1
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Park C, Han B, Choi Y, Jin Y, Kim KP, Choi SI, Seong BL. RNA-dependent proteome solubility maintenance in Escherichia coli lysates analysed by quantitative mass spectrometry: Proteomic characterization in terms of isoelectric point, structural disorder, functional hub, and chaperone network. RNA Biol 2024; 21:1-18. [PMID: 38361426 PMCID: PMC10878026 DOI: 10.1080/15476286.2024.2315383] [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] [Accepted: 02/02/2024] [Indexed: 02/17/2024] Open
Abstract
Protein aggregation, a consequence of misfolding and impaired proteostasis, can lead to cellular malfunctions such as various proteinopathies. The mechanisms protecting proteins from aggregation in complex cellular environments have long been investigated, often from a protein-centric viewpoint. However, our study provides insights into a crucial, yet overlooked actor: RNA. We found that depleting RNAs from Escherichia coli lysates induces global protein aggregation. Our quantitative mass spectrometry analysis identified over 900 statistically significant proteins from the Escherichia coli proteome whose solubility depends on RNAs. Proteome-wide characterization showed that the RNA dependency is particularly enriched among acidic proteins, intrinsically disordered proteins, and structural hub proteins. Moreover, we observed distinct differences in RNA-binding mode and Gene Ontology categories between RNA-dependent acidic and basic proteins. Notably, the solubility of key molecular chaperones [Trigger factor, DnaJ, and GroES] is largely dependent on RNAs, suggesting a yet-to-be-explored hierarchical relationship between RNA-based chaperone (termed as chaperna) and protein-based chaperones, both of which constitute the whole chaperone network. These findings provide new insights into the RNA-centric role in maintaining healthy proteome solubility in vivo, where proteins associate with a variety of RNAs, either stably or transiently.
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Affiliation(s)
- Chan Park
- Department of Microbiology, College of Medicine, Yonsei University, Seoul, Korea
- Vaccine Innovative Technology ALliance (VITAL)-Korea, Yonsei University, Seoul, Korea
| | - Bitnara Han
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, Korea
| | - Yura Choi
- Vaccine Innovative Technology ALliance (VITAL)-Korea, Yonsei University, Seoul, Korea
- The Interdisciplinary Graduate Program in Integrative Biotechnology and Translational Medicine, Yonsei University, Incheon, Korea
| | - Yoontae Jin
- Vaccine Innovative Technology ALliance (VITAL)-Korea, Yonsei University, Seoul, Korea
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea
| | - Kwang Pyo Kim
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, Korea
- Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, Seoul, Republic of Korea
| | - Seong Il Choi
- Department of Pediatrics, Severance Hospital, Institute of Allergy, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Baik L. Seong
- Department of Microbiology, College of Medicine, Yonsei University, Seoul, Korea
- Vaccine Innovative Technology ALliance (VITAL)-Korea, Yonsei University, Seoul, Korea
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2
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Fedorov AN. Biosynthetic Protein Folding and Molecular Chaperons. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S128-S19. [PMID: 35501992 DOI: 10.1134/s0006297922140115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The problem of linear polypeptide chain folding into a unique tertiary structure is one of the fundamental scientific challenges. The process of folding cannot be fully understood without its biological context, especially for big multidomain and multisubunit proteins. The principal features of biosynthetic folding are co-translational folding of growing nascent polypeptide chains and involvement of molecular chaperones in the process. The review summarizes available data on the early events of nascent chain folding, as well as on later advanced steps, including formation of elements of native structure. The relationship between the non-uniformity of translation rate and folding of the growing polypeptide is discussed. The results of studies on the effect of biosynthetic folding features on the parameters of folding as a physical process, its kinetics and mechanisms, are presented. Current understanding and hypotheses on the relationship of biosynthetic folding with the fundamental physical parameters and current views on polypeptide folding in the context of energy landscapes are discussed.
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Affiliation(s)
- Alexey N Fedorov
- Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia.
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3
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Bevilacqua PC, Williams AM, Chou HL, Assmann SM. RNA multimerization as an organizing force for liquid-liquid phase separation. RNA (NEW YORK, N.Y.) 2022; 28:16-26. [PMID: 34706977 PMCID: PMC8675289 DOI: 10.1261/rna.078999.121] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
RNA interactions are exceptionally strong and highly redundant. As such, nearly any two RNAs have the potential to interact with one another over relatively short stretches, especially at high RNA concentrations. This is especially true for pairs of RNAs that do not form strong self-structure. Such phenomena can drive liquid-liquid phase separation, either solely from RNA-RNA interactions in the presence of divalent or organic cations, or in concert with proteins. RNA interactions can drive multimerization of RNA strands via both base-pairing and tertiary interactions. In this article, we explore the tendency of RNA to form stable monomers, dimers, and higher order structures as a function of RNA length and sequence through a focus on the intrinsic thermodynamic, kinetic, and structural properties of RNA. The principles we discuss are independent of any specific type of biomolecular condensate, and thus widely applicable. We also speculate how external conditions experienced by living organisms can influence the formation of nonmembranous compartments, again focusing on the physical and structural properties of RNA. Plants, in particular, are subject to diverse abiotic stresses including extreme temperatures, drought, and salinity. These stresses and the cellular responses to them, including changes in the concentrations of small molecules such as polyamines, salts, and compatible solutes, have the potential to regulate condensate formation by melting or strengthening base-pairing. Reversible condensate formation, perhaps including regulation by circadian rhythms, could impact biological processes in plants, and other organisms.
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Affiliation(s)
- Philip C Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry, Microbiology, and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Allison M Williams
- Department of Biochemistry, Microbiology, and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Hong-Li Chou
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Sarah M Assmann
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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4
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TAR RNA Mediated Folding of a Single-Arginine-Mutant HIV-1 Tat Protein within HeLa Cells Experiencing Intracellular Crowding. Int J Mol Sci 2021; 22:ijms22189998. [PMID: 34576162 PMCID: PMC8468913 DOI: 10.3390/ijms22189998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/03/2021] [Accepted: 09/11/2021] [Indexed: 11/17/2022] Open
Abstract
The various effects of native protein folding on the stability and folding rate of intrinsically disordered proteins (IDPs) in crowded intracellular environments are important in biomedicine. Although most studies on protein folding have been conducted in vitro, providing valuable insights, studies on protein folding in crowded intracellular environments are scarce. This study aimed to explore the effects of intracellular molecular crowding on the folding of mutant transactivator HIV-1 Tat based on intracellular interactions, including TAR RNA, as proof of the previously reported chaperna-RNA concept. Considering that the Tat-TAR RNA motif binds RNA, we assessed the po tential function of TAR RNA as a chaperna for the refolding of R52Tat, a mutant in which the argi nine (R) residues at R52 have been replaced with alanine (A) by site-directed mutagenesis. We mon itored Tat-EGFP and Tat folding in HeLa cells via time-lapse fluorescence microscopy and biolayer interferometry using EGFP fusion as an indicator for folding status. These results show that the refolding of R52A Tat was stimulated well at a 0.3 μM TAR RNA concentration; wild-type Tat refolding was essentially abolished because of a reduction in the affinity for TAR RNA at that con centration. The folding and refolding of R52Tat were mainly promoted upon stimulation with TAR RNA. Our findings provide novel insights into the therapeutic potential of chaperna-mediated fold ing through the examination of as-yet-unexplored RNA-mediated protein folding as well as viral genetic variants that modulate viral evolutionary linkages for viral diseases inside a crowded intra cellular environment.
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5
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Hutchinson RB, Chen X, Zhou N, Cavagnero S. Fluorescence Anisotropy Decays and Microscale-Volume Viscometry Reveal the Compaction of Ribosome-Bound Nascent Proteins. J Phys Chem B 2021; 125:6543-6558. [PMID: 34110829 PMCID: PMC8741338 DOI: 10.1021/acs.jpcb.1c04473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This work introduces a technology that combines fluorescence anisotropy decay with microscale-volume viscometry to investigate the compaction and dynamics of ribosome-bound nascent proteins. Protein folding in the cell, especially when nascent chains emerge from the ribosomal tunnel, is poorly understood. Previous investigations based on fluorescence anisotropy decay determined that a portion of the ribosome-bound nascent protein apomyoglobin (apoMb) forms a compact structure. This work, however, could not assess the size of the compact region. The combination of fluorescence anisotropy with microscale-volume viscometry, presented here, enables identifying the size of compact nascent-chain subdomains using a single fluorophore label. Our results demonstrate that the compact region of nascent apoMb contains 57-83 amino acids and lacks residues corresponding to the two native C-terminal helices. These amino acids are necessary for fully burying the nonpolar residues in the native structure, yet they are not available for folding before ribosome release. Therefore, apoMb requires a significant degree of post-translational folding for the generation of its native structure. In summary, the combination of fluorescence anisotropy decay and microscale-volume viscometry is a powerful approach to determine the size of independently tumbling compact regions of biomolecules. This technology is of general applicability to compact macromolecules linked to larger frameworks.
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Affiliation(s)
| | - Xi Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Ningkun Zhou
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
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6
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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.
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7
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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.
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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
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8
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Ferdosh S, Banerjee S, Pathak BK, Sengupta J, Barat C. Hibernating ribosomes exhibit chaperoning activity but can resist unfolded protein-mediated subunit dissociation. FEBS J 2020; 288:1305-1324. [PMID: 32649051 DOI: 10.1111/febs.15479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/24/2020] [Accepted: 07/07/2020] [Indexed: 02/03/2023]
Abstract
Ribosome hibernation is a prominent cellular strategy to modulate protein synthesis during starvation and the stationary phase of bacterial cell growth. Translational suppression involves the formation of either factor-bound inactive 70S monomers or dimeric 100S hibernating ribosomal complexes, the biological significance of which is poorly understood. Here, we demonstrate that the Escherichia coli 70S ribosome associated with stationary phase factors hibernation promoting factor or protein Y or ribosome-associated inhibitor A and the 100S ribosome isolated from both Gram-negative and Gram-positive bacteria are resistant to unfolded protein-mediated subunit dissociation and subsequent degradation by cellular ribonucleases. Considering that the increase in cellular stress is accompanied by accumulation of unfolded proteins, such resistance of hibernating ribosomes towards dissociation might contribute to their maintenance during the stationary phase. Analysis of existing structures provided clues on the mechanism of inhibition of the unfolded protein-mediated disassembly in case of hibernating factor-bound ribosome. Further, the factor-bound 70S and 100S ribosomes can suppress protein aggregation and assist in protein folding. The chaperoning activity of these ribosomes is the first evidence of a potential biological activity of the hibernating ribosome that might be crucial for cell survival under stress conditions.
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Affiliation(s)
- Sehnaz Ferdosh
- Department of Biotechnology, St. Xavier's College, Kolkata, India
| | - Senjuti Banerjee
- Department of Biotechnology, St. Xavier's College, Kolkata, India
| | - Bani K Pathak
- 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, Kolkata, India
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9
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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
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10
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Choi SI. A Simple Principle for Understanding the Combined Cellular Protein Folding and Aggregation. Curr Protein Pept Sci 2020; 21:3-21. [DOI: 10.2174/1389203720666190725114550] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 12/27/2022]
Abstract
Proteins can undergo kinetic/thermodynamic partitioning between folding and aggregation. Proper protein folding and thermodynamic stability are crucial for aggregation inhibition. Thus, proteinfolding principles have been widely believed to consistently underlie aggregation as a consequence of conformational change. However, this prevailing view appears to be challenged by the ubiquitous phenomena that the intrinsic and extrinsic factors including cellular macromolecules can prevent aggregation, independently of (even with sacrificing) protein folding rate and stability. This conundrum can be definitely resolved by ‘a simple principle’ based on a rigorous distinction between protein folding and aggregation: aggregation can be controlled by affecting the intermolecular interactions for aggregation, independently of the intramolecular interactions for protein folding. Aggregation is beyond protein folding. A unifying model that can conceptually reconcile and underlie the seemingly contradictory observations is described here. This simple principle highlights, in particular, the importance of intermolecular repulsive forces against aggregation, the magnitude of which can be correlated with the size and surface properties of molecules. The intermolecular repulsive forces generated by the common intrinsic properties of cellular macromolecules including chaperones, such as their large excluded volume and surface charges, can play a key role in preventing the aggregation of their physically connected polypeptides, thus underlying the generic intrinsic chaperone activity of soluble cellular macromolecules. Such intermolecular repulsive forces of bulky cellular macromolecules, distinct from protein conformational change and attractive interactions, could be the puzzle pieces for properly understanding the combined cellular protein folding and aggregation including how proteins can overcome their metastability to amyloid fibrils in vivo.
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Affiliation(s)
- Seong Il Choi
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
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11
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Dao Duc K, Batra SS, Bhattacharya N, Cate JHD, Song YS. Differences in the path to exit the ribosome across the three domains of life. Nucleic Acids Res 2019; 47:4198-4210. [PMID: 30805621 PMCID: PMC6486554 DOI: 10.1093/nar/gkz106] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 02/22/2019] [Indexed: 01/07/2023] Open
Abstract
The ribosome exit tunnel is an important structure involved in the regulation of translation and other essential functions such as protein folding. By comparing 20 recently obtained cryo-EM and X-ray crystallography structures of the ribosome from all three domains of life, we here characterize the key similarities and differences of the tunnel across species. We first show that a hierarchical clustering of tunnel shapes closely reflects the species phylogeny. Then, by analyzing the ribosomal RNAs and proteins, we explain the observed geometric variations and show direct association between the conservations of the geometry, structure and sequence. We find that the tunnel is more conserved in the upper part close to the polypeptide transferase center, while in the lower part, it is substantially narrower in eukaryotes than in bacteria. Furthermore, we provide evidence for the existence of a second constriction site in eukaryotic exit tunnels. Overall, these results have several evolutionary and functional implications, which explain certain differences between eukaryotes and prokaryotes in their translation mechanisms. In particular, they suggest that major co-translational functions of bacterial tunnels were externalized in eukaryotes, while reducing the tunnel size provided some other advantages, such as facilitating the nascent chain elongation and enabling antibiotic resistance.
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Affiliation(s)
- Khanh Dao Duc
- Computer Science Division, University of California, Berkeley, CA 94720, USA
| | - Sanjit S Batra
- Computer Science Division, University of California, Berkeley, CA 94720, USA
| | | | - Jamie H D Cate
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.,Department of Chemistry, University of California, Berkeley, CA 94720, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yun S Song
- Computer Science Division, University of California, Berkeley, CA 94720, USA.,Department of Statistics, University of California, Berkeley, CA 94720, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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12
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Conversion of a soluble protein into a potent chaperone in vivo. Sci Rep 2019; 9:2735. [PMID: 30804538 PMCID: PMC6389997 DOI: 10.1038/s41598-019-39158-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 01/18/2019] [Indexed: 01/31/2023] Open
Abstract
Molecular chaperones play an important role in cellular protein-folding assistance and aggregation inhibition. As a different but complementary model, we previously proposed that, in general, soluble cellular macromolecules with large excluded volume and surface charges exhibit intrinsic chaperone activity to prevent aggregation of their connected polypeptides irrespective of the connection type, thereby contributing to efficient protein folding. As a proof of concept, we here demonstrated that a model recombinant protein with a specific sequence-binding domain robustly exerted chaperone activity toward various proteins harbouring a short recognition tag of 7 residues in Escherichia coli. The chaperone activity of this protein was comparable to that of representative E. coli chaperones in vivo. Furthermore, in vitro refolding experiments confirmed the in vivo results. Our findings reveal that a soluble protein exhibits the intrinsic chaperone activity to prevent off-pathway aggregation of its interacting proteins, leading to more productive folding while allowing them to fold according to their intrinsic folding pathways. This study gives new insights into the plausible chaperoning role of soluble cellular macromolecules in terms of aggregation inhibition and indirect folding assistance.
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13
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Yang SW, Jang YH, Kwon SB, Lee YJ, Chae W, Byun YH, Kim P, Park C, Lee YJ, Kim CK, Kim YS, Choi SI, Seong BL. Harnessing an RNA-mediated chaperone for the assembly of influenza hemagglutinin in an immunologically relevant conformation. FASEB J 2018; 32:2658-2675. [PMID: 29295864 PMCID: PMC5901386 DOI: 10.1096/fj.201700747rr] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 12/18/2017] [Indexed: 01/29/2023]
Abstract
A novel protein-folding function of RNA has been recognized, which can outperform previously known molecular chaperone proteins. The RNA as a molecular chaperone (chaperna) activity is intrinsic to some ribozymes and is operational during viral infections. Our purpose was to test whether influenza hemagglutinin (HA) can be assembled in a soluble, trimeric, and immunologically activating conformation by means of an RNA molecular chaperone (chaperna) activity. An RNA-interacting domain (RID) from the host being immunized was selected as a docking tag for RNA binding, which served as a transducer for the chaperna function for de novo folding and trimeric assembly of RID-HA1. Mutations that affect tRNA binding greatly increased the soluble aggregation defective in trimer assembly, suggesting that RNA interaction critically controls the kinetic network in the folding/assembly pathway. Immunization of mice resulted in strong hemagglutination inhibition and high titers of a neutralizing antibody, providing sterile protection against a lethal challenge and confirming the immunologically relevant HA conformation. The results may be translated into a rapid response to a new influenza pandemic. The harnessing of the novel chaperna described herein with immunologically tailored antigen-folding functions should serve as a robust prophylactic and diagnostic tool for viral infections.-Yang, S. W., Jang, Y. H., Kwon, S. B., Lee, Y. J., Chae, W., Byun, Y. H., Kim, P., Park, C., Lee, Y. J., Kim, C. K., Kim, Y. S., Choi, S. I., Seong, B. L. Harnessing an RNA-mediated chaperone for the assembly of influenza hemagglutinin in an immunologically relevant conformation.
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MESH Headings
- Animals
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- Female
- Hemagglutinin Glycoproteins, Influenza Virus/biosynthesis
- Hemagglutinin Glycoproteins, Influenza Virus/chemistry
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Immunization
- Influenza A virus/genetics
- Influenza A virus/immunology
- Influenza A virus/metabolism
- Mice
- Mice, Inbred BALB C
- Molecular Chaperones/chemistry
- Molecular Chaperones/genetics
- Molecular Chaperones/immunology
- Molecular Chaperones/metabolism
- Mutation
- Protein Folding
- Protein Multimerization
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/immunology
- RNA, Transfer/metabolism
- Rabbits
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Affiliation(s)
- Seung Won Yang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Yo Han Jang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Soon Bin Kwon
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Yoon Jae Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Wonil Chae
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Young Ho Byun
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Paul Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Chan Park
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Young Jae Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Choon Kang Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Young Seok Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Seong Il Choi
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Baik Lin Seong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
- Vaccine Translational Research Center, Yonsei University, Seoul, South Korea
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14
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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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15
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Kim JM, Choi HS, Seong BL. The folding competence of HIV-1 Tat mediated by interaction with TAR RNA. RNA Biol 2017; 14:926-937. [PMID: 28418268 DOI: 10.1080/15476286.2017.1311455] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
The trans-activator Tat protein of HIV-1 belongs to the large family of intrinsically disordered proteins (IDPs), and is known to recruit various host proteins for the transactivation of viral RNA synthesis. Tat protein interacts with the transactivator response RNA (TAR RNA), exhibiting RNA chaperone activities for structural rearrangement of interacting RNAs. Here, considering that Tat-TAR RNA interaction is mutually cooperative, we examined the potential role of TAR RNA as Chaperna - RNA that provides chaperone function to proteins - for the folding of HIV-1 Tat. Using EGFP fusion as an indirect indicator for folding status, we monitored Tat-EGFP folding in HeLa cells via time-lapse fluorescence microscopy. The live cell imaging showed that the rate and the extent of folding of Tat-EGFP were stimulated by TAR RNA. The purified Tat-EGFP was denatured and the fluorescence was monitored in vitro under renaturation condition. The fluorescence was significantly increased by TAR RNA, and the mutations in TAR RNA that affected the interaction with Tat protein failed to promote Tat refolding. The results suggest that TAR RNA stabilizes Tat as unfolded, but prevents it from misfolding, and maintaining its folding competence for interaction with multiple host factors toward its transactivation. The Chaperna function of virally encoded RNA in establishing proteome link at the viral-host interface provides new insights to as yet largely unexplored RNA mediated protein folding in normal and dysregulated cellular metabolism.
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Affiliation(s)
- Jung Min Kim
- a Department of Biotechnology , College of Life Science and Biotechnology, Yonsei University , Seoul , South Korea.,b Vaccine Translational Research Center , Yonsei University , Seoul , South Korea
| | - Hee Sun Choi
- c Department of Pathology , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Baik Lin Seong
- a Department of Biotechnology , College of Life Science and Biotechnology, Yonsei University , Seoul , South Korea.,b Vaccine Translational Research Center , Yonsei University , Seoul , South Korea
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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.
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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:
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17
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Chakraborty B, Bhakta S, Sengupta J. Disassembly of yeast 80S ribosomes into subunits is a concerted action of ribosome-assisted folding of denatured protein. Biochem Biophys Res Commun 2016; 469:923-9. [DOI: 10.1016/j.bbrc.2015.12.107] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 12/22/2015] [Indexed: 11/27/2022]
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18
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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: 20] [Impact Index Per Article: 2.2] [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.
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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
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19
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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.
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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.
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20
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Nguyen PH, Hammoud H, Halliez S, Pang Y, Evrard J, Schmitt M, Oumata N, Bourguignon JJ, Sanyal S, Beringue V, Blondel M, Bihel F, Voisset C. Structure-activity relationship study around guanabenz identifies two derivatives retaining antiprion activity but having lost α2-adrenergic receptor agonistic activity. ACS Chem Neurosci 2014; 5:1075-82. [PMID: 25244284 DOI: 10.1021/cn5001588] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Guanabenz (GA) is an orally active α2-adrenergic agonist that has been used for many years for the treatment of hypertension. We recently described that GA is also active against both yeast and mammalian prions in an α2-adrenergic receptor-independent manner. These data suggest that this side-activity of GA could be explored for the treatment of prion-based diseases and other amyloid-based disorders. In this perspective, the potent antihypertensive activity of GA happens to be an annoying side-effect that could limit its use. In order to get rid of GA agonist activity at α2-adrenergic receptors, we performed a structure-activity relationship study around GA based on changes of the chlorine positions on the benzene moiety and then on the modifications of the guanidine group. Hence, we identified the two derivatives 6 and 7 that still possess a potent antiprion activity but were totally devoid of any agonist activity at α2-adrenergic receptors. Similarly to GA, 6 and 7 were also able to inhibit the protein folding activity of the ribosome (PFAR) which has been suggested to be involved in prion appearance/maintenance. Therefore, these two GA derivatives are worth being considered as drug candidates.
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Affiliation(s)
- 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, 29200 Brest, France
| | - Hassan Hammoud
- Laboratoire d’Innovation
Thérapeutique, UMR7200, CNRS, Université de Strasbourg, Faculté
de pharmacie, 74, route
du Rhin, 67400 Illkirch, France
| | - Sophie Halliez
- Virologie
Immunologie Moléculaires, UR892, Institut National de la Recherche Agronomique (INRA), 78352 Jouy-en-Josas, France
| | - Yanhong Pang
- Department
of Cell and Molecular Biology, Box-596, BMC, Uppsala University, 751 05 Uppsala, Sweden
| | - 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, 29200 Brest, France
| | - Martine Schmitt
- Laboratoire d’Innovation
Thérapeutique, UMR7200, CNRS, Université de Strasbourg, Faculté
de pharmacie, 74, route
du Rhin, 67400 Illkirch, France
| | - Nassima Oumata
- Laboratoire
de Chimie Organique 2, Inserm U1022, Université Paris Descartes, 75006 Paris, France
| | - Jean-Jacques Bourguignon
- Laboratoire d’Innovation
Thérapeutique, UMR7200, CNRS, Université de Strasbourg, Faculté
de pharmacie, 74, route
du Rhin, 67400 Illkirch, France
| | - Suparna Sanyal
- Department
of Cell and Molecular Biology, Box-596, BMC, Uppsala University, 751 05 Uppsala, Sweden
| | - Vincent Beringue
- Virologie
Immunologie Moléculaires, UR892, Institut National de la Recherche Agronomique (INRA), 78352 Jouy-en-Josas, France
| | - 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, 29200 Brest, France
| | - Frédéric Bihel
- Laboratoire d’Innovation
Thérapeutique, UMR7200, CNRS, Université de Strasbourg, Faculté
de pharmacie, 74, route
du Rhin, 67400 Illkirch, France
| | - 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, 29200 Brest, France
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21
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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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22
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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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Oumata N, Nguyen PH, Beringue V, Soubigou F, Pang Y, Desban N, Massacrier C, Morel Y, Paturel C, Contesse MA, Bouaziz S, Sanyal S, Galons H, Blondel M, Voisset C. The toll-like receptor agonist imiquimod is active against prions. PLoS One 2013; 8:e72112. [PMID: 23977222 PMCID: PMC3745460 DOI: 10.1371/journal.pone.0072112] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 07/11/2013] [Indexed: 12/11/2022] Open
Abstract
Using a yeast-based assay, a previously unsuspected antiprion activity was found for imiquimod (IQ), a potent Toll-like receptor 7 (TLR7) agonist already used for clinical applications. The antiprion activity of IQ was first detected against yeast prions [PSI+] and [URE3], and then against mammalian prion both ex vivo in a cell-based assay and in vivo in a transgenic mouse model for prion diseases. In order to facilitate structure-activity relationship studies, we conducted a new synthetic pathway which provides a more efficient means of producing new IQ chemical derivatives, the activity of which was tested against both yeast and mammalian prions. The comparable antiprion activity of IQ and its chemical derivatives in the above life forms further emphasizes the conservation of prion controlling mechanisms throughout evolution. Interestingly, this study also demonstrated that the antiprion activity of IQ and IQ-derived compounds is independent from their ability to stimulate TLRs. Furthermore, we found that IQ and its active chemical derivatives inhibit the protein folding activity of the ribosome (PFAR) in vitro.
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Affiliation(s)
- Nassima Oumata
- Laboratoire de Chimie Organique 2, INSERM U1022, Université Paris Descartes, Paris, France
| | - Phu hai Nguyen
- Institut National de la Sante et de la recherche Medicale UMR1078, 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
| | - Vincent Beringue
- Virologie Immunologie Moléculaires, UR892, Institut National de la Recherche Agronomique (INRA), Jouy-en-Josas, France
| | - Flavie Soubigou
- Institut National de la Sante et de la recherche Medicale UMR1078, 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
| | - Yanhong Pang
- Department of Cell and Molecular Biology, BMC, Uppsala University, Uppsala, Sweden
| | - Nathalie Desban
- Protein Phosphorylation & Disease Laboratory, CNRS UPS2682, Roscoff, France
| | | | | | | | - Marie-Astrid Contesse
- Institut National de la Sante et de la recherche Medicale UMR1078, 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
| | - Serge Bouaziz
- UMR 8015 CNRS, Laboratoire de Cristallographie et RMN Biologiques, Université Paris Descartes, Paris, France
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, BMC, Uppsala University, Uppsala, Sweden
| | - Hervé Galons
- Laboratoire de Chimie Organique 2, INSERM U1022, Université Paris Descartes, Paris, France
| | - Marc Blondel
- Institut National de la Sante et de la recherche Medicale UMR1078, 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
- * E-mail: (CV); (MB)
| | - Cécile Voisset
- Institut National de la Sante et de la recherche Medicale UMR1078, 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
- * E-mail: (CV); (MB)
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24
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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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25
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Chronic treatment with long acting phosphodiesterase-5 inhibitor tadalafil alters proteomic changes associated with cytoskeletal rearrangement and redox regulation in Type 2 diabetic hearts. Basic Res Cardiol 2012; 107:249. [PMID: 22311732 DOI: 10.1007/s00395-012-0249-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Revised: 01/16/2012] [Accepted: 01/27/2012] [Indexed: 01/09/2023]
Abstract
Diabetic patients are prone to metabolic perturbations that progressively contribute to structural, functional and proteomic alterations in the myocardium. Phosphodiesterase-5 (PDE-5) inhibitors exhibit cardioprotective effects against ischemic/reperfusion injury, however the effects of chronic administration of PDE-5 inhibitors, particularly under diabetic conditions, remain unknown. Hence, the present study was designed to identify novel protein targets related to long-acting PDE-5 inhibitor tadalafil-induced cardioprotection in diabetes. Using two-dimensional differential in-gel electrophoresis with 3 CyDye labeling and MALDI-TOF/TOF tandem mass spectrometry we identified alterations in the expressions of cardiac proteins in diabetic db/db mice treated with tadalafil. Tadalafil reversed the coordinated alterations of cytoskeletal/contractile proteins such as myosin light chain (MLY) 2 and 4, myosin heavy chain α and myosin-binding protein C which contributes to contractile dysfunction. The expression of intermediate filament protein vimentin and extra-cellular matrix proteins like cysteine and glycine rich protein-3 and collagen type VI α were upregulated in db/db mice indicating cardiac remodeling in diabetes. These detrimental proteomic alterations were reflected in cardiac function which were reversed in tadalafil treated mice. Tadalafil also enhanced antioxidant enzyme glutathione S-transferase Kappa-1 (GSKT-1) and downregulated redox regulatory chaperones like heat shock protein 8 (HSPA8), and 75 kD glucose regulatory protein (75GRP). Furthermore, tadalafil treatment significantly attenuated GSSG/GSH ratio and improved the metabolic status of db/db mice. Chronic treatment with tadalafil in db/db mice modulates proteins involved in cytoskeletal rearrangement and redox signaling of the heart, which may explain the beneficial effects of PDE-5 inhibition in diabetes.
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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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27
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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]
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28
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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.
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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
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29
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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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30
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Abstract
Over five decades of research have yielded a large body of information on how purified proteins attain their native state when refolded in the test tube, starting from a chemically or thermally denatured state. Nevertheless, we still know little about how proteins fold and unfold in their natural biological habitat: the living cell. Indeed, a variety of cellular components, including molecular chaperones, the ribosome, and crowding of the intracellular medium, modulate folding mechanisms in physiologically relevant environments. This review focuses on the current state of knowledge in protein folding in the cell with emphasis on the early stage of a protein's life, as the nascent polypeptide traverses and emerges from the ribosomal tunnel. Given the vectorial nature of ribosome-assisted translation, the transient degree of chain elongation becomes a relevant variable expected to affect nascent protein foldability, aggregation propensity and extent of interaction with chaperones and the ribosome.
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Affiliation(s)
- Daria V Fedyukina
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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31
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Weinreis SA, Ellis JP, Cavagnero S. Dynamic fluorescence depolarization: a powerful tool to explore protein folding on the ribosome. Methods 2010; 52:57-73. [PMID: 20685617 PMCID: PMC2934862 DOI: 10.1016/j.ymeth.2010.06.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 05/28/2010] [Accepted: 06/01/2010] [Indexed: 11/25/2022] Open
Abstract
Protein folding is a fundamental biological process of great significance for cell function and life-related processes. Surprisingly, very little is presently known about how proteins fold in vivo. The influence of the cellular environment is of paramount importance, as molecular chaperones, the ribosome, and the crowded medium affect both folding pathways and potentially even equilibrium structures. Studying protein folding in physiologically relevant environments, however, poses a number of technical challenges due to slow tumbling rates, low concentrations and potentially non-homogenous populations. Early work in this area relied on biological assays based on antibody recognition, proteolysis, and activity studies. More recently, it has been possible to directly observe the structure and dynamics of nascent polypeptides at high resolution by spectroscopic and microscopic techniques. The fluorescence depolarization decay of nascent polypeptides labeled with a small extrinsic fluorophore is a particularly powerful tool to gain insights into the dynamics of newly synthesized proteins. The fluorophore label senses both its own local mobility and the motions of the macromolecule to which it is attached. Fluorescence anisotropy decays can be measured both in the time and frequency domains. The latter mode of data collection is extremely convenient to capture the nanosecond motions in ribosome-bound nascent proteins, indicative of the development of independent structure and folding on the ribosome. In this review, we discuss the theory of fluorescence depolarization and its exciting applications to the study of the dynamics of nascent proteins in the cellular environment.
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Affiliation(s)
- Sarah A. Weinreis
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
| | | | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
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32
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Smirnov A, Comte C, Mager-Heckel AM, Addis V, Krasheninnikov IA, Martin RP, Entelis N, Tarassov I. Mitochondrial enzyme rhodanese is essential for 5 S ribosomal RNA import into human mitochondria. J Biol Chem 2010; 285:30792-803. [PMID: 20663881 DOI: 10.1074/jbc.m110.151183] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
5 S rRNA is an essential component of ribosomes. In eukaryotic cells, it is distinguished by particularly complex intracellular traffic, including nuclear export and re-import. The finding that in mammalian cells 5 S rRNA can eventually escape its usual circuit toward nascent ribosomes to get imported into mitochondria has made the scheme more complex, and it has raised questions about both the mechanism of 5 S rRNA mitochondrial targeting and its function inside the organelle. Previously, we showed that import of 5 S rRNA into mitochondria requires unknown cytosolic proteins. Here, one of them was identified as mitochondrial thiosulfate sulfurtransferase, rhodanese. Rhodanese in its misfolded form was found to possess a strong and specific 5 S rRNA binding activity, exploiting sites found earlier to function as signals of 5 S rRNA mitochondrial localization. The interaction with 5 S rRNA occurs cotranslationally and results in formation of a stable complex in which rhodanese is preserved in a compact enzymatically inactive conformation. Human 5 S rRNA in a branched Mg(2+)-free form, upon its interaction with misfolded rhodanese, demonstrates characteristic functional traits of Hsp40 cochaperones implicated in mitochondrial precursor protein targeting, suggesting that it may use this mechanism to ensure its own mitochondrial localization. Finally, silencing of the rhodanese gene caused not only a proportional decrease of 5 S rRNA import but also a general inhibition of mitochondrial translation, indicating the functional importance of the imported 5 S rRNA inside the organelle.
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Affiliation(s)
- Alexandre Smirnov
- Department of Molecular and Cellular Genetics, UMR 7156, CNRS-University of Strasbourg, Strasbourg 67084, France
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33
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Clark PL, Ugrinov KG. Measuring cotranslational folding of nascent polypeptide chains on ribosomes. Methods Enzymol 2009; 466:567-90. [PMID: 21609877 DOI: 10.1016/s0076-6879(09)66024-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein folding has been studied extensively in vitro, but much less is known about how folding proceeds in vivo. A particular distinction of folding in vivo is that folding begins while the nascent polypeptide chain is still undergoing synthesis by the ribosome. Studies of cotranslational protein folding are inherently much more complex than classical in vitro protein folding studies, and historically there have been few methods available to produce the quantities of pure material required for biophysical studies of the nascent chain, or assays to specifically interrogate its conformation. However, the past few years have produced dramatic methodological advances, which now place cotranslational folding studies within reach of more biochemists, enabling a detailed comparison of the earliest stages of protein folding on the ribosome to the wealth of information available for the refolding of full-length polypeptide chains in vitro.
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Affiliation(s)
- Patricia L Clark
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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34
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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.
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Affiliation(s)
- Dibyendu Samanta
- Department of Biophysics, Molecular Biology and Genetics, University College of Science, Kolkata 700009, India.
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35
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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.
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36
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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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37
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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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38
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Ribosomal acrobatics in post-transcriptional control. Biochem Soc Trans 2008; 36:677-83. [PMID: 18631139 DOI: 10.1042/bst0360677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
High-resolution structures have given an extremely detailed view of aspects of ribosomes, including some near-functional states. Here, we review the importance of cryo-electron microscopy, among other techniques, in giving an understanding of the higher dynamics of the ribosome accompanying active recruitment of mRNA to the small subunit and translocation of tRNAs. Recent data show that careful use of a variety of different techniques is necessary for a proper understanding of the basis of function in systems such as the ribosome.
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39
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Choi SI, Han KS, Kim CW, Ryu KS, Kim BH, Kim KH, Kim SI, Kang TH, Shin HC, Lim KH, Kim HK, Hyun JM, Seong BL. Protein solubility and folding enhancement by interaction with RNA. PLoS One 2008; 3:e2677. [PMID: 18628952 PMCID: PMC2444022 DOI: 10.1371/journal.pone.0002677] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2008] [Accepted: 06/17/2008] [Indexed: 11/18/2022] Open
Abstract
While basic mechanisms of several major molecular chaperones are well understood, this machinery has been known to be involved in folding of only limited number of proteins inside the cells. Here, we report a chaperone type of protein folding facilitated by interaction with RNA. When an RNA-binding module is placed at the N-terminus of aggregation-prone target proteins, this module, upon binding with RNA, further promotes the solubility of passenger proteins, potentially leading to enhancement of proper protein folding. Studies on in vitro refolding in the presence of RNA, coexpression of RNA molecules in vivo and the mutants with impaired RNA binding ability suggests that RNA can exert chaperoning effect on their bound proteins. The results suggest that RNA binding could affect the overall kinetic network of protein folding pathway in favor of productive folding over off-pathway aggregation. In addition, the RNA binding-mediated solubility enhancement is extremely robust for increasing soluble yield of passenger proteins and could be usefully implemented for high-throughput protein expression for functional and structural genomic research initiatives. The RNA-mediated chaperone type presented here would give new insights into de novo folding in vivo.
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Affiliation(s)
- Seong Il Choi
- Institute of Life Science and Biotechnology, Yonsei University, Seodaemun-Gu, Seoul, Korea
- Department of Biotechnology, College of Engineering, Yonsei University, Seoul, Korea
| | - Kyoung Sim Han
- Department of Biotechnology, College of Engineering, Yonsei University, Seoul, Korea
| | - Chul Woo Kim
- Department of Biotechnology, College of Engineering, Yonsei University, Seoul, Korea
| | - Ki-Sun Ryu
- Department of Biotechnology, College of Engineering, Yonsei University, Seoul, Korea
| | - Byung Hee Kim
- Department of Biotechnology, College of Engineering, Yonsei University, Seoul, Korea
| | - Kyun-Hwan Kim
- Department of Pharmacology, School of Medicine, and Center for Diagnostic Medicine, Institute of Biomedical Science and Technology, Konkuk University, Seoul, Korea
| | - Seo-Il Kim
- Department of Biotechnology, College of Engineering, Yonsei University, Seoul, Korea
| | - Tae Hyun Kang
- Department of Biotechnology, College of Engineering, Yonsei University, Seoul, Korea
| | - Hang-Cheol Shin
- Department of Bioinformatics and Life Science, and CAMDRC, Soongsil University, Seoul, Korea
| | - Keo-Heun Lim
- Department of Biotechnology, College of Engineering, Yonsei University, Seoul, Korea
| | - Hyo Kyung Kim
- Department of Biotechnology, College of Engineering, Yonsei University, Seoul, Korea
| | - Jeong-Min Hyun
- Department of Biotechnology, College of Engineering, Yonsei University, Seoul, Korea
| | - Baik L. Seong
- Institute of Life Science and Biotechnology, Yonsei University, Seodaemun-Gu, Seoul, Korea
- Department of Biotechnology, College of Engineering, Yonsei University, Seoul, Korea
- * E-mail:
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40
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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.
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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
- * E-mail:
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41
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Barzegar A, Yousefi R, Sharifzadeh A, Dalgalarrondo M, Chobert JM, Ganjali MR, Norouzi P, Ehsani MR, Niasari-Naslaji A, Saboury AA, Haertlé T, Moosavi-Movahedi AA. Chaperone activities of bovine and camel β-caseins: Importance of their surface hydrophobicity in protection against alcohol dehydrogenase aggregation. Int J Biol Macromol 2008; 42:392-9. [DOI: 10.1016/j.ijbiomac.2008.01.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2007] [Revised: 01/25/2008] [Accepted: 01/28/2008] [Indexed: 10/22/2022]
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42
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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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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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Contreras Martínez LM, Martínez-Veracoechea FJ, Pohkarel P, Stroock AD, Escobedo FA, DeLisa MP. Protein translocation through a tunnel induces changes in folding kinetics: a lattice model study. Biotechnol Bioeng 2006; 94:105-17. [PMID: 16528757 DOI: 10.1002/bit.20832] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Compaction of a nascent polypeptide chain inside the ribosomal exit tunnel, before it leaves the ribosome, has been proposed to accelerate the folding of newly synthesized proteins following their release from the ribosome. Thus, we used Kinetic Monte Carlo simulations of a minimalist on-lattice model to explore the effect that polypeptide translocation through a variety of channels has on protein folding kinetics. Our results demonstrate that tunnel confinement promotes faster folding of a well-designed protein relative to its folding in free space by displacing the unfolded state towards more compact structures that are closer to the transition state. Since the tunnel only forbids rarely visited, extended configurations, it has little effect on a "poorly designed" protein whose unfolded state is largely composed of low-energy, compact, misfolded configurations. The beneficial effect of the tunnel depends on its width; for example, a too-narrow tunnel enforces unfolded states with limited or no access to the transition state, while a too-wide tunnel has no effect on the unfolded state entropy. We speculate that such effects are likely to play an important role in the folding of some proteins or protein domains in the cellular environment and might dictate whether a protein folds co-translationally or post-translationally.
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Fisher MT. Molecular roles of chaperones in assisted folding and assembly of proteins. GENETIC ENGINEERING 2006; 27:191-229. [PMID: 16382878 DOI: 10.1007/0-387-25856-6_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Affiliation(s)
- Mark T Fisher
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
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Lukash TO, Turkivska HV, Negrutskii BS, El'skaya AV. Chaperone-like activity of mammalian elongation factor eEF1A: renaturation of aminoacyl-tRNA synthetases. Int J Biochem Cell Biol 2004; 36:1341-7. [PMID: 15109577 DOI: 10.1016/j.biocel.2003.11.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2002] [Revised: 11/17/2003] [Accepted: 11/17/2003] [Indexed: 11/29/2022]
Abstract
Eukaryotic translational elongation factor eEF1A is known to be responsible for the binding of codon-specific aminoacyl-tRNAs to the ribosome. In this study, we report that in addition to this canonical function, eEF1A is able to promote the renaturation of aminoacyl-tRNA synthetases (ARS) and protect them against denaturation by dilution. The full recovery of the phenylalanyl- (PheRS) and seryl-tRNA synthetase (SerRS) activities was achieved in the presence of 4 microM eEF1A, while bovine serum albumin at similar concentration had no renaturation effect. Remarkably, in vitro renaturation occurs at the molar ratio of eEF1A to ARS equivalent to that found in the cytoplasm of higher eukaryotic cells. The eEF1A.GDP and eEF1A.GTP complexes were shown to be similar in their effect on the phenylalanyl-tRNA synthetase renaturation. Thus, we conclude that the chaperone-like activity of eEF1A might be important for maintaining the enzymes activity in the protein synthesis compartments of mammalian cells.
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Affiliation(s)
- T O Lukash
- Department of Translation Mechanisms, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnogo Str., Kiev 03143, Ukraine
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Abstract
An ion channel protein begins life as a nascent peptide inside a ribosome, moves to the endoplasmic reticulum where it becomes integrated into the lipid bilayer, and ultimately forms a functional unit that conducts ions in a well-regulated fashion. Here, I discuss the nascent peptide and its tasks as it wends its way through ribosomal tunnels and exit ports, through translocons, and into the bilayer. We are just beginning to explore the sequence of these events, mechanisms of ion channel structure formation, when biogenic decisions are made, and by which participants. These decisions include when to exit the endoplasmic reticulum and with whom to associate. Such issues govern the expression of ion channels at the cell surface and thus the electrical activity of a cell.
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Affiliation(s)
- Carol Deutsch
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, 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: 18] [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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Abstract
Ribosomes have been shown to mediate refolding of proteins in vitro. In order to understand the mechanism of action, we have explored the 70S ribosome surface for hydrophobicity, one of the important aspects in chaperone-target protein interaction. We find that the 70S ribosome displays significant hydrophobicity on its surface when probed with the hydrophobic fluorophore 8-anilino-1-naphthalene sulfonate. To understand the functional significance of this hydrophobicity we investigated the ability of the ribosome to prevent aggregation of insulin B chain and alpha-lactalbumin induced by reducing the interchain and intrachain disulfide bond respectively with dithiothreitol (DTT) and photo aggregation of gamma-crystallin at 37 degrees C. The 70S ribosome offers complete protection towards light-induced aggregation of gamma-crystallin (at 1:2 (w/w) ratio of crystallin:ribosome) and DTT-induced aggregation of alpha-lactalbumin (at 1:3) and there is appreciable protection (at 1:3) against the aggregation of insulin B chain. We also investigated the role of 70S ribosome in refolding of bovine carbonic anhydrase. Ribosomes improved the folding yield in a concentration-dependent manner. These results clearly demonstrate a general chaperone-like activity of 70S ribosome and implicate its surface hydrophobicity.
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Affiliation(s)
- Ranvir Singh
- Centre for Cellular and Molecular Biology, Uppal Road, 500 007, Hyderabad, India
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