of the protein folding process through another conserved function: the protein folding activity of the ribosome (PFAR). This ribozyme activity, discovered more than 2 decades ago, depends upon the domain V of the large rRNA within the large subunit of the ribosome. Surprisingly, we discovered that anti-prion compounds are also potent PFAR inhibitors, highlighting an unexpected link between PFAR and prion propagation. In this review, we discuss the ancestral origin of PFAR in the light of the ancient RNA world hypothesis. We also consider how this ribosomal activity fits into the landscape of cellular protein chaperones involved in the appearance and propagation of prions and other amyloids in mammals. Finally, we examine how drugs targeting the protein folding activity of the ribosome could be active against mammalian prion and other protein aggregation-based diseases, making PFAR a promising therapeutic target for various human protein misfolding diseases.
Collapse
Affiliation(s)
- Cécile Voisset
- a Inserm UMR 1078 , Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé, Etablissement Français du Sang (EFS) Bretagne, CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire , Brest , France
| | - Marc Blondel
- a Inserm UMR 1078 , Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé, Etablissement Français du Sang (EFS) Bretagne, CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire , Brest , France
| | - Gary W Jones
- b School of Clinical and Applied Sciences , Faculty of Health and Social Sciences, Leeds Beckett University , Leeds , UK
| | - Gaëlle Friocourt
- a Inserm UMR 1078 , Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé, Etablissement Français du Sang (EFS) Bretagne, CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire , Brest , France
| | - Guillaume Stahl
- c Laboratoire de Biologie Moléculaire Eucaryotes , CNRS, Université de Toulouse , Toulouse , France
| | - Stéphane Chédin
- d Institute for Integrative Biology of the Cell (I2BC), UMR 9198, CEA, CNRS, Université Paris-Sud, CEA/Saclay, SBIGeM , Gif-sur-Yvette , France
| | | | - Reynald Gillet
- f Université de Rennes 1, CNRS UMR 6290 IGDR , Rennes , France
| |
Collapse
|
11
|
Kovachev PS, Banerjee D, Rangel LP, Eriksson J, Pedrote MM, Martins-Dinis MMDC, Edwards K, Cordeiro Y, Silva JL, Sanyal S. Distinct modulatory role of RNA in the aggregation of the tumor suppressor protein p53 core domain. J Biol Chem 2017; 292:9345-9357. [PMID: 28420731 DOI: 10.1074/jbc.m116.762096] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 04/12/2017] [Indexed: 01/05/2023] Open
Abstract
Inactivation of the tumor suppressor protein p53 by mutagenesis, chemical modification, protein-protein interaction, or aggregation has been associated with different human cancers. Although DNA is the typical substrate of p53, numerous studies have reported p53 interactions with RNA. Here, we have examined the effects of RNA of varied sequence, length, and origin on the mechanism of aggregation of the core domain of p53 (p53C) using light scattering, intrinsic fluorescence, transmission electron microscopy, thioflavin-T binding, seeding, and immunoblot assays. Our results are the first to demonstrate that RNA can modulate the aggregation of p53C and full-length p53. We found bimodal behavior of RNA in p53C aggregation. A low RNA:protein ratio (∼1:50) facilitates the accumulation of large amorphous aggregates of p53C. By contrast, at a high RNA:protein ratio (≥1:8), the amorphous aggregation of p53C is clearly suppressed. Instead, amyloid p53C oligomers are formed that can act as seeds nucleating de novo aggregation of p53C. We propose that structured RNAs prevent p53C aggregation through surface interaction and play a significant role in the regulation of the tumor suppressor protein.
Collapse
Affiliation(s)
- Petar Stefanov Kovachev
- From the Department of Cell and Molecular Biology, Uppsala University, Uppsala, Box-596, 75124, Sweden
| | - Debapriya Banerjee
- From the Department of Cell and Molecular Biology, Uppsala University, Uppsala, Box-596, 75124, Sweden
| | - Luciana Pereira Rangel
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Jonny Eriksson
- Department of Chemistry, Uppsala University, Uppsala, 75124, Sweden, and
| | - Murilo M Pedrote
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Ciência Tecnologia de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Mafalda Maria D C Martins-Dinis
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Ciência Tecnologia de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Katarina Edwards
- Department of Chemistry, Uppsala University, Uppsala, 75124, Sweden, and
| | - Yraima Cordeiro
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Jerson L Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Ciência Tecnologia de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Suparna Sanyal
- From the Department of Cell and Molecular Biology, Uppsala University, Uppsala, Box-596, 75124, Sweden,
| |
Collapse
|
12
|
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.
Collapse
|
13
|
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.
Collapse
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:
| |
Collapse
|
14
|
Blondel M, Soubigou F, Evrard J, Nguyen PH, Hasin N, Chédin S, Gillet R, Contesse MA, Friocourt G, Stahl G, Jones GW, Voisset C. Protein Folding Activity of the Ribosome is involved in Yeast Prion Propagation. Sci Rep 2016; 6:32117. [PMID: 27633137 PMCID: PMC5025663 DOI: 10.1038/srep32117] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 08/02/2016] [Indexed: 11/09/2022] Open
Abstract
6AP and GA are potent inhibitors of yeast and mammalian prions and also specific inhibitors of PFAR, the protein-folding activity borne by domain V of the large rRNA of the large subunit of the ribosome. We therefore explored the link between PFAR and yeast prion [PSI(+)] using both PFAR-enriched mutants and site-directed methylation. We demonstrate that PFAR is involved in propagation and de novo formation of [PSI(+)]. PFAR and the yeast heat-shock protein Hsp104 partially compensate each other for [PSI(+)] propagation. Our data also provide insight into new functions for the ribosome in basal thermotolerance and heat-shocked protein refolding. PFAR is thus an evolutionarily conserved cell component implicated in the prion life cycle, and we propose that it could be a potential therapeutic target for human protein misfolding diseases.
Collapse
Affiliation(s)
- Marc Blondel
- Inserm UMR 1078, Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest, France
| | - Flavie Soubigou
- Inserm UMR 1078, Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest, France
| | - Justine Evrard
- Inserm UMR 1078, Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest, France
| | - Phu hai Nguyen
- Inserm UMR 1078, Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest, France
| | - Naushaba Hasin
- Yeast Genetics Laboratory, Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
| | - Stéphane Chédin
- Institute for Integrative Biology of the Cell (I2BC), UMR 9198, CEA, CNRS, Université Paris-Sud, CEA/Saclay, SBIGeM, Gif-sur-Yvette, France
| | - Reynald Gillet
- Université de Rennes 1, CNRS UMR 6290 IGDR, Translation and Folding Team, Rennes, France
| | - Marie-Astrid Contesse
- Inserm UMR 1078, Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest, France
| | - Gaëlle Friocourt
- Inserm UMR 1078, Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest, France
| | - Guillaume Stahl
- Laboratoire de Biologie Moléculaire Eucaryotes, CNRS, Université de Toulouse, Toulouse, France
| | - Gary W. Jones
- Yeast Genetics Laboratory, Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
| | - Cécile Voisset
- Inserm UMR 1078, Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest, France
| |
Collapse
|
15
|
Chakraborty B, Bhakta S, Sengupta J. Mechanistic Insight into the Reactivation of BCAII Enzyme from Denatured and Molten Globule States by Eukaryotic Ribosomes and Domain V rRNAs. PLoS One 2016; 11:e0153928. [PMID: 27099964 PMCID: PMC4839638 DOI: 10.1371/journal.pone.0153928] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 04/06/2016] [Indexed: 12/29/2022] Open
Abstract
In all life forms, decoding of messenger-RNA into polypeptide chain is accomplished by the ribosome. Several protein chaperones are known to bind at the exit of ribosomal tunnel to ensure proper folding of the nascent chain by inhibiting their premature folding in the densely crowded environment of the cell. However, accumulating evidence suggests that ribosome may play a chaperone role in protein folding events in vitro. Ribosome-mediated folding of denatured proteins by prokaryotic ribosomes has been studied extensively. The RNA-assisted chaperone activity of the prokaryotic ribosome has been attributed to the domain V, a span of 23S rRNA at the intersubunit side of the large subunit encompassing the Peptidyl Transferase Centre. Evidently, this functional property of ribosome is unrelated to the nascent chain protein folding at the exit of the ribosomal tunnel. Here, we seek to scrutinize whether this unique function is conserved in a primitive kinetoplastid group of eukaryotic species Leishmania donovani where the ribosome structure possesses distinct additional features and appears markedly different compared to other higher eukaryotic ribosomes. Bovine Carbonic Anhydrase II (BCAII) enzyme was considered as the model protein. Our results manifest that domain V of the large subunit rRNA of Leishmania ribosomes preserves chaperone activity suggesting that ribosome-mediated protein folding is, indeed, a conserved phenomenon. Further, we aimed to investigate the mechanism underpinning the ribosome-assisted protein reactivation process. Interestingly, the surface plasmon resonance binding analyses exhibit that rRNA guides productive folding by directly interacting with molten globule-like states of the protein. In contrast, native protein shows no notable affinity to the rRNA. Thus, our study not only confirms conserved, RNA-mediated chaperoning role of ribosome but also provides crucial insight into the mechanism of the process.
Collapse
Affiliation(s)
- Biprashekhar Chakraborty
- Structural Biology & Bio-Informatics Division, Indian Institute of Chemical Biology (Council of Scientific & Industrial Research), 4, Raja S.C. Mullick Road, Kolkata, 700 032, India
| | - Sayan Bhakta
- Structural Biology & Bio-Informatics Division, Indian Institute of Chemical Biology (Council of Scientific & Industrial Research), 4, Raja S.C. Mullick Road, Kolkata, 700 032, India
| | - Jayati Sengupta
- Structural Biology & Bio-Informatics Division, Indian Institute of Chemical Biology (Council of Scientific & Industrial Research), 4, Raja S.C. Mullick Road, Kolkata, 700 032, India
- * E-mail:
| |
Collapse
|
16
|
Docter BE, Horowitz S, Gray MJ, Jakob U, Bardwell JCA. Do nucleic acids moonlight as molecular chaperones? Nucleic Acids Res 2016; 44:4835-45. [PMID: 27105849 PMCID: PMC4889950 DOI: 10.1093/nar/gkw291] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/08/2016] [Indexed: 01/17/2023] Open
Abstract
Organisms use molecular chaperones to combat the unfolding and aggregation of proteins. While protein chaperones have been widely studied, here we demonstrate that DNA and RNA exhibit potent chaperone activity in vitro Nucleic acids suppress the aggregation of classic chaperone substrates up to 300-fold more effectively than the protein chaperone GroEL. Additionally, RNA cooperates with the DnaK chaperone system to refold purified luciferase. Our findings reveal a possible new role for nucleic acids within the cell: that nucleic acids directly participate in maintaining proteostasis by preventing protein aggregation.
Collapse
Affiliation(s)
- Brianne E Docter
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Scott Horowitz
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael J Gray
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ursula Jakob
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - James C A Bardwell
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
17
|
Son A, Choi SI, Han G, Seong BL. M1 RNA is important for the in-cell solubility of its cognate C5 protein: Implications for RNA-mediated protein folding. RNA Biol 2015; 12:1198-208. [PMID: 26517763 DOI: 10.1080/15476286.2015.1096487] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
It is one of the fundamental questions in biology how proteins efficiently fold into their native conformations despite off-pathway events such as misfolding and aggregation in living cells. Although molecular chaperones have been known to assist the de novo folding of certain types of proteins, the role of a binding partner (or a ligand) in the folding and in-cell solubility of its interacting protein still remains poorly defined. RNase P is responsible for the maturation of tRNAs as adaptor molecules of amino acids in ribosomal protein synthesis. The RNase P from Escherichia coli, composed of M1 RNA and C5 protein, is a prototypical ribozyme in which the RNA subunit contains the catalytic activity. Using E. coli RNase P, we demonstrate that M1 RNA plays a pivotal role in the in-cell solubility of C5 protein both in vitro and in vivo. Mutations in either the C5 protein or M1 RNA that affect their interactions significantly abolished the folding of C5 protein. Moreover, we find that M1 RNA provides quality insurance of interacting C5 protein, either by promoting the degradation of C5 mutants in the presence of functional proteolytic machinery, or by abolishing their solubility if the machinery is non-functional. Our results describe a crucial role of M1 RNA in the folding, in-cell solubility, and, consequently, the proteostasis of the client C5 protein, giving new insight into the biological role of RNAs as chaperones and mediators that ensure the quality of interacting proteins.
Collapse
Affiliation(s)
- Ahyun Son
- a Department of Integrated OMICS for Biomedical Science ; College of World Class University; Yonsei University ; Seoul , Korea.,b Vaccine Translational Research Center; Yonsei University ; Seoul , Korea
| | - Seong Il Choi
- c Department of Biotechnology ; College of Bioscience and Biotechnology; Yonsei University ; Seoul , Korea
| | - Gyoonhee Han
- a Department of Integrated OMICS for Biomedical Science ; College of World Class University; Yonsei University ; Seoul , Korea.,c Department of Biotechnology ; College of Bioscience and Biotechnology; Yonsei University ; Seoul , Korea
| | - Baik L Seong
- b Vaccine Translational Research Center; Yonsei University ; Seoul , Korea.,c Department of Biotechnology ; College of Bioscience and Biotechnology; Yonsei University ; Seoul , Korea
| |
Collapse
|
18
|
Banerjee D, Sanyal S. Protein folding activity of the ribosome (PFAR) -- a target for antiprion compounds. Viruses 2014; 6:3907-24. [PMID: 25341659 PMCID: PMC4213570 DOI: 10.3390/v6103907] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 10/13/2014] [Accepted: 10/15/2014] [Indexed: 12/18/2022] Open
Abstract
Prion diseases are fatal neurodegenerative diseases affecting mammals. Prions are misfolded amyloid aggregates of the prion protein (PrP), which form when the alpha helical, soluble form of PrP converts to an aggregation-prone, beta sheet form. Thus, prions originate as protein folding problems. The discovery of yeast prion(s) and the development of a red-/white-colony based assay facilitated safe and high-throughput screening of antiprion compounds. With this assay three antiprion compounds; 6-aminophenanthridine (6AP), guanabenz acetate (GA), and imiquimod (IQ) have been identified. Biochemical and genetic studies reveal that these compounds target ribosomal RNA (rRNA) and inhibit specifically the protein folding activity of the ribosome (PFAR). The domain V of the 23S/25S/28S rRNA of the large ribosomal subunit constitutes the active site for PFAR. 6AP and GA inhibit PFAR by competition with the protein substrates for the common binding sites on the domain V rRNA. PFAR inhibition by these antiprion compounds opens up new possibilities for understanding prion formation, propagation and the role of the ribosome therein. In this review, we summarize and analyze the correlation between PFAR and prion processes using the antiprion compounds as tools.
Collapse
Affiliation(s)
- Debapriya Banerjee
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, Uppsala SE-75124, Sweden.
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, Uppsala SE-75124, Sweden.
| |
Collapse
|
19
|
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.
Collapse
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:
| |
Collapse
|
20
|
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.
Collapse
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:
| |
Collapse
|
21
|
Halder S, Bhattacharyya D. RNA structure and dynamics: a base pairing perspective. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 113:264-83. [PMID: 23891726 DOI: 10.1016/j.pbiomolbio.2013.07.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 06/25/2013] [Accepted: 07/16/2013] [Indexed: 12/12/2022]
Abstract
RNA is now known to possess various structural, regulatory and enzymatic functions for survival of cellular organisms. Functional RNA structures are generally created by three-dimensional organization of small structural motifs, formed by base pairing between self-complementary sequences from different parts of the RNA chain. In addition to the canonical Watson-Crick or wobble base pairs, several non-canonical base pairs are found to be crucial to the structural organization of RNA molecules. They appear within different structural motifs and are found to stabilize the molecule through long-range intra-molecular interactions between basic structural motifs like double helices and loops. These base pairs also impart functional variation to the minor groove of A-form RNA helices, thus forming anchoring site for metabolites and ligands. Non-canonical base pairs are formed by edge-to-edge hydrogen bonding interactions between the bases. A large number of theoretical studies have been done to detect and analyze these non-canonical base pairs within crystal or NMR derived structures of different functional RNA. Theoretical studies of these isolated base pairs using ab initio quantum chemical methods as well as molecular dynamics simulations of larger fragments have also established that many of these non-canonical base pairs are as stable as the canonical Watson-Crick base pairs. This review focuses on the various structural aspects of non-canonical base pairs in the organization of RNA molecules and the possible applications of these base pairs in predicting RNA structures with more accuracy.
Collapse
Affiliation(s)
- Sukanya Halder
- Biophysics division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700 064, India
| | | |
Collapse
|
22
|
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.
Collapse
Affiliation(s)
- Yanhong Pang
- Department of Cell and Molecular Biology, Uppsala University, 75124 Uppsala, Sweden
| | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Chen C, Wang E, Liu P, Xiao Y. Simulation study of the role of the ribosomal exit tunnel on protein folding. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:022701. [PMID: 23496542 DOI: 10.1103/physreve.87.022701] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 01/14/2013] [Indexed: 06/01/2023]
Abstract
To investigate the role of the ribosomal exit tunnel on protein folding, we simulate the initial-stage folding behavior of the protein villin headpiece subdomain HP35 (PDB id: 1yrf) with and without prefolding in the exit tunnel by using an all-atom model and find that prefolding in the exit tunnel could effectively help the protein form native secondary structures. Furthermore, our results show that, after releasing from the exit tunnel, the prefolded chains may have a tendency to form more native contacts than those only in free space and this reduces the conformational space of sampling. Our results may provide an alternative way to explain the fast folding mechanism of proteins in vivo.
Collapse
Affiliation(s)
- Changjun Chen
- Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | | | | | | |
Collapse
|
24
|
Das D, Samanta D, Hasan S, Das A, Bhattacharya A, Dasgupta S, Chakrabarti A, Ghorai P, Das Gupta C. Identical RNA-protein interactions in vivo and in vitro and a scheme of folding the newly synthesized proteins by ribosomes. J Biol Chem 2012; 287:37508-21. [PMID: 22932895 DOI: 10.1074/jbc.m112.396127] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A distinct three-dimensional shape of rRNA inside the ribosome is required for the peptidyl transfer activity of its peptidyltransferase center (PTC). In contrast, even the in vitro transcribed PTC RNA interacts with unfolded protein(s) at about five sites to let them attain their native states. We found that the same set of conserved nucleotides in the PTC interact identically with nascent and chemically unfolded proteins in vivo and in vitro, respectively. The time course of this interaction, difficult to follow in vivo, was observed in vitro. It suggested nucleation of folding of cytosolic globular proteins vectorially from hydrophilic N to hydrophobic C termini, consistent with our discovery of a regular arrangement of cumulative hydrophobic indices of the peptide segments of cytosolic proteins from N to C termini. Based on this observation, we propose a model here for the nucleation of folding of the nascent protein chain by the PTC.
Collapse
Affiliation(s)
- Debasis Das
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, 92-A.P.C. Road, Kolkata 700 009, India
| | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Choi SI, Son A, Lim KH, Jeong H, Seong BL. Macromolecule-assisted de novo protein folding. Int J Mol Sci 2012; 13:10368-10386. [PMID: 22949867 PMCID: PMC3431865 DOI: 10.3390/ijms130810368] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/14/2012] [Accepted: 08/17/2012] [Indexed: 01/24/2023] Open
Abstract
In the processes of protein synthesis and folding, newly synthesized polypeptides are tightly connected to the macromolecules, such as ribosomes, lipid bilayers, or cotranslationally folded domains in multidomain proteins, representing a hallmark of de novo protein folding environments in vivo. Such linkage effects on the aggregation of endogenous polypeptides have been largely neglected, although all these macromolecules have been known to effectively and robustly solubilize their linked heterologous proteins in fusion or display technology. Thus, their roles in the aggregation of linked endogenous polypeptides need to be elucidated and incorporated into the mechanisms of de novo protein folding in vivo. In the classic hydrophobic interaction-based stabilizing mechanism underlying the molecular chaperone-assisted protein folding, it has been assumed that the macromolecules connected through a simple linkage without hydrophobic interactions and conformational changes would make no effect on the aggregation of their linked polypeptide chains. However, an increasing line of evidence indicates that the intrinsic properties of soluble macromolecules, especially their surface charges and excluded volume, could be important and universal factors for stabilizing their linked polypeptides against aggregation. Taken together, these macromolecules could act as folding helpers by keeping their linked nascent chains in a folding-competent state. The folding assistance provided by these macromolecules in the linkage context would give new insights into de novo protein folding inside the cell.
Collapse
Affiliation(s)
- Seong Il Choi
- Translational Research Center for Protein Function Control, Yonsei University, Seoul 120-749, Korea
- Department of Biotechnology, College of Bioscience and Biotechnology, Yonsei University, Seoul 120-749, Korea; E-Mails: (A.S.); (K.-H.L.)
- Authors to whom correspondence should be addressed; E-Mails: (S.I.C.); (H.J.); (B.L.S.); Tel.: +82-2-393-4631 (S.I.C.)
| | - Ahyun Son
- Department of Biotechnology, College of Bioscience and Biotechnology, Yonsei University, Seoul 120-749, Korea; E-Mails: (A.S.); (K.-H.L.)
| | - Keo-Heun Lim
- Department of Biotechnology, College of Bioscience and Biotechnology, Yonsei University, Seoul 120-749, Korea; E-Mails: (A.S.); (K.-H.L.)
| | - Hotcherl Jeong
- Vismer Co., Ltd., Ansan, Kyeonggi-do 426-791, Korea
- Authors to whom correspondence should be addressed; E-Mails: (S.I.C.); (H.J.); (B.L.S.); Tel.: +82-2-393-4631 (S.I.C.)
| | - Baik L. Seong
- Translational Research Center for Protein Function Control, Yonsei University, Seoul 120-749, Korea
- Department of Biotechnology, College of Bioscience and Biotechnology, Yonsei University, Seoul 120-749, Korea; E-Mails: (A.S.); (K.-H.L.)
- Authors to whom correspondence should be addressed; E-Mails: (S.I.C.); (H.J.); (B.L.S.); Tel.: +82-2-393-4631 (S.I.C.)
| |
Collapse
|
26
|
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.
Collapse
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.
| |
Collapse
|
27
|
Voisset C, Saupe SJ, Blondel M. The various facets of the protein-folding activity of the ribosome. Biotechnol J 2011; 6:668-73. [DOI: 10.1002/biot.201100021] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 03/16/2011] [Accepted: 04/04/2011] [Indexed: 11/11/2022]
|
28
|
Jha S, Komar AA. Birth, life and death of nascent polypeptide chains. Biotechnol J 2011; 6:623-40. [PMID: 21538896 PMCID: PMC3130931 DOI: 10.1002/biot.201000327] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 02/26/2011] [Accepted: 03/15/2011] [Indexed: 01/16/2023]
Abstract
The journey of nascent polypeptides from synthesis at the peptidyl transferase center of the ribosome (“birth”) to full function (“maturity”) involves multiple interactions, constraints, modifications and folding events. Each step of this journey impacts the ultimate expression level and functional capacity of the translated protein. It has become clear that the kinetics of protein translation is predominantly modulated by synonymous codon usage along the mRNA, and that this provides an active mechanism for coordinating the synthesis, maturation and folding of nascent polypeptides. Multiple quality control systems ensure that proteins achieve their native, functional form. Unproductive co-translational folding intermediates that arise during protein synthesis may undergo enhanced interaction with components of these systems, such as chaperones, and/or be subjects of co-translational degradation (“death”). This review provides an overview of our current understanding of the complex co-translational events that accompany the synthesis, maturation, folding and degradation of nascent polypeptide chains.
Collapse
Affiliation(s)
- Sujata Jha
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | | |
Collapse
|
29
|
Barbezier N, Chartier A, Bidet Y, Buttstedt A, Voisset C, Galons H, Blondel M, Schwarz E, Simonelig M. Antiprion drugs 6-aminophenanthridine and guanabenz reduce PABPN1 toxicity and aggregation in oculopharyngeal muscular dystrophy. EMBO Mol Med 2011; 3:35-49. [PMID: 21204267 PMCID: PMC3044817 DOI: 10.1002/emmm.201000109] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Oculopharyngeal muscular dystrophy (OPMD) is an adult-onset syndrome characterized by progressive degeneration of specific muscles. OPMD is caused by extension of a polyalanine tract in poly(A) binding protein nuclear 1 (PABPN1). Insoluble nuclear inclusions form in diseased muscles. We have generated a Drosophila model of OPMD that recapitulates the features of the disorder. Here, we show that the antiprion drugs 6-aminophenanthridine (6AP) and guanabenz acetate (GA), which prevent formation of amyloid fibers by prion proteins in cell models, alleviate OPMD phenotypes in Drosophila, including muscle degeneration and nuclear inclusion formation. The large ribosomal RNA and its activity in protein folding were recently identified as a specific cellular target of 6AP and GA. We show that deletions of the ribosomal DNA locus reduce OPMD phenotypes and act synergistically with sub-effective doses of 6AP. In a complementary approach, we demonstrate that ribosomal RNA accelerates in vitro fibril formation of PABPN1 N-terminal domain. These results reveal the conserved role of ribosomal RNA in different protein aggregation disorders and identify 6AP and GA as general anti-aggregation molecules.
Collapse
Affiliation(s)
- Nicolas Barbezier
- mRNA Regulation and Development, Institut de Génétique Humaine, CNRS UPR 1142, Montpellier Cedex 5, France
| | | | | | | | | | | | | | | | | |
Collapse
|
30
|
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.
Collapse
Affiliation(s)
- Suzana Dos Reis
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124 Uppsala, Sweden
| | | | | | | | | | | | | |
Collapse
|
31
|
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.
Collapse
Affiliation(s)
- Angela Bekesi
- Institute of Enzymology, Biological Research Centre, Hungarian Academy of Sciences, Budapest, Hungary.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Sabate R, de Groot NS, Ventura S. Protein folding and aggregation in bacteria. Cell Mol Life Sci 2010; 67:2695-715. [PMID: 20358253 PMCID: PMC11115605 DOI: 10.1007/s00018-010-0344-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Revised: 02/19/2010] [Accepted: 03/05/2010] [Indexed: 01/31/2023]
Abstract
Proteins might experience many conformational changes and interactions during their lifetimes, from their synthesis at ribosomes to their controlled degradation. Because, in most cases, only folded proteins are functional, protein folding in bacteria is tightly controlled genetically, transcriptionally, and at the protein sequence level. In addition, important cellular machinery assists the folding of polypeptides to avoid misfolding and ensure the attainment of functional structures. When these redundant protective strategies are overcome, misfolded polypeptides are recruited into insoluble inclusion bodies. The protein embedded in these intracellular deposits might display different conformations including functional and beta-sheet-rich structures. The latter assemblies are similar to the amyloid fibrils characteristic of several human neurodegenerative diseases. Interestingly, bacteria exploit the same structural principles for functional properties such as adhesion or cytotoxicity. Overall, this review illustrates how prokaryotic organisms might provide the bedrock on which to understand the complexity of protein folding and aggregation in the cell.
Collapse
Affiliation(s)
- Raimon Sabate
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Natalia S. de Groot
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Salvador Ventura
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| |
Collapse
|
33
|
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]
|
34
|
Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a Nonnative carbon source, L-1,2-propanediol. Appl Environ Microbiol 2010; 76:4158-68. [PMID: 20435762 DOI: 10.1128/aem.00373-10] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Laboratory adaptive evolution studies can provide key information to address a wide range of issues in evolutionary biology. Such studies have been limited thus far by the inability of workers to readily detect mutations in evolved microbial strains on a genome scale. This limitation has now been overcome by recently developed genome sequencing technology that allows workers to identify all accumulated mutations that appear during laboratory adaptive evolution. In this study, we evolved Escherichia coli K-12 MG1655 with a nonnative carbon source, l-1,2-propanediol (l-1,2-PDO), for approximately 700 generations. We found that (i) experimental evolution of E. coli for approximately 700 generations in 1,2-PDO-supplemented minimal medium resulted in acquisition of the ability to use l-1,2-PDO as a sole carbon and energy source so that the organism changed from an organism that did not grow at all initially to an organism that had a growth rate of 0.35 h(-1); (ii) six mutations detected by whole-genome resequencing accumulated in the evolved E. coli mutant over the course of adaptive evolution on l-1,2-PDO; (iii) five of the six mutations were within coding regions, and IS5 was inserted between two fuc regulons; (iv) two major mutations (mutations in fucO and its promoter) involved in l-1,2-PDO catabolism appeared early during adaptive evolution; and (v) multiple defined knock-in mutant strains with all of the mutations had growth rates essentially matching that of the evolved strain. These results provide insight into the genetic basis underlying microbial evolution for growth on a nonnative substrate.
Collapse
|
35
|
Kim HK, Choi SI, Seong BL. 5S rRNA-assisted DnaK refolding. Biochem Biophys Res Commun 2009; 391:1177-81. [PMID: 19962961 DOI: 10.1016/j.bbrc.2009.11.176] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Accepted: 11/29/2009] [Indexed: 10/20/2022]
Abstract
Although accumulating evidence has revealed that most proteins can fold without the assistance of molecular chaperones, little attention has been paid to other types of chaperoning macromolecules. A variety of proteins interact with diverse RNA molecules in vivo, suggesting a potential role of RNAs for folding of their interacting proteins. Here we show that the in vitro refolding of a representative molecular chaperone, DnaK, an Escherichia coli homolog of Hsp70, could be assisted by its interacting 5S rRNA. The folding enhancement occurred in RNA concentration and its size dependent manner whereas neither the RNA with the reverse sequence of 5S rRNA nor the RNase pretreated 5S rRNA stimulated the folding in vitro. Based on our results, we propose that 5S rRNA could exert the chaperoning activity on DnaK during the folding process. The results suggest an interesting possibility that the folding of RNA-interacting proteins could be assisted by their cognate RNA ligands.
Collapse
Affiliation(s)
- Hyo Kyung Kim
- Department of Biotechnology, College of Bioscience and Biotechnology, Yonsei University, Seoul 120-749, South Korea
| | | | | |
Collapse
|
36
|
Davidovich C, Belousoff M, Bashan A, Yonath A. The evolving ribosome: from non-coded peptide bond formation to sophisticated translation machinery. Res Microbiol 2009; 160:487-92. [PMID: 19619641 DOI: 10.1016/j.resmic.2009.07.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Revised: 07/02/2009] [Accepted: 07/04/2009] [Indexed: 11/25/2022]
Abstract
Structural analysis supported by biochemical, mutagenesis and computational evidence, revealed that the contemporary ribosome's active site is a universal symmetrical pocket made of ribosomal RNA. This pocket seems to be the remnant of the proto-ribosome, a dimeric RNA assembly evolved by gene duplication, capable of autonomously catalyzing peptide bond formation and non-coded amino acid polymerization.
Collapse
Affiliation(s)
- Chen Davidovich
- The Department of Structural Biology, Weizmann Institute, Rehovot, Israel
| | | | | | | |
Collapse
|
37
|
The dimeric proto-ribosome: Structural details and possible implications on the origin of life. Int J Mol Sci 2009; 10:2921-2934. [PMID: 19742176 PMCID: PMC2738903 DOI: 10.3390/ijms10072921] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 06/25/2009] [Indexed: 11/16/2022] Open
Abstract
A symmetric pocket-like entity, composed of two L-shaped RNA units, encircles the peptide synthesis site within the contemporary ribosome. This entity was suggested to be the vestige of a dimeric proto-ribosome, which could have formed spontaneously in the prebiotic world, catalyzing non-coded peptide bond formation and elongation. This structural element, beyond offering the initial step in the evolution of translation, is hypothesized here to be linked to the origin of life. By catalyzing the production of random peptide chains, the proto-ribosome could have enabled the formation of primary enzymes, launching a process of co-evolution of the translation apparatus and the proteins, thus presenting an alternative to the RNA world hypothesis.
Collapse
|
38
|
Samanta D, Das A, Bhattacharya A, Basu A, Das D, DasGupta C. Mechanism of ribosome assisted protein folding: a new insight into rRNA functions. Biochem Biophys Res Commun 2009; 384:137-40. [PMID: 19401192 DOI: 10.1016/j.bbrc.2009.04.106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Accepted: 04/19/2009] [Indexed: 11/26/2022]
Abstract
The peptidyl transferase center (PTC), present in the domain V of 23S rRNA of bacteria can act as a general protein folding modulator. Any general function of a nucleic acid polymer (DNA or RNA) is always related to specific sequence/sequences. The ribosome mediated protein folding also involves a specific interaction between the nucleotides of peptidyl transferase center and the amino acids of an unfolded protein. In this article the mechanism of rRNA assisted protein folding and its significance in the light of high resolution crystal structure of ribosome are discussed.
Collapse
Affiliation(s)
- Dibyendu Samanta
- Department of Biophysics, Molecular Biology and Genetics, University College of Science, Kolkata 700009, India.
| | | | | | | | | | | |
Collapse
|
39
|
Voisset C, Thuret JY, Tribouillard-Tanvier D, Saupe SJ, Blondel M. Tools for the study of ribosome-borne protein folding activity. Biotechnol J 2008; 3:1033-40. [PMID: 18683165 DOI: 10.1002/biot.200800134] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In addition to its role in protein synthesis, which involves a peptidyl transferase activity, the ribosome has also been described to be able to assist protein folding, at least in vitro, as presented in a Research Highlight (Das, et al., Biotechnol. J. 2008). This in vitro-described ribosome-borne protein folding activity (RPFA) is yet poorly characterized in vivo, in part because of the lack of tools to study its biological significance. There is substantial evidence documenting RPFA in vitro, and an assay intended to detect this activity in vivo has been set up in bacteria, but this assay is indirect. In this review, we describe the different tools and tests currently available to study RPFA. We put a special emphasis on the various available inhibitors of this activity and in particular, we discuss the use of 6-aminophenanthridine (6AP) and guanabenz (GA), two antiprion drugs that were very recently shown to specifically inhibit RPFA in vitro without any significant effect on the activity of the ribosome in protein synthesis. Therefore, these drugs should allow determining the potential biological role of RPFA. Importantly, the biological activity of 6AP and GA suggest a possible involvement of RPFA in human proteinopathies.
Collapse
|
40
|
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.
Collapse
Affiliation(s)
- Debasis Das
- Department of Biophysics, Molecular Biology and Genetics, University College of Science, Kolkata, India
| | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Tribouillard-Tanvier D, Dos Reis S, Gug F, Voisset C, Béringue V, Sabate R, Kikovska E, Talarek N, Bach S, Huang C, Desban N, Saupe SJ, Supattapone S, Thuret JY, Chédin S, Vilette D, Galons H, Sanyal S, Blondel M. Protein folding activity of ribosomal RNA is a selective target of two unrelated antiprion drugs. PLoS One 2008; 3:e2174. [PMID: 18478094 PMCID: PMC2374897 DOI: 10.1371/journal.pone.0002174] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Accepted: 04/04/2008] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND 6-Aminophenanthridine (6AP) and Guanabenz (GA, a drug currently in use for the treatment of hypertension) were isolated as antiprion drugs using a yeast-based assay. These structurally unrelated molecules are also active against mammalian prion in several cell-based assays and in vivo in a mouse model for prion-based diseases. METHODOLOGY/PRINCIPAL FINDINGS Here we report the identification of cellular targets of these drugs. Using affinity chromatography matrices for both drugs, we demonstrate an RNA-dependent interaction of 6AP and GA with the ribosome. These specific interactions have no effect on the peptidyl transferase activity of the ribosome or on global translation. In contrast, 6AP and GA specifically inhibit the ribosomal RNA-mediated protein folding activity of the ribosome. CONCLUSION/SIGNIFICANCE 6AP and GA are therefore the first compounds to selectively inhibit the protein folding activity of the ribosome. They thus constitute precious tools to study the yet largely unexplored biological role of this protein folding activity.
Collapse
Affiliation(s)
- Déborah Tribouillard-Tanvier
- INSERM U613, Brest, France
- Univ Brest, Faculté de Médecine et des Sciences de la Santé, UMR-S613, Brest, France
- Etablissement Français du Sang (EFS) Bretagne, Brest, France
- CHU Brest, Hop Morvan, Laboratoire de Génétique Moléculaire, Brest, France
- CNRS UPS2682, Station Biologique, Protein Phosphorylation & Disease Laboratory, Roscoff, France
| | - Suzana Dos Reis
- Institute of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Fabienne Gug
- INSERM U648, Laboratoire de Chimie Organique 2, Université Paris Descartes, Paris, France
| | - Cécile Voisset
- INSERM U613, Brest, France
- Univ Brest, Faculté de Médecine et des Sciences de la Santé, UMR-S613, Brest, France
- Etablissement Français du Sang (EFS) Bretagne, Brest, France
- CHU Brest, Hop Morvan, Laboratoire de Génétique Moléculaire, Brest, France
| | - Vincent Béringue
- Institut National de la Recherche Agronomique (INRA), UR892, Virologie Immunologie Moléculaires, Jouy-en-Josas, France
| | - Raimon Sabate
- Laboratoire de Génétique Moléculaire des Champignons, IBGC UMR CNRS 5095, Université de Bordeaux 2, Bordeaux, France
| | - Ema Kikovska
- Institute of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Nicolas Talarek
- Department of Medicine/Biochemistry, University of Fribourg, Fribourg, Switzerland
| | - Stéphane Bach
- CNRS UPS2682, Station Biologique, Protein Phosphorylation & Disease Laboratory, Roscoff, France
| | - Chenhui Huang
- Institute of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Nathalie Desban
- CNRS UPS2682, Station Biologique, Protein Phosphorylation & Disease Laboratory, Roscoff, France
| | - Sven J. Saupe
- Laboratoire de Génétique Moléculaire des Champignons, IBGC UMR CNRS 5095, Université de Bordeaux 2, Bordeaux, France
| | - Surachai Supattapone
- Department of Medicine, Dartmouth Medical School, Hanover, New Hampshire, United States of America
- Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire, United States of America
| | | | | | - Didier Vilette
- Institut National de la Recherche Agronomique (INRA), UR892, Virologie Immunologie Moléculaires, Jouy-en-Josas, France
| | - Hervé Galons
- INSERM U648, Laboratoire de Chimie Organique 2, Université Paris Descartes, Paris, France
| | - Suparna Sanyal
- Institute of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Marc Blondel
- INSERM U613, Brest, France
- Univ Brest, Faculté de Médecine et des Sciences de la Santé, UMR-S613, Brest, France
- Etablissement Français du Sang (EFS) Bretagne, Brest, France
- CHU Brest, Hop Morvan, Laboratoire de Génétique Moléculaire, Brest, France
| |
Collapse
|