1
|
Hossain KR, Clayton D, Goodchild SC, Rodger A, Payne RJ, Cornelius F, Clarke RJ. Order-disorder transitions of cytoplasmic N-termini in the mechanisms of P-type ATPases. Faraday Discuss 2021; 232:172-187. [PMID: 34549220 DOI: 10.1039/d0fd00040j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Membrane protein structure and function are modulated via interactions with their lipid environment. This is particularly true for integral membrane pumps, the P-type ATPases. These ATPases play vital roles in cell physiology, where they are associated with the transport of cations and lipids, thereby generating and maintaining crucial (electro-)chemical potential gradients across the membrane. Several pumps (Na+, K+-ATPase, H+, K+-ATPase and the plasma membrane Ca2+-ATPase) which are located in the asymmetric animal plasma membrane have been found to possess polybasic (lysine-rich) domains on their cytoplasmic surfaces, which are thought to act as phosphatidylserine (PS) binding domains. In contrast, the sarcoplasmic reticulum Ca2+-ATPase, located within an intracellular organelle membrane, does not possess such a domain. Here we focus on the lysine-rich N-termini of the plasma-membrane-bound Na+, K+- and H+, K+-ATPases. Synthetic peptides corresponding to the N-termini of these proteins were found, via quartz crystal microbalance and circular dichroism measurements, to interact via an electrostatic interaction with PS-containing membranes, thereby undergoing an increase in helical or other secondary structure content. As well as influencing ion pumping activity, it is proposed that this interaction could provide a mechanism for sensing the lipid asymmetry of the plasma membrane, which changes drastically when a cell undergoes apoptosis, i.e. programmed cell death. Thus, polybasic regions of plasma membrane-bound ion pumps could potentially perform the function of a "death sensor", signalling to a cell to reduce pumping activity and save energy.
Collapse
Affiliation(s)
| | - Daniel Clayton
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia.
| | - Sophia C Goodchild
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Alison Rodger
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Richard J Payne
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia.
| | - Flemming Cornelius
- Department of Biomedicine, University of Aarhus, DK-8000 Aarhus C, Denmark
| | - Ronald J Clarke
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia. .,The University of Sydney Nano Institute, Sydney, NSW 2006, Australia
| |
Collapse
|
2
|
Lim J, Cheong Y, Kim YS, Chae W, Hwang BJ, Lee J, Jang YH, Roh YH, Seo SU, Seong BL. RNA-dependent assembly of chimeric antigen nanoparticles as an efficient H5N1 pre-pandemic vaccine platform. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2021; 37:102438. [PMID: 34256061 DOI: 10.1016/j.nano.2021.102438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/12/2021] [Accepted: 05/25/2021] [Indexed: 11/17/2022]
Abstract
Highly pathogenic avian influenza viruses (HPAIVs) pose a significant threat to human health, with high mortality rates, and require effective vaccines. We showed that, harnessed with novel RNA-mediated chaperone function, hemagglutinin (HA) of H5N1 HPAIV could be displayed as an immunologically relevant conformation on self-assembled chimeric nanoparticles (cNP). A tri-partite monomeric antigen was designed including: i) an RNA-interaction domain (RID) as a docking tag for RNA to enable chaperna function (chaperna: chaperone + RNA), ii) globular head domain (gd) of HA as a target antigen, and iii) ferritin as a scaffold for 24 mer-assembly. The immunization of mice with the nanoparticles (~46 nm) induced a 25-30 fold higher neutralizing capacity of the antibody and provided cross-protection from homologous and heterologous lethal challenges. This study suggests that cNP assembly is conducive to eliciting antibodies against the conserved region in HA, providing potent and broad protective efficacy.
Collapse
MESH Headings
- Animals
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/therapeutic use
- Antibodies, Viral/immunology
- Antibodies, Viral/therapeutic use
- Birds/virology
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Hemagglutinin Glycoproteins, Influenza Virus/therapeutic use
- Humans
- Influenza A Virus, H5N1 Subtype/drug effects
- Influenza A Virus, H5N1 Subtype/immunology
- Influenza A Virus, H5N1 Subtype/pathogenicity
- Influenza Vaccines/chemistry
- Influenza Vaccines/immunology
- Influenza Vaccines/therapeutic use
- Influenza in Birds/immunology
- Influenza in Birds/prevention & control
- Influenza in Birds/virology
- Mice
- Nanoparticles/chemistry
- Nanoparticles/therapeutic use
- Pandemics
- RNA/genetics
- RNA/immunology
- RNA/therapeutic use
Collapse
Affiliation(s)
- Jongkwan Lim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Yucheol Cheong
- Department of Biotechnology, College of Life Sciences and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Young-Seok Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Wonil Chae
- Department of Biotechnology, College of Life Sciences and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Beom Jeung Hwang
- Department of Biotechnology, College of Life Sciences and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Jinhee Lee
- Department of Integrated OMICS for Biomedical Science, College of Life Sciences and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Yo Han Jang
- Department of Biological Sciences and Biotechnology, College of Life Sciences and Biotechnology, Andong National University, Andong, Republic of Korea
| | - Young Hoon Roh
- Department of Biotechnology, College of Life Sciences and Biotechnology, Yonsei University, Seoul, Republic of Korea.
| | - Sang-Uk Seo
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
| | - Baik L Seong
- Department of Biotechnology, College of Life Sciences and Biotechnology, Yonsei University, Seoul, Republic of Korea; Department of Microbiology, College of Medicine, Yonsei University, Seoul, Republic of Korea; Vaccine Innovative Technology Alliance-Korea, Yonsei University, Seoul, Republic of Korea.
| |
Collapse
|
3
|
Hwang BJ, Jang Y, Kwon SB, Yu JE, Lim J, Roh YH, Seong BL. RNA-assisted self-assembly of monomeric antigens into virus-like particles as a recombinant vaccine platform. Biomaterials 2021; 269:120650. [PMID: 33465537 DOI: 10.1016/j.biomaterials.2021.120650] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 12/15/2020] [Accepted: 12/30/2020] [Indexed: 12/11/2022]
Abstract
Representing highly ordered repetitive structures of antigen macromolecular assemblies, virus-like particles (VLPs) serve as a high-priority vaccine platform against emerging viral infections, as alternatives to traditional cell culture-based vaccines. RNAs can function as chaperones (Chaperna) and are extremely effective in promoting protein folding. Beyond their canonical function as translational adaptors, tRNAs may moonlight as chaperones for the kinetic control of macromolecular antigen assembly. Capitalizing on genomic RNA co-assembly in infectious virions, we present the first report of a biomimetic assembly of viral capsids that was assisted by non-viral host RNAs into genome-free, non-infectious empty particles. Here, we demonstrate the assembly of bacterially-produced soluble norovirus VP1 forming VLPs (n = 180) in vitro. A tRNA-interacting domain (tRID) was genetically fused with the VP1 capsid protein, as a tRNA docking tag, in the bacterial host to transduce chaperna function for de novo viral antigen folding. tRID/tRNA removal prompted the in vitro assembly of monomeric antigens into highly ordered repetitive structures that elicited robust protective immune responses after immunization. The chaperna-based assembly of monomeric antigens will impact the development and deployment of VLP vaccines for emerging and re-emerging viral infections.
Collapse
Affiliation(s)
- Beom Jeung Hwang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea; Vaccine Innovative Technology Alliance-Korea, Yonsei University, Seoul, 03722, Republic of Korea
| | - Yohan Jang
- Department of Biological Sciences and Biotechnology Major in Bio-Vaccine Engineering, Andong National University, Andong, South Korea
| | - Soon Bin Kwon
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Ji Eun Yu
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Jongkwan Lim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Young Hoon Roh
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
| | - Baik L Seong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea; Vaccine Innovative Technology Alliance-Korea, Yonsei University, Seoul, 03722, Republic of Korea.
| |
Collapse
|
4
|
Liu S, Refaei M, Liu S, Decker A, Hinerman JM, Herr AB, Howell M, Musier-Forsyth K, Tsang P. Hairpin RNA-induced conformational change of a eukaryotic-specific lysyl-tRNA synthetase extension and role of adjacent anticodon-binding domain. J Biol Chem 2020; 295:12071-12085. [PMID: 32611767 PMCID: PMC7443506 DOI: 10.1074/jbc.ra120.013852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 06/26/2020] [Indexed: 11/06/2022] Open
Abstract
Human lysyl-tRNA synthetase (hLysRS) is essential for aminoacylation of tRNALys Higher eukaryotic LysRSs possess an N-terminal extension (Nterm) previously shown to facilitate high-affinity tRNA binding and aminoacylation. This eukaryote-specific appended domain also plays a critical role in hLysRS nuclear localization, thus facilitating noncanonical functions of hLysRS. The structure is intrinsically disordered and therefore remains poorly characterized. Findings of previous studies are consistent with the Nterm domain undergoing a conformational transition to an ordered structure upon nucleic acid binding. In this study, we used NMR to investigate how the type of RNA, as well as the presence of the adjacent anticodon-binding domain (ACB), influences the Nterm conformation. To explore the latter, we used sortase A ligation to produce a segmentally labeled tandem-domain protein, Nterm-ACB. In the absence of RNA, Nterm remained disordered regardless of ACB attachment. Both alone and when attached to ACB, Nterm structure remained unaffected by titration with single-stranded RNAs. The central region of the Nterm domain adopted α-helical structure upon titration of Nterm and Nterm-ACB with RNA hairpins containing double-stranded regions. Nterm binding to the RNA hairpins resulted in CD spectral shifts consistent with an induced helical structure. NMR and fluorescence anisotropy revealed that Nterm binding to hairpin RNAs is weak but that the binding affinity increases significantly upon covalent attachment to ACB. We conclude that the ACB domain facilitates induced-fit conformational changes and confers high-affinity RNA hairpin binding, which may be advantageous for functional interactions of LysRS with a variety of different binding partners.
Collapse
Affiliation(s)
- Sheng Liu
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA
| | - Maryanne Refaei
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA
| | - Shuohui Liu
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, Ohio, USA
| | - Aaron Decker
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA
| | - Jennifer M. Hinerman
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Andrew B. Herr
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Mike Howell
- Protein Express, Inc., Cincinnati, Ohio, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, Ohio, USA
| | - Pearl Tsang
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA
| |
Collapse
|
5
|
Sridhar A, Orozco M, Collepardo-Guevara R. Protein disorder-to-order transition enhances the nucleosome-binding affinity of H1. Nucleic Acids Res 2020; 48:5318-5331. [PMID: 32356891 PMCID: PMC7261198 DOI: 10.1093/nar/gkaa285] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/02/2020] [Accepted: 04/14/2020] [Indexed: 12/18/2022] Open
Abstract
Intrinsically disordered proteins are crucial elements of chromatin heterogenous organization. While disorder in the histone tails enables a large variation of inter-nucleosome arrangements, disorder within the chromatin-binding proteins facilitates promiscuous binding to a wide range of different molecular targets, consistent with structural heterogeneity. Among the partially disordered chromatin-binding proteins, the H1 linker histone influences a myriad of chromatin characteristics including compaction, nucleosome spacing, transcription regulation, and the recruitment of other chromatin regulating proteins. Although it is now established that the long C-terminal domain (CTD) of H1 remains disordered upon nucleosome binding and that such disorder favours chromatin fluidity, the structural behaviour and thereby the role/function of the N-terminal domain (NTD) within chromatin is yet unresolved. On the basis of microsecond-long parallel-tempering metadynamics and temperature-replica exchange atomistic molecular dynamics simulations of different H1 NTD subtypes, we demonstrate that the NTD is completely unstructured in solution but undergoes an important disorder-to-order transition upon nucleosome binding: it forms a helix that enhances its DNA binding ability. Further, we show that the helical propensity of the H1 NTD is subtype-dependent and correlates with the experimentally observed binding affinity of H1 subtypes, suggesting an important functional implication of this disorder-to-order transition.
Collapse
Affiliation(s)
- Akshay Sridhar
- Maxwell Centre, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - Modesto Orozco
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri i Reixac, 19, 08028 Barcelona, Spain
- Department of Biochemistry and Biomedicine, University of Barcelona, Av. Diagonal 647. 08028 Barcelona, Spain
| | - Rosana Collepardo-Guevara
- Maxwell Centre, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| |
Collapse
|
6
|
Kim YS, Lim J, Sung J, Cheong Y, Lee EY, Kim J, Oh H, Kim YS, Cho NH, Choi S, Kang SM, Nam JH, Chae W, Seong BL. Built-in RNA-mediated chaperone (chaperna) for antigen folding tailored to immunized hosts. Biotechnol Bioeng 2020; 117:1990-2007. [PMID: 32297972 PMCID: PMC7262357 DOI: 10.1002/bit.27355] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 01/25/2023]
Abstract
High‐quality antibody (Ab) production depends on the availability of immunologically relevant antigens. We present a potentially universal platform for generating soluble antigens from bacterial hosts, tailored to immunized animals for Ab production. A novel RNA‐dependent chaperone, in which the target antigen is genetically fused with an RNA‐interacting domain (RID) docking tag derived from the immunized host, promotes the solubility and robust folding of the target antigen. We selected the N‐terminal tRNA‐binding domain of lysyl‐tRNA synthetase (LysRS) as the RID for fusion with viral proteins and demonstrated the expression of the RID fusion proteins in their soluble and native conformations; immunization predominantly elicited Ab responses to the target antigen, whereas the “self” RID tag remained nonimmunogenic. Differential immunogenicity of the fusion proteins greatly enriched and simplified the screening of hybridoma clones of monoclonal antibodies (mAbs), enabling specific and sensitive serodiagnosis of MERS‐CoV infection. Moreover, mAbs against the consensus influenza hemagglutinin stalk domain enabled a novel assay for trivalent seasonal influenza vaccines. The Fc‐mediated effector function was demonstrated, which could be harnessed for the design of next‐generation “universal” influenza vaccines. The nonimmunogenic built‐in antigen folding module tailored to a repertoire of immunized animal hosts will drive immunochemical diagnostics, therapeutics, and designer vaccines.
Collapse
Affiliation(s)
- Young-Seok Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Jongkwan Lim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Jemin Sung
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Yucheol Cheong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Eun-Young Lee
- Department of Biotechnology, The Catholic University of Korea, Bucheon, Republic of Korea
| | - Jihoon Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Hana Oh
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Yeon-Sook Kim
- Division of Infectious Diseases, Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, Republic of Korea
| | - Nam-Hyuk Cho
- Department of Microbiology and Immunology, Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seongil Choi
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Sang-Moo Kang
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia
| | - Jae-Hwan Nam
- Department of Biotechnology, The Catholic University of Korea, Bucheon, Republic of Korea
| | - Wonil Chae
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Baik L Seong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| |
Collapse
|
7
|
Kwon SB, Yu JE, Park C, Lee J, Seong BL. Nucleic Acid-Dependent Structural Transition of the Intrinsically Disordered N-Terminal Appended Domain of Human Lysyl-tRNA Synthetase. Int J Mol Sci 2018; 19:ijms19103016. [PMID: 30282926 PMCID: PMC6213541 DOI: 10.3390/ijms19103016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 09/27/2018] [Accepted: 09/29/2018] [Indexed: 12/22/2022] Open
Abstract
Eukaryotic lysyl-tRNA synthetases (LysRS) have an N-terminal appended tRNA-interaction domain (RID) that is absent in their prokaryotic counterparts. This domain is intrinsically disordered and lacks stable structures. The disorder-to-order transition is induced by tRNA binding and has implications on folding and subsequent assembly into multi-tRNA synthetase complexes. Here, we expressed and purified RID from human LysRS (hRID) in Escherichia coli and performed a detailed mutagenesis of the appended domain. hRID was co-purified with nucleic acids during Ni-affinity purification, and cumulative mutations on critical amino acid residues abolished RNA binding. Furthermore, we identified a structural ensemble between disordered and helical structures in non-RNA-binding mutants and an equilibrium shift for wild-type into the helical conformation upon RNA binding. Since mutations that disrupted RNA binding led to an increase in non-functional soluble aggregates, a stabilized RNA-mediated structural transition of the N-terminal appended domain may have implications on the functional organization of human LysRS and multi-tRNA synthetase complexes in vivo.
Collapse
Affiliation(s)
- Soon Bin Kwon
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea.
| | - Ji Eun Yu
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea.
| | - Chan Park
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea.
| | - Jiseop Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea.
| | - Baik L Seong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea.
| |
Collapse
|
8
|
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.
Collapse
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
Collapse
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
| |
Collapse
|
9
|
Dias J, Octobre G, Kobbi L, Comisso M, Flisiak S, Mirande M. Activation of human mitochondrial lysyl-tRNA synthetase upon maturation of its premitochondrial precursor. Biochemistry 2012; 51:909-16. [PMID: 22235746 DOI: 10.1021/bi201337b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The cytoplasmic and mitochondrial species of human lysyl-tRNA synthetase are encoded by a single gene by means of alternative splicing of the KARS1 gene. The cytosolic enzyme possesses a eukaryote-specific N-terminal polypeptide extension that confers on the native enzyme potent tRNA binding properties required for the vectorial transfer of tRNA from the synthetase to elongation factor EF1A within the eukaryotic translation machinery. The mitochondrial enzyme matures from its precursor upon being targeted to that organelle. To understand how the cytosolic and mitochondrial enzymes are adapted to participate in two distinct translation machineries, of eukaryotic or bacterial origin, we characterized the mitochondrial LysRS species. Here we report that cleavage of the precursor of mitochondrial LysRS leads to a mature enzyme with reduced tRNA binding properties compared to those of the cytoplasmic counterpart. This adaptation mechanism may prevent inhibition of translation through sequestration of lysyl-tRNA on the synthetase in a compartment where the bacterial-like elongation factor EF-Tu could not assist in its dissociation from the synthetase. We also observed that the RxxxKRxxK tRNA-binding motif of mitochondrial LysRS is not functional in the precursor form of that enzyme and becomes operational after cleavage of the mitochondrial targeting sequence. The finding that maturation of the precursor is needed to reveal the potent tRNA binding properties of this enzyme has strong implications for the spatiotemporal regulation of its activities and is consistent with previous studies suggesting that the only LysRS species able to promote packaging of tRNA(Lys) into HIV-1 viral particles is the mature form of the mitochondrial enzyme.
Collapse
Affiliation(s)
- José Dias
- Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, Gif-sur-Yvette, France
| | | | | | | | | | | |
Collapse
|
10
|
Processivity of translation in the eukaryote cell: role of aminoacyl-tRNA synthetases. FEBS Lett 2009; 584:443-7. [PMID: 19914240 DOI: 10.1016/j.febslet.2009.11.027] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Accepted: 11/10/2009] [Indexed: 11/21/2022]
Abstract
Several lines of evidence led to the conclusion that mammalian ribosomal protein synthesis is a highly organized biological process in vivo. A wealth of data support the concept according to which tRNA aminoacylation, formation of the ternary complex on EF1A and delivery of aminoacyl-tRNA to the ribosome is a processive mechanism where tRNA is vectorially transferred from one component to another. Polypeptide extensions, referred to as tRBDs (tRNA binding domains), are appended to mammalian and yeast aminoacyl-tRNA synthetases. The involvement of these domains in the capture of deacylated tRNA and in the sequestration of aminoacylated tRNA, suggests that cycling of tRNA in translation is mediated by the processivity of the consecutive steps. The possible origin of the tRBDs is discussed.
Collapse
|
11
|
Healy S, Heightman TD, Hohmann L, Schriemer D, Gravel RA. Nonenzymatic biotinylation of histone H2A. Protein Sci 2009; 18:314-28. [PMID: 19160459 DOI: 10.1002/pro.37] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Holocarboxylase synthetase (HCS, eukaryotic enzyme) and BirA (prokaryotic) are biotin protein ligases that catalyze the ATP-dependent attachment of biotin to apocarboxylases via the reactive intermediate, bio-5'-AMP. In this study, we examined the in vitro mechanism of biotin attachment to histone H2A in the presence of HCS and BirA. The experiment derives from our observations that HCS is found in the nucleus of cells in addition to the cytoplasm, and it has the ability to attach biotin to histones in vitro (Narang et al., Hum Mol Genet 2004; 13:15-23). Using recombinant HCS or BirA, the rate of biotin attachment was considerably slower with histone H2A than with the biotin binding domain of an apocarboxylase. However, on incubation of recombinant H2A with chemically synthesized bio-5'-AMP, H2A was observed to be rapidly labeled with biotin in the absence of enzyme. Nonenzymatic biotinylation of a truncated apocarboxylase (BCCP87) has been previously reported (Streaker and Beckett, Protein Sci 2006; 15:1928-1935), though at a much slower rate than we observe for H2A. The specific attachment sites of nonenzymatically biotinylated recombinant H2A at different time points were identified using mass spectrometry, and were found to consist of a similar pattern of biotin attachment as seen in the presence of HCS, with preference for lysines in the highly basic N-terminal region of the histone. None of the lysine sites within H2A resembles the biotin attachment consensus sequence seen in carboxylases, suggesting a novel mechanism for histone biotinylation.
Collapse
Affiliation(s)
- Shannon Healy
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta, Canada.
| | | | | | | | | |
Collapse
|
12
|
Bour T, Akaddar A, Lorber B, Blais S, Balg C, Candolfi E, Frugier M. Plasmodial aspartyl-tRNA synthetases and peculiarities in Plasmodium falciparum. J Biol Chem 2009; 284:18893-903. [PMID: 19443655 DOI: 10.1074/jbc.m109.015297] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Distinctive features of aspartyl-transfer RNA (tRNA) synthetases (AspRS) from the protozoan Plasmodium genus are described. These apicomplexan AspRSs contain 29-31 amino acid insertions in their anticodon binding domains, a remarkably long N-terminal appendix that varies in size from 110 to 165 amino acids and two potential initiation codons. This article focuses on the atypical functional and structural properties of Plasmodium falciparum cytosolic AspRS, the causative parasite of human malaria. This species encodes a 626 or 577 amino acids AspRS depending on whether initiation starts on the first or second in-frame initiation codon. The longer protein has poor solubility and a propensity to aggregate. Production of the short version was favored as shown by the comparison of the recombinant protein with endogenous AspRS. Comparison of the tRNA aminoacylation activity of wild-type and mutant parasite AspRSs with those of yeast and human AspRSs revealed unique properties. The N-terminal extension contains a motif that provides unexpectedly strong RNA binding to plasmodial AspRS. Furthermore, experiments demonstrated the requirement of the plasmodial insertion for AspRS dimerization and, therefore, tRNA aminoacylation and other putative functions. Implications for the parasite biology are proposed. These data provide a robust background for unraveling the precise functional properties of the parasite AspRS and for developing novel lead compounds against malaria, targeting its idiosyncratic domains.
Collapse
Affiliation(s)
- Tania Bour
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg Cedex, France
| | | | | | | | | | | | | |
Collapse
|
13
|
Massey SE. ScanMoment: a web server for combinatorial analysis of basic residues in nucleic acid binding sites. Bioinformation 2009; 3:293-5. [PMID: 19293994 PMCID: PMC2655046 DOI: 10.6026/97320630003293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Accepted: 01/31/2009] [Indexed: 12/02/2022] Open
Abstract
UNLABELLED ScanMoment is a webserver designed to identify the presence of the basic faced alpha-helix (BFAH) motif in the nucleic acid binding sites of proteins. The program calculates the 'Basic Moment', a parameter that quantitizes the distribution of basic residues on the surface of an alpha-helix. A sliding window is used to generate a plot displaying regions of the protein sequence that possesses a high Basic Moment and hus likely to possess a BFAH motif. The user may vary the periodicity from that of an alpha-helix (100 degrees ), to those of other secondary structures such as beta sheets and 3(10) helices. The program can also plot the periodicity of basic residues in a protein sequence using a Fourier transformation. The procedure has been used to characterize the presence of BFAHs in the N-terminal extensions of the eukaryotic aminoacyl-tRNA synthetases and to indicate the presence of a BFAH in the tRNA binding site of alanyl-tRNA synthetase. AVAILABILITY www.scanmoment.org.
Collapse
Affiliation(s)
- Steven E Massey
- Department of Biology, University of Puerto Rico - Rio Piedras, PO Box 23360, San Juan, Puerto Rico 00931.
| |
Collapse
|
14
|
Frugier M, Ryckelynck M, Giegé R. tRNA-balanced expression of a eukaryal aminoacyl-tRNA synthetase by an mRNA-mediated pathway. EMBO Rep 2006; 6:860-5. [PMID: 16113655 PMCID: PMC1369159 DOI: 10.1038/sj.embor.7400481] [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] [Received: 04/22/2005] [Revised: 06/09/2005] [Accepted: 06/09/2005] [Indexed: 11/09/2022] Open
Abstract
Aminoacylation of transfer RNAs is a key step during translation. It is catalysed by the aminoacyl-tRNA synthetases (aaRSs) and requires the specific recognition of their cognate substrates, one or several tRNAs, ATP and the amino acid. Whereas the control of certain aaRS genes is well known in prokaryotes, little is known about the regulation of eukaryotic aaRS genes. Here, it is shown that expression of AspRS is regulated in yeast by a feedback mechanism that necessitates the binding of AspRS to its messenger RNA. This regulation leads to a synchronized expression of AspRS and tRNA(Asp). The correlation between AspRS expression and mRNA(AspRS) and tRNA(Asp) concentrations, as well as the presence of AspRS in the nucleus, suggests an original regulation mechanism. It is proposed that the surplus of AspRS, not sequestered by tRNA(Asp), is imported into the nucleus where it binds to mRNA(AspRS) and thus inhibits its accumulation.
Collapse
Affiliation(s)
- Magali Frugier
- Département Machineries Traductionnelles, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, 67084 Strasbourg Cedex, France.
| | | | | |
Collapse
|
15
|
Cheong HK, Park JY, Kim EH, Lee C, Kim S, Kim Y, Choi BS, Cheong C. Structure of the N-terminal extension of human aspartyl-tRNA synthetase: implications for its biological function. Int J Biochem Cell Biol 2003; 35:1548-57. [PMID: 12824064 DOI: 10.1016/s1357-2725(03)00070-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human aspartyl-tRNA synthetase (hDRS) contains an extension at the N-terminus, which is involved in the transfer of Asp-tRNA to elongation factor alpha1 (EF1alpha). The structure of the N-terminal extension is critical to its function. Conformational studies on the synthetic, 21-residue N-terminal extension peptide (Thr5-Lys25) of human aspartyl-tRNA synthetase using 1H nuclear magnetic resonance (NMR) spectroscopy, showed that the C-terminus adopts a regular alpha-helix with amphiphilicity, while the N-terminus shows a less-ordered structure with a flexible beta-turn. The observed characteristics suggest a structural switch model, such that when the tRNA is in the stretched conformation, the peptide reduces the rate of dissociation of Asp-tRNA from human aspartyl-tRNA synthetase, and provides enough time for elongation factor 1alpha to interact with the Asp-tRNA. Following Asp-tRNA transfer to EF1alpha, the peptide assumes the folded conformation. The structural switch model supports the direct transfer mechanism.
Collapse
Affiliation(s)
- Hae-Kap Cheong
- Magnetic Resonance Team, Korea Basic Science Institute, Daejeon 305-333, South Korea.
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Abstract
Dimeric class II aspartyl-tRNA synthetase (AspRS) from yeast has a modular architecture and includes an N-terminal appendix of 70 amino acid residues that protrudes from the anticodon-binding module. This extension, of predicted helical structure, is not essential for aminoacylation but contains an RNA-binding motif that promotes non-specific interactions with tRNAs. As shown here, this protein extension can also interact with the 5' end of the AspRS mRNA. In vitro, optimal binding occurs on an mRNA domain comprising part of the 87 nucleotide long 5'UTR and the sequence encoding the N-terminal appendix. At the protein side, only the appendix and the anticodon-binding module participate in the interaction between AspRS and the mRNA domain. Binding is specific, since only tRNA(Asp) can dissociate the complex. In vivo, AspRS also binds specifically this mRNA domain and in doing so triggers a reduced translation of a fused GFP mRNA. From that, a mechanism for the regulation of this eukaryotic aminoacyl-tRNA synthetase is proposed. Implications for aspartylation accuracy in yeast are given.
Collapse
Affiliation(s)
- Magali Frugier
- Département "Mécanismes et Macromolécules de la Synthèse Protéique et Cristallogenèse", UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
| | | |
Collapse
|
17
|
Yiadom KPAB, Hammamieh R, Ukpabi N, Tsang P, Yang DCH. A peptide from the extension of Lys-tRNA synthetase binds to transfer RNA and DNA. Peptides 2003; 24:987-98. [PMID: 14499277 DOI: 10.1016/s0196-9781(03)00188-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Eukaryotic aminoacyl-tRNA synthetases have dispensable extensions appended at the amino- or carboxyl-terminus as compared to their bacterial counterparts. While a synthetic peptide corresponding to the basic amino-terminal extension in yeast Asp-tRNA synthetase binds to DNA, the extension in the intact protein evidently binds to tRNA and enhances the tRNA specificity of Asp-tRNA synthetase. On the other hand, the amino-terminal extension in human Asp-tRNA synthetase, both within the intact protein and as a synthetic peptide, binds to tRNA. Here, the tRNA binding of a synthetic peptide, hKRS(Arg(25)-Glu(42)), corresponding to the amino-terminal extension of human Lys-tRNA synthetase (hKRS) was analyzed. This basic peptide bound to tRNA(Phe) and the apparent-binding constant increased with increasing concentrations of Mg(2+). The hKRS peptide also bound to DNA and polyphosphate; however, the apparent DNA-binding constants decreased at increasing concentrations of Mg(2+). The ability of the hKRS peptide to adopt alpha-helical conformation was demonstrated by NMR and circular dichroism. A Lys-rich peptide derived from the elongation factor 1alpha was also examined and bound to DNA but not to tRNA.
Collapse
MESH Headings
- Amino Acid Sequence
- Cations, Divalent/chemistry
- Circular Dichroism
- DNA/chemistry
- DNA/metabolism
- DNA-Binding Proteins/chemical synthesis
- DNA-Binding Proteins/chemistry
- DNA-Binding Proteins/metabolism
- Humans
- Hydrogen-Ion Concentration
- Lysine-tRNA Ligase/chemistry
- Magnesium Chloride/chemistry
- Magnetic Resonance Spectroscopy
- Models, Molecular
- Molecular Sequence Data
- Molecular Weight
- Peptide Elongation Factor 1/chemistry
- Peptides/chemical synthesis
- Peptides/chemistry
- Peptides/metabolism
- Polyphosphates/chemistry
- Protein Binding
- Protein Structure, Secondary
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- RNA, Transfer, Met/chemistry
- RNA, Transfer, Met/metabolism
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/metabolism
- RNA-Binding Proteins/chemical synthesis
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/metabolism
- Sodium Chloride/chemistry
- Spectrometry, Fluorescence
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Trifluoroethanol/chemistry
Collapse
|
18
|
Ryckelynck M, Giegé R, Frugier M. Yeast tRNA(Asp) charging accuracy is threatened by the N-terminal extension of aspartyl-tRNA synthetase. J Biol Chem 2003; 278:9683-90. [PMID: 12486031 DOI: 10.1074/jbc.m211035200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
This study evaluates the role of the N-terminal extension from yeast aspartyl-tRNA synthetase in tRNA aspartylation. The presence of an RNA-binding motif in this extension, conserved in eukaryotic class IIb aminoacyl-tRNA synthetases, provides nonspecific tRNA binding properties to this enzyme. Here, it is assumed that the additional contacts the 70 amino acid-long appendix of aspartyl-tRNA synthetase makes with tRNA could be important in expression of aspartate identity in yeast. Using in vitro transcripts mutated at identity positions, it is demonstrated that the extension grants better aminoacylation efficiency but reduced specificity to the synthetase, increasing considerably the risk of noncognate tRNA mischarging. Yeast tRNA(Glu(UUC)) and tRNA(Asn(GUU)) were identified as the most easily mischarged tRNA species. Both have a G at the discriminator position, and their anticodon differs only by one change from the GUC aspartate anticodon.
Collapse
Affiliation(s)
- Michaël Ryckelynck
- Département Mécanismes et Macromolécules de la Synthèse Protéique et Cristallogenèse, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
| | | | | |
Collapse
|
19
|
Francin M, Mirande M. Functional dissection of the eukaryotic-specific tRNA-interacting factor of lysyl-tRNA synthetase. J Biol Chem 2003; 278:1472-9. [PMID: 12417586 DOI: 10.1074/jbc.m208802200] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the cytoplasm of higher eukaryotic cells, aminoacyl-tRNA synthetases (aaRSs) have polypeptide chain extensions appended to conventional prokaryotic-like synthetase domains. The supplementary domains, referred to as tRNA-interacting factors (tIFs), provide the core synthetases with potent tRNA-binding capacities, a functional requirement related to the low concentration of free tRNA prevailing in the cytoplasm of eukaryotic cells. Lysyl-tRNA synthetase is a component of the multi-tRNA synthetase complex. It exhibits a lysine-rich N-terminal polypeptide extension that increases its catalytic efficiency. The functional characterization of this new type of tRNA-interacting factor has been conducted. Here we describe the systematic substitution of the 13 lysine or arginine residues located within the general RNA-binding domain of hamster LysRS made of 70 residues. Our data show that three lysine and one arginine residues are major building blocks of the tRNA-binding site. Their mutation into alanine led to a reduced affinity for tRNA(3)(Lys) or minimalized tRNA mimicking the acceptor-TPsiC stem-loop of tRNA(3)(Lys) and a decrease in catalytic efficiency similar to that observed after a complete deletion of the N-terminal domain. Moreover, covalent continuity between the tRNA-binding and core domain is a prerequisite for providing LysRS with a tRNA binding capacity. Thus, our results suggest that the ability of LysRS to promote tRNA(Lys) networking during translation or to convey tRNA(3)(Lys) into the human immunodeficiency virus type 1 viral particles rests on the addition in evolution of this tRNA-interacting factor.
Collapse
Affiliation(s)
- Mathilde Francin
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, 1 Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | | |
Collapse
|
20
|
Agou F, Ye F, Goffinont S, Courtois G, Yamaoka S, Israël A, Véron M. NEMO trimerizes through its coiled-coil C-terminal domain. J Biol Chem 2002; 277:17464-75. [PMID: 11877453 DOI: 10.1074/jbc.m201964200] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
NEMO/IkappaB kinase (IKK) gamma is the regulatory component of the IKK complex comprising the two protein kinases, IKKalpha and IKKbeta. To investigate the self-assembly properties of NEMO and to understand further the mechanism of activation of the IKK complex, we purified wild-type and mutant NEMO expressed in Escherichia coli. In the absence of its IKK partners, recombinant NEMO (rNEMO) is a metastable functional monomer correctly folded, according to its fluorescence and far-UV CD spectra, which is binding specifically to the IKK complex. A minor fraction of rNEMO was found tightly associated with DnaK (E. coli Hsp70). We also examined the interaction of NEMO with prokaryotic and eukaryotic Hsp70, and we showed that the Hsp70-NEMO complex forms a supramolecular structure probably corresponding to an assembly intermediate. In vivo cross-linking experiments indicate that native NEMO in association with IKK is in equilibrium between a dimeric and a trimeric form. Similarly to native NEMO, a NEMO mutant deleted from its IKK binding N-terminal domain (residues 242-388) forms a stable trimeric coiled-coil, suggesting that the association of NEMO with IKK or with Hsp70 prevents incorrect interdomain pairing reactions that could lead to aggregation or to an non-native oligomeric state of rNEMO. We propose a model in which the activation of the IKK complex occurs through the trimerization of NEMO upon binding to a not yet identified upstream activator.
Collapse
Affiliation(s)
- Fabrice Agou
- Unité de Régulation Enzymatique des Activités Cellulaires, Paris Cedex 15, France.
| | | | | | | | | | | | | |
Collapse
|
21
|
Hammamieh R, Yang DC. Magnesium ion-mediated binding to tRNA by an amino-terminal peptide of a class II tRNA synthetase. J Biol Chem 2001; 276:428-33. [PMID: 11035022 DOI: 10.1074/jbc.m007570200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aspartyl-tRNA synthetase is a class II tRNA synthetase and occurs in a multisynthetase complex in mammalian cells. Human Asp-tRNA synthetase contains a short 32-residue amino-terminal extension that can control the release of charged tRNA and its direct transfer to elongation factor 1 alpha; however, whether the extension binds to tRNA directly or interacts with the synthetase active site is not known. Full-length human AspRS, but not amino-terminal 32 residue-deleted, fully active AspRS, was found to bind to noncognate tRNA(fMet) in the presence of Mg(2+). Synthetic amino-terminal peptides bound similarly to tRNA(fMet), whereas little or no binding of polynucleotides, poly(dA-dT), or polyphosphate to the peptides was found. The apparent binding constants to tRNA by the peptide increased with increasing concentrations of Mg(2+), suggesting Mg(2+) mediates the binding as a new mode of RNA.peptide interactions. The binding of tRNA(fMet) to amino-terminal peptides was also observed using fluorescence-labeled tRNAs and circular dichroism. These results suggest that a small peptide can bind to tRNA selectively and that evolution of class II tRNA synthetases may involve structural changes of amino-terminal extensions for enhanced selective binding of tRNA.
Collapse
Affiliation(s)
- R Hammamieh
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA
| | | |
Collapse
|
22
|
Frugier M, Moulinier L, Giegé R. A domain in the N-terminal extension of class IIb eukaryotic aminoacyl-tRNA synthetases is important for tRNA binding. EMBO J 2000; 19:2371-80. [PMID: 10811628 PMCID: PMC384352 DOI: 10.1093/emboj/19.10.2371] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cytoplasmic aspartyl-tRNA synthetase (AspRS) from Saccharomyces cerevisiae is a homodimer of 64 kDa subunits. Previous studies have emphasized the high sensitivity of the N-terminal region to proteolytic cleavage, leading to truncated species that have lost the first 20-70 residues but that retain enzymatic activity and dimeric structure. In this work, we demonstrate that the N-terminal extension in yeast AspRS participates in tRNA binding and we generalize this finding to eukaryotic class IIb aminoacyl-tRNA synthetases. By gel retardation studies and footprinting experiments on yeast tRNA(Asp), we show that the extension, connected to the anticodon-binding module of the synthetase, contacts tRNA on the minor groove side of its anticodon stem. Sequence comparison of eukaryotic class IIb synthetases identifies a lysine-rich 11 residue sequence ((29)LSKKALKKLQK(39) in yeast AspRS with the consensus xSKxxLKKxxK in class IIb synthetases) that is important for this binding. Direct proof of the role of this sequence comes from a mutagenesis analysis and from binding studies using the isolated peptide.
Collapse
Affiliation(s)
- M Frugier
- Département 'Mécanismes et Macromolécules de la Synthèse Protéique et Cristallogenèse', UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, 67084 Strasbourg Cedex, France
| | | | | |
Collapse
|
23
|
Shiba K, Motegi H, Yoshida M, Noda T. Human asparaginyl-tRNA synthetase: molecular cloning and the inference of the evolutionary history of Asx-tRNA synthetase family. Nucleic Acids Res 1998; 26:5045-51. [PMID: 9801298 PMCID: PMC147956 DOI: 10.1093/nar/26.22.5045] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We have cloned and sequenced a cDNA encoding human cytoplasmic asparaginyl-tRNA synthetase (AsnRS). The N-terminal appended domain of 112 amino acid represents the signature sequence for the eukaryotic AsnRS and is absent from archaebacterial or eubacterial enzymes. The canonical ortholog for AsnRS is absent from most archaebacterial and some eubacterial genomes, indicating that in those organisms, formation of asparaginyl-tRNA is independent of the enzyme. The high degree of sequence conservation among asparaginyl- and aspartyl-tRNA synthetases (AsxRS) made it possible to infer the evolutionary paths of the two enzymes. The data show the neighbor relationship between AsnRS and eubacterial aspartyl-tRNA synthetase, and support the occurrence of AsnRS early in the course of evolution, which is in contrast to the proposed late occurrence of glutaminyl-tRNA synthetase.
Collapse
Affiliation(s)
- K Shiba
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, 1-37-1 Kami-Ikebukuro, Toshima, Tokyo 170-8455, Japan.
| | | | | | | |
Collapse
|
24
|
Dong A, Matsuura J, Manning MC, Carpenter JF. Intermolecular beta-sheet results from trifluoroethanol-induced nonnative alpha-helical structure in beta-sheet predominant proteins: infrared and circular dichroism spectroscopic study. Arch Biochem Biophys 1998; 355:275-81. [PMID: 9675038 DOI: 10.1006/abbi.1998.0718] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
2,2,2-Trifluoroethanol (TFE)-induced nonnative alpha-helical structure in peptides and proteins has been extensively studied with circular dichroism (CD) spectroscopy. However, to date, complementary information from infrared (IR) spectroscopy has not been reported. Using both IR and CD spectroscopy, we demonstrate here that the TFE-induced nonnative alpha-helical structure in two beta-sheet-predominant proteins, beta-lactoglobulin and alpha-chymotrypsin, is unstable in comparison with those found in the alpha-helix-predominant proteins myoglobin and cytochrome c under identical conditions. IR spectra showed that, immediately after dissolution of the beta-sheet proteins in 50% (v/v) TFE, a strong amide I band component appears at 1654 cm-1 in H2O and at 1650 cm-1 in D2O, which is ascribed to alpha-helical structure. However, the intensities of the alpha-helical bands decrease as a function of time, concomitant with the appearance of two new band components near 1620 and 1695 cm-1 in H2O and 1612 and 1684 cm-1 in D2O, a typical IR spectral pattern for an intermolecular beta-sheet aggregate. Clear gels begin to develop within 30 min. No similar spectral changes were observed for the alpha-helical proteins. CD spectra suggested initially that the TFE-induced alpha-helix was retained in the gelled state. However, further analysis of the spectra, and Gaussian function modeling with basic spectra, indicated that the apparent alpha-helix signal was actually due to a combination of signals from intermolecular beta-sheet and residual alpha-helix. These results indicate that the TFE-induced nonnative alpha-helix structure in predominantly beta-sheet proteins is unstable and readily converts to an intermolecular beta-sheet aggregate.
Collapse
Affiliation(s)
- A Dong
- Department of Chemistry and Biochemistry, University of Northern Colorado, Greeley, Colorado, 80639, USA
| | | | | | | |
Collapse
|
25
|
Weygand-Durasević I, Lenhard B, Filipić S, Söll D. The C-terminal extension of yeast seryl-tRNA synthetase affects stability of the enzyme and its substrate affinity. J Biol Chem 1996; 271:2455-61. [PMID: 8576207 DOI: 10.1074/jbc.271.5.2455] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Saccharomyces cerevisiae seryl-tRNA synthetase (SerRS) contains a 20-amino acid C-terminal extension, which is not found in prokaryotic SerRS enzymes. A truncated yeast SES1 gene, lacking the 60 base pairs that encode this C-terminal domain, is able to complement a yeast SES1 null allele strain; thus, the C-terminal extension in SerRS is dispensable for the viability of the cell. However, the removal of the C-terminal peptide affects both stability of the enzyme and its affinity for the substrates. The truncation mutant binds tRNA with 3.6-fold higher affinity, while the Km for serine is 4-fold increased relative to the wild-type SerRS. This indicates the importance of the C-terminal extension in maintaining the overall structure of SerRS.
Collapse
Affiliation(s)
- I Weygand-Durasević
- Department of Molecular Genetics, Rudjer Bosković Institute, Zagreb, Croatia
| | | | | | | |
Collapse
|
26
|
Abstract
Structure/function relationships accounting for specific tRNA charging by class II aspartyl-tRNA synthetases from Saccharomyces cerevisiae, Escherichia coli and Thermus thermophilus are reviewed. Effects directly linked to tRNA features are emphasized and aspects about synthetase contribution in expression of tRNA(Asp) identity are also covered. Major identity nucleotides conferring aspartate specificity to yeast, E coli and T thermophilus tRNAs comprise G34, U35, C36, C38 and G73, a set of nucleotides conserved in tRNA(Asp) molecules of other biological origin. Aspartate specificity can be enhanced by negative discrimination preventing, eg mischarging of native yeast tRNA(Asp by yeast arginyl-tRNA synthetase. In the yeast system crystallography shows that identity nucleotides are in contact with identity amino acids located in the catalytic and anticodon binding domains of the synthetase. Specificity of RNA/protein interaction involves a conformational change of the tRNA that optimizes the H-bonding potential of the identity signals on both partners of the complex. Mutation of identity nucleotides leads to decreased aspartylation efficiencies accompanied by a loss of specific H-bonds and an altered adaptation of tRNA on the synthetase. Species-specific characteristics of aspartate systems are the number, location and nature of minor identity signals. These features and the structural variations in aspartate tRNAs and synthetases are correlated with mechanistic differences in the aminoacylation reactions catalyzed by the various aspartyl-tRNA synthetases. The reality of the aspartate identity set is verified by its functional expression in a variety of RNA frameworks. Inversely a number of identities can be expressed within a tRNA(Asp) framework. From this emerged the concept of the RNA structural frameworks underlying expression of identities which is illustrated with data obtained with engineered tRNAs. Efficient aspartylation of minihelices is explained by the primordial role of G73. From this and other considerations it is suggested that aspartate identity appeared early in the history of tRNA aminoacylation systems.
Collapse
Affiliation(s)
- R Giegé
- Unité Structure des Macromolécules Biologioues et Mécanismes de Reconnaissance, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
| | | | | | | | | | | |
Collapse
|