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Yang L, Lee KM, Yu CWH, Imai H, Choi AH, Banfield D, Ito K, Uchiumi T, Wong KB. The flexible N-terminal motif of uL11 unique to eukaryotic ribosomes interacts with P-complex and facilitates protein translation. Nucleic Acids Res 2022; 50:5335-5348. [PMID: 35544198 PMCID: PMC9122527 DOI: 10.1093/nar/gkac292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 04/08/2022] [Accepted: 04/13/2022] [Indexed: 11/25/2022] Open
Abstract
Eukaryotic uL11 contains a conserved MPPKFDP motif at the N-terminus that is not found in archaeal and bacterial homologs. Here, we determined the solution structure of human uL11 by NMR spectroscopy and characterized its backbone dynamics by 15N-1H relaxation experiments. We showed that these N-terminal residues are unstructured and flexible. Structural comparison with ribosome-bound uL11 suggests that the linker region between the N-terminal domain and C-terminal domain of human uL11 is intrinsically disordered and only becomes structured when bound to the ribosomes. Mutagenesis studies show that the N-terminal conserved MPPKFDP motif is involved in interacting with the P-complex and its extended protuberant domain of uL10 in vitro. Truncation of the MPPKFDP motif also reduced the poly-phenylalanine synthesis in both hybrid ribosome and yeast mutagenesis studies. In addition, G→A/P substitutions to the conserved GPLG motif of helix-1 reduced poly-phenylalanine synthesis to 9-32% in yeast ribosomes. We propose that the flexible N-terminal residues of uL11, which could extend up to ∼25 Å from the N-terminal domain of uL11, can form transient interactions with the uL10 that help to fetch and fix it into a position ready for recruiting the incoming translation factors and facilitate protein synthesis.
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Affiliation(s)
- Lei Yang
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Ka-Ming Lee
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Conny Wing-Heng Yu
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Hirotatsu Imai
- Department of Biology, Faculty of Science, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan
| | - Andrew Kwok-Ho Choi
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - David K Banfield
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Kosuke Ito
- Department of Biology, Faculty of Science, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan
| | - Toshio Uchiumi
- Department of Biology, Faculty of Science, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan
- The Institute of Science and Technology, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan
| | - Kam-Bo Wong
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
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Istiaq A, Ohta K. Ribosome-Induced Cellular Multipotency, an Emerging Avenue in Cell Fate Reversal. Cells 2021; 10:cells10092276. [PMID: 34571922 PMCID: PMC8469204 DOI: 10.3390/cells10092276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 08/25/2021] [Accepted: 08/30/2021] [Indexed: 01/23/2023] Open
Abstract
The ribosome, which is present in all three domains of life, plays a well-established, critical role in the translation process by decoding messenger RNA into protein. Ribosomal proteins, in contrast, appear to play non-translational roles in growth, differentiation, and disease. We recently discovered that ribosomes are involved in reverting cellular potency to a multipotent state. Ribosomal incorporation (the uptake of free ribosome by living cells) can direct the fate of both somatic and cancer cells into multipotency, allowing them to switch cell lineage. During this process, both types of cells experienced cell-cycle arrest and cellular stress while remaining multipotent. This review provides a molecular perspective on current insights into ribosome-induced multipotency and sheds light on how a common stress-associated mechanism may be involved. We also discuss the impact of this phenomenon on cancer cell reprogramming and its potential in cancer therapy.
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Affiliation(s)
- Arif Istiaq
- Department of Stem Cell Biology, Faculty of Arts and Science, Kyushu University, Fukuoka 819-0395, Japan;
- Department of Brain Morphogenesis, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-8555, Japan
- HIGO Program, Kumamoto University, Kumamoto 860-8555, Japan
| | - Kunimasa Ohta
- Department of Stem Cell Biology, Faculty of Arts and Science, Kyushu University, Fukuoka 819-0395, Japan;
- Correspondence: ; Tel.: +81-92-802-6014
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Gabdulkhakov A, Mitroshin I, Garber M. Structure of the ribosomal P stalk base in archaean Methanococcus jannaschii. J Struct Biol 2020; 211:107559. [PMID: 32653645 DOI: 10.1016/j.jsb.2020.107559] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/18/2020] [Accepted: 06/28/2020] [Indexed: 11/29/2022]
Abstract
Complexes of archaeal ribosomal proteins uL11 and uL10/P0 (the two-domain N-terminal fragment of uL10, uL10NTF/P0NTF) with the adjacent 74 nucleotides of 23S rRNA fragment (23SrRNA(74)) from Methanococcus jannaschii (Mja) were obtained, crystallized and their structures were studied. The comparative structural analysis of the complexes of Mja uL10NTF•23SrRNA(74) and Mja uL10NTF•uL11•23SrRNA(74) shows that the insertion of uL11 in the binary complex does not change the conformation of the 23S rRNA fragment. On the other hand, the interaction with this specific RNA fragment leads to the restructuring of uL11 compared to the structure of this protein in the free state. Besides, although analysis confirmed the mobility of uL10/P0 domain II, disproved the assumption that it may be in contact with rRNA or uL11. In addition, the Mja uL10NTF•uL11•23SrRNA(74) complex was cocrystallized with the antibiotic thiostrepton, and the structure of this complex was solved. The thiostrepton binding site in this archaeal complex was found between the 23S rRNA and the N-terminal domain (NTD) of the Mja uL11 protein, similar to its binding site in the one of bacterial ribosome complex with thiostrepton. Upon binding of thiostrepton, the NTD of uL11 shifts toward rRNA by 7 Å. Such a shift may be the cause of the inhibitory effect of the antibiotic on the recruitment of translation factors to the GTPase-activating region in archaeal ribosomes, similar to its inhibitory effect on protein synthesis in bacterial ribosomes.
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Affiliation(s)
- Azat Gabdulkhakov
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, Pushchino, Moscow Region 142290, Russian Federation.
| | - Ivan Mitroshin
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, Pushchino, Moscow Region 142290, Russian Federation
| | - Maria Garber
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, Pushchino, Moscow Region 142290, Russian Federation
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Polikanov YS, Aleksashin NA, Beckert B, Wilson DN. The Mechanisms of Action of Ribosome-Targeting Peptide Antibiotics. Front Mol Biosci 2018; 5:48. [PMID: 29868608 PMCID: PMC5960728 DOI: 10.3389/fmolb.2018.00048] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 04/23/2018] [Indexed: 12/31/2022] Open
Abstract
The ribosome is one of the major targets in the cell for clinically used antibiotics. However, the increase in multidrug resistant bacteria is rapidly reducing the effectiveness of our current arsenal of ribosome-targeting antibiotics, highlighting the need for the discovery of compounds with new scaffolds that bind to novel sites on the ribosome. One possible avenue for the development of new antimicrobial agents is by characterization and optimization of ribosome-targeting peptide antibiotics. Biochemical and structural data on ribosome-targeting peptide antibiotics illustrates the large diversity of scaffolds, binding interactions with the ribosome as well as mechanism of action to inhibit translation. The availability of high-resolution structures of ribosomes in complex with peptide antibiotics opens the way to structure-based design of these compounds as novel antimicrobial agents.
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Affiliation(s)
- Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States.,Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL, United States
| | - Nikolay A Aleksashin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, United States
| | - Bertrand Beckert
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
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Wawiórka L, Molestak E, Szajwaj M, Michalec-Wawiórka B, Boguszewska A, Borkiewicz L, Liudkovska V, Kufel J, Tchórzewski M. Functional analysis of the uL11 protein impact on translational machinery. Cell Cycle 2017; 15:1060-72. [PMID: 26939941 DOI: 10.1080/15384101.2016.1154245] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The ribosomal GTPase associated center constitutes the ribosomal area, which is the landing platform for translational GTPases and stimulates their hydrolytic activity. The ribosomal stalk represents a landmark structure in this center, and in eukaryotes is composed of uL11, uL10 and P1/P2 proteins. The modus operandi of the uL11 protein has not been exhaustively studied in vivo neither in prokaryotic nor in eukaryotic cells. Using a yeast model, we have brought functional insight into the translational apparatus deprived of uL11, filling the gap between structural and biochemical studies. We show that the uL11 is an important element in various aspects of 'ribosomal life'. uL11 is involved in 'birth' (biogenesis and initiation), by taking part in Tif6 release and contributing to ribosomal subunit-joining at the initiation step of translation. uL11 is particularly engaged in the 'active life' of the ribosome, in elongation, being responsible for the interplay with eEF1A and fidelity of translation and contributing to a lesser extent to eEF2-dependent translocation. Our results define the uL11 protein as a critical GAC element universally involved in trGTPase 'productive state' stabilization, being primarily a part of the ribosomal element allosterically contributing to the fidelity of the decoding event.
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Affiliation(s)
- Leszek Wawiórka
- a Department of Molecular Biology , Maria Curie-Skłodowska University , Lublin , Poland
| | - Eliza Molestak
- a Department of Molecular Biology , Maria Curie-Skłodowska University , Lublin , Poland
| | - Monika Szajwaj
- a Department of Molecular Biology , Maria Curie-Skłodowska University , Lublin , Poland
| | | | | | - Lidia Borkiewicz
- a Department of Molecular Biology , Maria Curie-Skłodowska University , Lublin , Poland
| | - Vladyslava Liudkovska
- b Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw , Warsaw , Poland
| | - Joanna Kufel
- b Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw , Warsaw , Poland
| | - Marek Tchórzewski
- a Department of Molecular Biology , Maria Curie-Skłodowska University , Lublin , Poland
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Tu WY, Huang YC, Liu LF, Chang LH, Tam MF. Rpl12p affects the transcription of the PHO pathway high-affinity inorganic phosphate transporters and repressible phosphatases. Yeast 2011; 28:481-93. [DOI: 10.1002/yea.1852] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 02/22/2011] [Indexed: 11/08/2022] Open
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Miller JL, Cimen H, Koc H, Koc EC. Phosphorylated proteins of the mammalian mitochondrial ribosome: implications in protein synthesis. J Proteome Res 2010; 8:4789-98. [PMID: 19702336 DOI: 10.1021/pr9004844] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mitochondria, the powerhouse of eukaryotic cells, have their own translation machinery that is solely responsible for synthesis of 13 mitochondrially encoded protein subunits of oxidative phosphorylation complexes. Phosphorylation is a well-known post-translational modification in regulation of many processes in mammalian mitochondria including oxidative phosphorylation. However, there is still very limited knowledge on phosphorylation of mitochondrial ribosomal proteins and their role(s) in ribosome function. In this study, we have identified the mitochondrial ribosomal proteins that are phosphorylated at serine, threonine or tyrosine residues. Twenty-four phosphorylated proteins were visualized by phosphorylation-specific techniques including in vitro radiolabeling, residue specific antibodies for phosphorylated residues, or ProQ phospho dye and identified by tandem mass spectrometry. Translation assays with isolated ribosomes that were phosphorylated in vitro by kinases PKA, PKCdelta, or Abl Tyr showed up to 30% inhibition due to phosphorylation. Findings from this study should serve as the framework for future studies addressing the regulation mechanisms of mitochondrial translation machinery by phosphorylation and other post-translational modifications.
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Affiliation(s)
- Jennifer L Miller
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Abstract
Protein synthesis is one of the major targets in the cell for antibiotics. This review endeavors to provide a comprehensive "post-ribosome structure" A-Z of the huge diversity of antibiotics that target the bacterial translation apparatus, with an emphasis on correlating the vast wealth of biochemical data with more recently available ribosome structures, in order to understand function. The binding site, mechanism of action, and modes of resistance for 26 different classes of protein synthesis inhibitors are presented, ranging from ABT-773 to Zyvox. In addition to improving our understanding of the process of translation, insight into the mechanism of action of antibiotics is essential to the development of novel and more effective antimicrobial agents to combat emerging bacterial resistance to many clinically-relevant drugs.
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Affiliation(s)
- Daniel N Wilson
- Gene Center and Department of Chemistry and Biochemistry, University of Munich, LMU, Munich, Germany.
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Chiou JC, Li XP, Remacha M, Ballesta JPG, Tumer NE. The ribosomal stalk is required for ribosome binding, depurination of the rRNA and cytotoxicity of ricin A chain in Saccharomyces cerevisiae. Mol Microbiol 2008; 70:1441-52. [PMID: 19019145 DOI: 10.1111/j.1365-2958.2008.06492.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ribosome inactivating proteins (RIPs) like ricin, pokeweed antiviral protein (PAP) and Shiga-like toxins 1 and 2 (Stx1 and Stx2) share the same substrate, the alpha-sarcin/ricin loop, but differ in their specificities towards prokaryotic and eukaryotic ribosomes. Ricin depurinates the eukaryotic ribosomes more efficiently than the prokaryotic ribosomes, while PAP can depurinate both types of ribosomes. Accumulating evidence suggests that different docking sites on the ribosome might be used by different RIPs, providing a basis for understanding the mechanism underlying their kingdom specificity. Our previous results demonstrated that PAP binds to the ribosomal protein L3 to depurinate the alpha-sarcin/ricin loop and binding of PAP to L3 was critical for its cytotoxicity. Here, we used surface plasmon resonance to demonstrate that ricin toxin A chain (RTA) binds to the P1 and P2 proteins of the ribosomal stalk in Saccharomyces cerevisiae. Ribosomes from the P protein mutants were depurinated less than the wild-type ribosomes when treated with RTA in vitro. Ribosome depurination was reduced when RTA was expressed in the DeltaP1 and DeltaP2 mutants in vivo and these mutants were more resistant to the cytotoxicity of RTA than the wild-type cells. We further show that while RTA, Stx1 and Stx2 have similar requirements for ribosome depurination, PAP has different requirements, providing evidence that the interaction of RIPs with different ribosomal proteins is responsible for their ribosome specificity.
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Affiliation(s)
- Jia-Chi Chiou
- Biotechnology Center for the Agriculture and the Environment, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901-8520 USA
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