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Horbowicz-Drożdżal P, Kamel K, Kmiecik S, Borkiewicz L, Tumer NE, Shaw PC, Tchórzewski M, Grela P. Phosphorylation of the conserved C-terminal domain of ribosomal P-proteins impairs the mode of interaction with plant toxins. FEBS Lett 2021; 595:2221-2236. [PMID: 34328639 DOI: 10.1002/1873-3468.14170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/14/2021] [Accepted: 07/21/2021] [Indexed: 11/12/2022]
Abstract
The ribosome is subjected to post-translational modifications, including phosphorylation, that affect its biological activity. Among ribosomal elements, the P-proteins undergo phosphorylation within the C terminus, the element which interacts with trGTPases or ribosome-inactivating proteins (RIPs); however, the role of phosphorylation has never been elucidated. Here, we probed the function of phosphorylation on the interaction of P-proteins with RIPs using the ribosomal P1-P2 dimer. We determined the kinetic parameters of the interaction with the toxins using biolayer interferometry and microscale thermophoresis. The results present the first mechanistic insight into the function of P-protein phosphorylation, showing that introduction of a negative charge into the C terminus of P1-P2 proteins promotes α-helix formation and decreases the affinity of the P-proteins for the RIPs.
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Affiliation(s)
- Patrycja Horbowicz-Drożdżal
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Karol Kamel
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Sebastian Kmiecik
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Poland
| | - Lidia Borkiewicz
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Poland
| | - Nilgun E Tumer
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Pang-Chui Shaw
- School of Life Sciences, The Chinese University of Hong Kong, China
| | - Marek Tchórzewski
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Przemysław Grela
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
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Zhang Y, Jin T. Almond allergens: update and perspective on identification and characterization. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:4657-4663. [PMID: 32270879 DOI: 10.1002/jsfa.10417] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 04/01/2020] [Accepted: 04/09/2020] [Indexed: 06/11/2023]
Abstract
Almond (Prunus dulcis) is not only widely used as a human food as a result of its flavor, nutrients, and health benefits, but it is also one of the most likely tree nuts to trigger allergies. Almond allergens, however, have not been studied as extensively as those of peanuts and other selected tree nuts. This review provides an update of the molecular properties of almond allergens to clarify some confusion about the identities of almond allergens and our perspective on characterizing putative almond allergens. At present, the following almond allergens have been designated by the World Health Organization/International Union of Immunological Societies Allergen Nomenclature Sub-Committee: Pru du 3 (a non-specific lipid transfer protein 1, nsLTP1), Pru du 4 (a profilin), Pru du 5 (60S acidic ribosomal protein 2), Pru du 6 (an 11S legumin known as prunin) and Pru du 8 (an antimicrobial protein with cC3C repeats). Besides, almond vicilin and almond γ-conglutin have been identified as food allergens, although further characterization of these allergens is still of interest. In addition, almond 2S albumin was reported as a food allergen as a result of the misidentification of Pru du 8. Two more almond proteins have been called allergens based on their sequence homology with known food allergens and their 'membership' in relevant protein families that contain allergens in many species. These include the pathogenesis related-10 protein (referred to as Pru du 1) and the thaumatin-like protein (referred to as Pru du 2). Almonds thus have five known food allergens and five more likely ones that need to be investigated further. Published 2020. This article is a U.S. Government work and is in the public domain in the USA.
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Affiliation(s)
- Yuzhu Zhang
- U.S. Department of Agriculture, Agricultural Research Service, Pacific West Area, Western Regional Research Center, Albany, CA, USA
| | - Tengchuan Jin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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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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Tcherkez G, Carroll A, Abadie C, Mainguet S, Davanture M, Zivy M. Protein synthesis increases with photosynthesis via the stimulation of translation initiation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 291:110352. [PMID: 31928674 DOI: 10.1016/j.plantsci.2019.110352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/13/2019] [Accepted: 11/21/2019] [Indexed: 05/09/2023]
Abstract
Leaf protein synthesis is an essential process at the heart of plant nitrogen (N) homeostasis and turnover that preferentially takes place in the light, that is, when N and CO2 fixation occur. The carbon allocation to protein synthesis in illuminated leaves generally accounts for ca. 1 % of net photosynthesis. It is likely that protein synthesis activity varies with photosynthetic conditions (CO2/O2 atmosphere composition) since changes in photorespiration and carbon provision should in principle impact on amino acid supply as well as metabolic regulation via leaf sugar content. However, possible changes in protein synthesis and translation activity when gaseous conditions vary are virtually unknown. Here, we address this question using metabolomics, isotopic techniques, phosphoproteomics and polysome quantitation, under different photosynthetic conditions that were varied with atmospheric CO2 and O2 mole fraction, using illuminated Arabidopsis rosettes under controlled gas exchange conditions. We show that carbon allocation to proteins is within 1-2.5 % of net photosynthesis, increases with photosynthesis rate and is unrelated to total amino acid content. In addition, photosynthesis correlates to polysome abundance and phosphorylation of ribosomal proteins and translation initiation factors. Our results demonstrate that translation activity follows photosynthetic activity, showing the considerable impact of metabolism (carboxylation-oxygenation balance) on protein synthesis.
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Affiliation(s)
- Guillaume Tcherkez
- Research School of Biology, ANU Joint College of Sciences, Australian National University, 2601, Canberra, ACT, Australia(1); Institut de Recherche en Horticulture et Semences, INRA, Université d'Angers, 42 rue Georges Morel, 49070, Beaucouzé, France(2).
| | - Adam Carroll
- Joint Mass Spectrometry Facility, Research School of Chemistry, Australian National University, 2601, Canberra, ACT, Australia
| | - Cyril Abadie
- Institut de Recherche en Horticulture et Semences, INRA, Université d'Angers, 42 rue Georges Morel, 49070, Beaucouzé, France(2)
| | - Samuel Mainguet
- Institute of Plant Sciences of Saclay, INRA, University Paris-Sud, CNRS, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Marlène Davanture
- Plateforme d'Analyse de Protéomique Paris Sud-Ouest (PAPPSO), GQE Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Ferme du Moulon, 91190, Gif-sur-Yvette, France
| | - Michel Zivy
- Plateforme d'Analyse de Protéomique Paris Sud-Ouest (PAPPSO), GQE Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Ferme du Moulon, 91190, Gif-sur-Yvette, France
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Abstract
The large ribosomal subunit has a distinct feature, the stalk, extending outside the ribosome. In bacteria it is called the L12 stalk. The base of the stalk is protein uL10 to which two or three dimers of proteins bL12 bind. In archea and eukarya P1 and P2 proteins constitute the stalk. All these extending proteins, that have a high degree of flexibility due to a hinge between their N- and C-terminal parts, are essential for proper functionalization of some of the translation factors. The role of the stalk proteins has remained enigmatic for decades but is gradually approaching an understanding. In this review we summarise the knowhow about the structure and function of the ribosomal stalk till date starting from the early phase of ribosome research.
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Multiplication of Ribosomal P-Stalk Proteins Contributes to the Fidelity of Translation. Mol Cell Biol 2017; 37:MCB.00060-17. [PMID: 28606931 DOI: 10.1128/mcb.00060-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 06/06/2017] [Indexed: 12/30/2022] Open
Abstract
The P-stalk represents a vital element within the ribosomal GTPase-associated center, which represents a landing platform for translational GTPases. The eukaryotic P-stalk exists as a uL10-(P1-P2)2 pentameric complex, which contains five identical C-terminal domains, one within each protein, and the presence of only one such element is sufficient to stimulate factor-dependent GTP hydrolysis in vitro and to sustain cell viability. The functional contribution of the P-stalk to the performance of the translational machinery in vivo, especially the role of P-protein multiplication, has never been explored. Here, we show that ribosomes depleted of P1/P2 proteins exhibit reduced translation fidelity at elongation and termination steps. The elevated rate of the decoding error is inversely correlated with the number of the P-proteins present on the ribosome. Unexpectedly, the lack of P1/P2 has little effect in vivo on the efficiency of other translational GTPase (trGTPase)-dependent steps of protein synthesis, including translocation. We have shown that loss of accuracy of decoding caused by P1/P2 depletion is the major cause of translation slowdown, which in turn affects the metabolic fitness of the yeast cell. We postulate that the multiplication of P-proteins is functionally coupled with the qualitative aspect of ribosome action, i.e., the recoding phenomenon shaping the cellular proteome.
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Human ribosomal P1-P2 heterodimer represents an optimal docking site for ricin A chain with a prominent role for P1 C-terminus. Sci Rep 2017; 7:5608. [PMID: 28717148 PMCID: PMC5514047 DOI: 10.1038/s41598-017-05675-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 06/15/2017] [Indexed: 12/26/2022] Open
Abstract
The eukaryotic P-stalk contains two P1-P2 protein dimers with a conserved C- terminal domain (CTD) critical for the interaction with external factors. To understand the role of the individual CTD of human P1/P2 proteins, we examined the interaction of reconstituted human P-protein complexes and C-terminally truncated forms with ricin A chain (RTA), which binds to the stalk to depurinate the sarcin/ricin loop (SRL). The interaction between P-protein complexes and RTA was examined by surface plasmon resonance, isothermal titration calorimetry, microscale thermophoresis and bio-layer interferometry. The P1-P2 heterodimer missing a CTD on P2 was able to bind RTA. In contrast, the P1-P2 heterodimer missing the CTD of P1 protein displayed almost no binding toward RTA. Very low interaction was detected between RTA and the non-truncated P2-P2 homodimer, suggesting that the structural architecture of the P1-P2 heterodimer is critical for binding RTA. The reconstituted pentameric human stalk complex had higher affinity for RTA than the P1-P2 dimer. Deletion of P1 CTD, but not P2 CTD reduced the affinity of the pentamer for RTA. These results highlight the importance of the heterodimeric organization of P1-P2 in the human stalk pentamer and functional non-equivalence of the individual P-protein CTDs in the interaction with RTA.
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Mosquera T, Alvarez MF, Jiménez-Gómez JM, Muktar MS, Paulo MJ, Steinemann S, Li J, Draffehn A, Hofmann A, Lübeck J, Strahwald J, Tacke E, Hofferbert HR, Walkemeier B, Gebhardt C. Targeted and Untargeted Approaches Unravel Novel Candidate Genes and Diagnostic SNPs for Quantitative Resistance of the Potato (Solanum tuberosum L.) to Phytophthora infestans Causing the Late Blight Disease. PLoS One 2016; 11:e0156254. [PMID: 27281327 PMCID: PMC4900573 DOI: 10.1371/journal.pone.0156254] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 05/08/2016] [Indexed: 11/18/2022] Open
Abstract
The oomycete Phytophthora infestans causes late blight of potato, which can completely destroy the crop. Therefore, for the past 160 years, late blight has been the most important potato disease worldwide. The identification of cultivars with high and durable field resistance to P. infestans is an objective of most potato breeding programs. This type of resistance is polygenic and therefore quantitative. Its evaluation requires multi-year and location trials. Furthermore, quantitative resistance to late blight correlates with late plant maturity, a negative agricultural trait. Knowledge of the molecular genetic basis of quantitative resistance to late blight not compromised by late maturity is very limited. It is however essential for developing diagnostic DNA markers that facilitate the efficient combination of superior resistance alleles in improved cultivars. We used association genetics in a population of 184 tetraploid potato cultivars in order to identify single nucleotide polymorphisms (SNPs) that are associated with maturity corrected resistance (MCR) to late blight. The population was genotyped for almost 9000 SNPs from three different sources. The first source was candidate genes specifically selected for their function in the jasmonate pathway. The second source was novel candidate genes selected based on comparative transcript profiling (RNA-Seq) of groups of genotypes with contrasting levels of quantitative resistance to P. infestans. The third source was the first generation 8.3k SolCAP SNP genotyping array available in potato for genome wide association studies (GWAS). Twenty seven SNPs from all three sources showed robust association with MCR. Some of those were located in genes that are strong candidates for directly controlling quantitative resistance, based on functional annotation. Most important were: a lipoxygenase (jasmonate pathway), a 3-hydroxy-3-methylglutaryl coenzyme A reductase (mevalonate pathway), a P450 protein (terpene biosynthesis), a transcription factor and a homolog of a major gene for resistance to P. infestans from the wild potato species Solanum venturii. The candidate gene approach and GWAS complemented each other as they identified different genes. The results of this study provide new insight in the molecular genetic basis of quantitative resistance in potato and a toolbox of diagnostic SNP markers for breeding applications.
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Affiliation(s)
- Teresa Mosquera
- Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
- Faculty of Agricultural Sciences, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Maria Fernanda Alvarez
- Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
- Faculty of Agricultural Sciences, Universidad Nacional de Colombia, Bogotá, Colombia
| | - José M. Jiménez-Gómez
- Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
- Institute Jean-Pierre Bourgin, INRA, AgroParis Tech, CNRS, Université Paris-Saclay, Versailles, France
| | - Meki Shehabu Muktar
- Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Sebastian Steinemann
- Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jinquan Li
- Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Astrid Draffehn
- Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Andrea Hofmann
- Department of Genomics, Life & Brain Center, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Jens Lübeck
- SaKa-Pflanzenzucht GmbH & Co. KG, 24340, Windeby, Germany
| | | | | | | | - Birgit Walkemeier
- Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Christiane Gebhardt
- Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
- * E-mail:
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Lomonosova AV, Ovchinnikova EV, Kazakov AS, Denesyuk AI, Sofin AD, Mikhailov RV, Ulitin AB, Mirzabekov TA, Permyakov EA, Permyakov SE. Extremophilic 50S Ribosomal RNA-Binding Protein L35Ae as a Basis for Engineering of an Alternative Protein Scaffold. PLoS One 2015; 10:e0134906. [PMID: 26247602 PMCID: PMC4527664 DOI: 10.1371/journal.pone.0134906] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/15/2015] [Indexed: 01/05/2023] Open
Abstract
Due to their remarkably high structural stability, proteins from extremophiles are particularly useful in numerous biological applications. Their utility as alternative protein scaffolds could be especially valuable in small antibody mimetic engineering. These artificial binding proteins occupy a specific niche between antibodies and low molecular weight substances, paving the way for development of innovative approaches in therapeutics, diagnostics, and reagent use. Here, the 50S ribosomal RNA-binding protein L35Ae from the extremophilic archaea Pyrococcus horikoshii has been probed for its potential to serve as a backbone in alternative scaffold engineering. The recombinant wild type L35Ae has a native-like secondary structure, extreme thermal stability (mid-transition temperature of 90°C) and a moderate resistance to the denaturation by guanidine hydrochloride (half-transition at 2.6 M). Chemical crosslinking and dynamic light scattering data revealed that the wild type L35Ae protein has a propensity for multimerization and aggregation correlating with its non-specific binding to a model cell surface of HEK293 cells, as evidenced by flow cytometry. To suppress these negative features, a 10-amino acid mutant (called L35Ae 10X) was designed, which lacks the interaction with HEK293 cells, is less susceptible to aggregation, and maintains native-like secondary structure and thermal stability. However, L35Ae 10X also shows lowered resistance to guanidine hydrochloride (half-transition at 2.0M) and is more prone to oligomerization. This investigation of an extremophile protein’s scaffolding potential demonstrates that lowered resistance to charged chemical denaturants and increased propensity to multimerization may limit the utility of extremophile proteins as alternative scaffolds.
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Affiliation(s)
- Anna V. Lomonosova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
| | - Elena V. Ovchinnikova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
| | - Alexei S. Kazakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
| | - Alexander I. Denesyuk
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
- Department of Biosciences, Åbo Akademi University, Turku, 20520, Finland
| | - Alexander D. Sofin
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
| | - Roman V. Mikhailov
- Antherix, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
| | - Andrei B. Ulitin
- Antherix, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
| | - Tajib A. Mirzabekov
- Antherix, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
- Biomirex Inc., 304 Pleasant Street, Watertown, Massachusetts, 02472, United States of America
| | - Eugene A. Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
| | - Sergei E. Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
- * E-mail:
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Basu D, Tumer NE. Do the A subunits contribute to the differences in the toxicity of Shiga toxin 1 and Shiga toxin 2? Toxins (Basel) 2015; 7:1467-85. [PMID: 25938272 PMCID: PMC4448158 DOI: 10.3390/toxins7051467] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/23/2015] [Accepted: 04/27/2015] [Indexed: 12/25/2022] Open
Abstract
Shiga toxin producing Escherichia coli O157:H7 (STEC) is one of the leading causes of food-poisoning around the world. Some STEC strains produce Shiga toxin 1 (Stx1) and/or Shiga toxin 2 (Stx2) or variants of either toxin, which are critical for the development of hemorrhagic colitis (HC) or hemolytic uremic syndrome (HUS). Currently, there are no therapeutic treatments for HC or HUS. E. coli O157:H7 strains carrying Stx2 are more virulent and are more frequently associated with HUS, which is the most common cause of renal failure in children in the US. The basis for the increased potency of Stx2 is not fully understood. Shiga toxins belong to the AB5 family of protein toxins with an A subunit, which depurinates a universally conserved adenine residue in the α-sarcin/ricin loop (SRL) of the 28S rRNA and five copies of the B subunit responsible for binding to cellular receptors. Recent studies showed differences in the structure, receptor binding, dependence on ribosomal proteins and pathogenicity of Stx1 and Stx2 and supported a role for the B subunit in differential toxicity. However, the current data do not rule out a potential role for the A1 subunits in the differential toxicity of Stx1 and Stx2. This review highlights the recent progress in understanding the differences in the A1 subunits of Stx1 and Stx2 and their role in defining toxicity.
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Affiliation(s)
- Debaleena Basu
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901-8520, USA.
| | - Nilgun E Tumer
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901-8520, USA.
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Wawiórka L, Krokowski D, Gordiyenko Y, Krowarsch D, Robinson CV, Adam I, Grankowski N, Tchórzewski M. In vivo formation of Plasmodium falciparum ribosomal stalk - a unique mode of assembly without stable heterodimeric intermediates. Biochim Biophys Acta Gen Subj 2014; 1850:150-8. [PMID: 25450178 DOI: 10.1016/j.bbagen.2014.10.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 09/19/2014] [Accepted: 10/15/2014] [Indexed: 11/25/2022]
Abstract
BACKGROUND The ribosomal stalk composed of P-proteins constitutes a structure on the large ribosomal particle responsible for recruitment of translation factors and stimulation of factor-dependent GTP hydrolysis during translation. The main components of the stalk are P-proteins, which form a pentamer. Despite the conserved basic function of the stalk, the P-proteins do not form a uniform entity, displaying heterogeneity in the primary structure across the eukaryotic lineage. The P-proteins from protozoan parasites are among the most evolutionarily divergent stalk proteins. METHODS We have assembled P-stalk complex of Plasmodium falciparum in vivo in bacterial system using tricistronic expression cassette and provided its characteristics by biochemical and biophysical methods. RESULTS All three individual P-proteins, namely uL10/P0, P1 and P2, are indispensable for acquisition of a stable structure of the P stalk complex and the pentameric uL10/P0-(P1-P2)₂form represents the most favorable architecture for parasite P-proteins. CONCLUSION The formation of P. falciparum P-stalk is driven by trilateral interaction between individual elements which represents unique mode of assembling, without stable P1-P2 heterodimeric intermediate. GENERAL SIGNIFICANCE On the basis of our mass-spectrometry analysis supported by the bacterial two-hybrid assay and biophysical analyses, a unique pathway of the parasite stalk assembling has been proposed. We suggest that the absence of P1/P2 heterodimer, and the formation of a stable pentamer in the presence of all three proteins, indicate a one-step formation to be the main pathway for the vital ribosomal stalk assembly, whereas the P2 homo-oligomer may represent an off-pathway product with physiologically important nonribosomal role.
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Affiliation(s)
- Leszek Wawiórka
- Department of Molecular Biology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - Dawid Krokowski
- Department of Molecular Biology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - Yuliya Gordiyenko
- Department of Chemistry, University of Oxford, South Parks Rd, Oxford OX1 3QZ, UK
| | - Daniel Krowarsch
- Department of Protein Biotechnology, Faculty of Biotechnology, University of Wroclaw, Tamka 2, 50-137 Wroclaw, Poland
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, South Parks Rd, Oxford OX1 3QZ, UK
| | - Ishag Adam
- Department of Obstetrics & Gynecology, Faculty of Medicine, AlKaser Street, University of Khartoum, Khartoum, Sudan
| | - Nikodem Grankowski
- Department of Molecular Biology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - Marek Tchórzewski
- Department of Molecular Biology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland.
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Sudarsan R, Chopra RK, Khan MA, Sharma S. Ribosomal protein P2 localizes to the parasite zoite-surface and is a target for invasion inhibitory antibodies in Toxoplasma gondii and Plasmodium falciparum. Parasitol Int 2014; 64:43-9. [PMID: 25280460 DOI: 10.1016/j.parint.2014.08.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 08/14/2014] [Accepted: 08/30/2014] [Indexed: 10/24/2022]
Abstract
In the malarial parasite Plasmodium falciparum, the conserved ribosomal stalk protein P2 (PfP2) exhibits extra-ribosomal stage-specific oligomerization and trafficking to the host red cell membrane. Antibodies directed against PfP2 arrested cell division. We sought to examine whether P2 from a closely related Apicomplexan parasite, Toxoplasma gondii, exhibits similar properties in terms of its oligomeric status as well as such unique host-cell localization. Circular dichroism spectroscopy of recombinant P2 from T. gondii (TgP2) showed a structure similar to that of PfP2, but unlike PfP2, which forms SDS- and DTT-resistant oligomers, TgP2 exhibited only a weak SDS-resistant dimerization. Also, unlike PfP2 localization to the infected erythrocyte surface, TgP2 did not localize to the host membrane in T. gondii infected human foreskin fibroblast cells. However, P2 protein was detected on the free tachyzoite surface, corroborated by localization of epitope-tagged P2 transfected in T. gondii. The presence of P2 on the surface of P. falciparum merozoites was also observed, and specific antibodies raised against the P2 protein blocked both T. gondii and P. falciparum zoite invasion of the host cells. Thus, although certain moonlighting functions of the acidic ribosomal protein P2 are different amongst P. falciparum and T. gondii, the P2 protein localizes to the surface of the invasive zoite form, and appears to constitute a potential target for host cell invasion inhibition in both the Apicomplexan infections.
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Affiliation(s)
- Rajagopal Sudarsan
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India.
| | - Reshma Korde Chopra
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Mudassar Ali Khan
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Shobhona Sharma
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
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13
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Functional divergence between the two P1-P2 stalk dimers on the ribosome in their interaction with ricin A chain. Biochem J 2014; 460:59-67. [PMID: 24576056 DOI: 10.1042/bj20140014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The eukaryotic stalk, which is responsible for the recruitment of translation factors, is a pentamer containing two P1-P2 dimers with unclear modes of action. In Saccharomyces cerevisiae, P1/P2 proteins (individual P1 and P2 proteins) are organized into two distinct dimers, P1A-P2B and P1B-P2A. To investigate the functional contribution of each dimer on the ribosome, RTA (ricin A chain), which binds to the stalk to depurinate the SRL (sarcin/ricin loop), was used as a molecular probe in yeast mutants in which the binding site for one or the other dimer on P0 was deleted. Ribosome depurination and toxicity of RTA were greatly reduced in mutants containing only P1A-P2B on the ribosome, whereas those with only P1B-P2A were reduced less in depurination and were unaffected in toxicity. Ribosomes bearing P1B-P2A were depurinated by RTA at a similar level as wild-type, but ribosomes bearing P1A-P2B were depurinated at a much lower level in vitro. The latter ribosomes showed the lowest association and almost no dissociation with RTA by surface plasmon resonance. These results indicate that the P1B-P2A dimer is more critical for facilitating the access of RTA to the SRL, providing the first in vivo evidence for functional divergence between the two stalk dimers on the ribosome.
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Lee KM, Yusa K, Chu LO, Yu CWH, Oono M, Miyoshi T, Ito K, Shaw PC, Wong KB, Uchiumi T. Solution structure of human P1•P2 heterodimer provides insights into the role of eukaryotic stalk in recruiting the ribosome-inactivating protein trichosanthin to the ribosome. Nucleic Acids Res 2013; 41:8776-87. [PMID: 23892290 PMCID: PMC3794596 DOI: 10.1093/nar/gkt636] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Lateral ribosomal stalk is responsible for binding and recruiting translation factors during protein synthesis. The eukaryotic stalk consists of one P0 protein with two copies of P1•P2 heterodimers to form a P0(P1•P2)2 pentameric P-complex. Here, we have solved the structure of full-length P1•P2 by nuclear magnetic resonance spectroscopy. P1 and P2 dimerize via their helical N-terminal domains, whereas the C-terminal tails of P1•P2 are unstructured and can extend up to ∼125 Å away from the dimerization domains. 15N relaxation study reveals that the C-terminal tails are flexible, having a much faster internal mobility than the N-terminal domains. Replacement of prokaryotic L10(L7/L12)4/L11 by eukaryotic P0(P1•P2)2/eL12 rendered Escherichia coli ribosome, which is insensitive to trichosanthin (TCS), susceptible to depurination by TCS and the C-terminal tail was found to be responsible for this depurination. Truncation and insertion studies showed that depurination of hybrid ribosome is dependent on the length of the proline-alanine rich hinge region within the C-terminal tail. All together, we propose a model that recruitment of TCS to the sarcin-ricin loop required the flexible C-terminal tail, and the proline-alanine rich hinge region lengthens this C-terminal tail, allowing the tail to sweep around the ribosome to recruit TCS.
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Affiliation(s)
- Ka-Ming Lee
- School of Life Sciences, Centre for Protein Science and Crystallography, The Chinese University of Hong Kong, Shatin, Hong Kong, China and Department of Biology, Faculty of Science, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan
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15
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Das S, Sudarsan R, Sivakami S, Sharma S. Erythrocytic stage-dependent regulation of oligomerization of Plasmodium ribosomal protein P2. J Biol Chem 2012; 287:41499-513. [PMID: 23060439 DOI: 10.1074/jbc.m112.384388] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The eukaryotic 60 S-ribosomal stalk consists of P0, P1, and P2 proteins, which associate in a pentameric structure (P1(2)-P0-P2(2)). The Plasmodium falciparum protein P2 (PfP2) appears to play nonribosomal roles. It gets exported to the infected erythrocyte (IE) surface at 30 h post-merozoite invasion (PMI), concomitant with extensive oligomerization. Here we present certain biophysical properties of PfP2. Recombinant P2 (rPfP2) protein showed SDS-resistant oligomerization, which could be significantly abolished under reducing conditions. However, the protein continued to oligomerize even when both cysteine residues were mutated, and with up to 40 amino acids (aa) deleted from the C-terminal end. CD analysis of P2 showed largely α-helical and random coil domains. The SDS- and DTT-resistant oligomerization was studied further as it occurred in a development-specific manner in Plasmodium. In a synchronized erythrocytic culture of P. falciparum, the PfP2 protein was detected as part of the ribosomal complex (∼96 kDa) at 18 and 30 h PMI, and was SDS sensitive. However, at 30 h, large amounts of SDS-sensitive aggregates of >600 kDa were also seen. At 30 h PMI, each of the parasites, IE cytosol and IE ghost contained 60-80-kDa PfP2 complexes, which resolved to a single 65-kDa species on SDS-PAGE. Tetramethylrhodamine-labeled rPfP2 protein exhibited DTT- and SDS-resistant oligomerization when treated with P. falciparum parasite extracts only from 24 to 36 h PMI, and multiple proteins appeared to be required for this oligomerization. Understanding the regulation of oligomerization of PfP2 may help in the elucidation of the novel structure-function relationship in the export of PfP2 to the red cell surface.
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Affiliation(s)
- Sudipta Das
- Department of Biological Sciences, Tata Institute of Fundamental Research, 400005 Mumbai, India
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16
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May KL, Li XP, Martínez-Azorín F, Ballesta JPG, Grela P, Tchórzewski M, Tumer NE. The P1/P2 proteins of the human ribosomal stalk are required for ribosome binding and depurination by ricin in human cells. FEBS J 2012; 279:3925-36. [PMID: 22909382 DOI: 10.1111/j.1742-4658.2012.08752.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Revised: 08/14/2012] [Accepted: 08/16/2012] [Indexed: 01/30/2023]
Abstract
Ricin A-chain (RTA) depurinates the sarcin-ricin loop of 28S ribosomal RNA and inhibits protein synthesis in mammalian cells. In yeast, the ribosomal stalk facilitates the interaction of RTA with the ribosome and subsequent depurination. Despite homology between the stalk structures from yeast and humans, there are notable differences. The human ribosomal stalk contains two identical heterodimers of P1 and P2 bound to P0, whereas the yeast stalk consists of two different heterodimers, P1α-P2β and P2α-P1β, bound to P0. RTA exhibits higher activity towards mammalian ribosomes than towards ribosomes from other organisms, suggesting that the mode of interaction with ribosomes may vary. Here, we examined whether the human ribosomal stalk proteins facilitate the interaction of RTA with human ribosomes and subsequent depurination of the sarcin-ricin loop. Using small interfering RNA-mediated knockdown of P1/P2 expression in human cells, we demonstrated that the depurination activity of RTA is lower when P1 and P2 levels are reduced. Biacore analysis showed that ribosomes from P1/P2-depleted cells have a reduced ability to bind RTA, which correlates with reduced depurination activity both in vitro and inside cells. RTA interacts directly with recombinant human P1-P2 dimer, further demonstrating the importance of human P1 and P2 in enabling RTA to bind and depurinate human ribosomes.
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Affiliation(s)
- Kerrie L May
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901, USA
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17
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Das S, Basu H, Korde R, Tewari R, Sharma S. Arrest of nuclear division in Plasmodium through blockage of erythrocyte surface exposed ribosomal protein P2. PLoS Pathog 2012; 8:e1002858. [PMID: 22912579 PMCID: PMC3415463 DOI: 10.1371/journal.ppat.1002858] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 06/27/2012] [Indexed: 12/24/2022] Open
Abstract
Malaria parasites reside inside erythrocytes and the disease manifestations are linked to the growth inside infected erythrocytes (IE). The growth of the parasite is mostly confined to the trophozoite stage during which nuclear division occurs followed by the formation of cell bodies (schizogony). The mechanism and regulation of schizogony are poorly understood. Here we show a novel role for a Plasmodium falciparum 60S stalk ribosomal acidic protein P2 (PfP2) (PFC0400w), which gets exported to the IE surface for 6-8 hrs during early schizogony, starting around 26-28 hrs post-merozoite invasion. The surface exposure is demonstrated using multiple PfP2-specific monoclonal antibodies, and is confirmed through transfection using PfP2-GFP. The IE surface-exposed PfP2-protein occurs mainly as SDS-resistant P2-homo-tetramers. Treatment with anti-PfP2 monoclonals causes arrest of IEs at the first nuclear division. Upon removal of the antibodies, about 80-85% of synchronized parasites can be released even after 24 hrs of antibody treatment. It has been reported that a tubovesicular network (TVN) is set up in early trophozoites which is used for nutrient import. Anti-P2 monoclonal antibodies cause a complete fragmentation of TVN by 36 hrs, and impairs lipid import in IEs. These may be downstream causes for the cell-cycle arrest. Upon antibody removal, the TVN is reconstituted, and the cell division progresses. Each of the above properties is observed in the rodent malaria parasite species P. yoelii and P. berghei. The translocation of the P2 protein to the IE surface is therefore likely to be of fundamental importance in Plasmodium cell division.
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Affiliation(s)
- Sudipta Das
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Himanish Basu
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Reshma Korde
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Rita Tewari
- Centre for Genetics and Genomics, Queen's Medical Centre, The University of Nottingham, Nottingham, United Kingdom
| | - Shobhona Sharma
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
- * E-mail:
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18
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NMR insights into folding and self-association of Plasmodium falciparum P2. PLoS One 2012; 7:e36279. [PMID: 22567147 PMCID: PMC3342256 DOI: 10.1371/journal.pone.0036279] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 04/04/2012] [Indexed: 11/19/2022] Open
Abstract
The eukaryotic 60S-ribosomal stalk is composed of acidic ribosomal proteins (P1 and P2) and neutral protein P0, which are thought to be associated as a pentameric structure, [2P1, 2P2, P0]. Plasmodium falciparum P2 (PfP2) appears to play additional non-ribosomal functions associated with its tendency for homo-oligomerization. Recombinant bacterially expressed PfP2 protein also undergoes self-association, as shown by SDS-PAGE analysis and light scattering studies. Secondary structure prediction algorithms predict the native PfP2 protein to be largely helical and this is corroborated by circular dichroism investigation. The 1H-15N HSQC spectrum of native P2 showed only 43 cross peaks compared to the expected 138. The observed peaks were found to belong to the C-terminal region, suggesting that this segment is flexible and solvent exposed. In 9 M urea denaturing conditions the chain exhibited mostly non-native β structural propensity. 15N Relaxation data for the denatured state indicated substantial variation in ms-µs time scale motion along the chain. Average area buried upon folding (AABUF) calculations on the monomer enabled identification of hydrophobic patches along the sequence. Interestingly, the segments of slower motion in the denatured state coincided with these hydrophobic patches, suggesting that in the denatured state the monomeric chain undergoes transient hydrophobic collapse. The implications of these results for the folding mechanism and self-association of PfP2 are discussed.
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Lee KM, Yu CWH, Chiu TYH, Sze KH, Shaw PC, Wong KB. Solution structure of the dimerization domain of the eukaryotic stalk P1/P2 complex reveals the structural organization of eukaryotic stalk complex. Nucleic Acids Res 2011; 40:3172-82. [PMID: 22135285 PMCID: PMC3326305 DOI: 10.1093/nar/gkr1143] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The lateral ribosomal stalk is responsible for the kingdom-specific binding of translation factors and activation of GTP hydrolysis during protein synthesis. The eukaryotic stalk is composed of three acidic ribosomal proteins P0, P1 and P2. P0 binds two copies of P1/P2 hetero-dimers to form a pentameric P-complex. The structure of the eukaryotic stalk is currently not known. To provide a better understanding on the structural organization of eukaryotic stalk, we have determined the solution structure of the N-terminal dimerization domain (NTD) of P1/P2 hetero-dimer. Helix-1, -2 and -4 from each of the NTD-P1 and NTD-P2 form the dimeric interface that buries 2200 A2 of solvent accessible surface area. In contrast to the symmetric P2 homo-dimer, P1/P2 hetero-dimer is asymmetric. Three conserved hydrophobic residues on the surface of NTD-P1 are replaced by charged residues in NTD-P2. Moreover, NTD-P1 has an extra turn in helix-1, which forms extensive intermolecular interactions with helix-1 and -4 of NTD-P2. Truncation of this extra turn of P1 abolished the formation of P1/P2 hetero-dimer. Systematic truncation studies suggest that P0 contains two spine-helices that each binds one copy of P1/P2 hetero-dimer. Modeling studies suggest that a large hydrophobic cavity, which can accommodate the loop between the spine-helices of P0, can be found on NTD-P1 but not on NTD-P2 when the helix-4 adopts an ‘open’ conformation. Based on the asymmetric properties of NTD-P1/NTD-P2, a structural model of the eukaryotic P-complex with P2/P1:P1/P2 topology is proposed.
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Affiliation(s)
- Ka-Ming Lee
- School of Life Sciences, Centre for Protein Science and Crystallography, The Chinese University of Hong Kong, Hong Kong, China
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20
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Chiou JC, Li XP, Remacha M, Ballesta JPG, Tumer NE. Shiga toxin 1 is more dependent on the P proteins of the ribosomal stalk for depurination activity than Shiga toxin 2. Int J Biochem Cell Biol 2011; 43:1792-801. [PMID: 21907821 DOI: 10.1016/j.biocel.2011.08.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 07/27/2011] [Accepted: 08/26/2011] [Indexed: 01/01/2023]
Abstract
Shiga toxins produced by Escherichia coli O157:H7 are responsible for food poisoning and hemolytic uremic syndrome (HUS). The A subunits of Shiga toxins (Stx1A and Stx2A) inhibit translation by depurinating a specific adenine in the large rRNA. To determine if Stx1A and Stx2A require the ribosomal stalk for depurination, their activity and cytotoxicity were examined in the yeast P protein deletion mutants. Stx1A and Stx2A were less toxic and depurinated ribosomes less in a strain lacking P1/P2 on the ribosome and in the cytosol (ΔP2) than in a strain lacking P1/P2 on the ribosome, but containing free P2 in the cytosol (ΔP1). To determine if cytoplasmic P proteins facilitated depurination, Stx1A and Stx2A were expressed in the P0ΔAB mutant, in which the binding sites for P1/P2 were deleted on the ribosome, and P1/P2 accumulated in the cytosol. Stx1A was less toxic and depurinated ribosomes less in P0ΔAB, suggesting that intact binding sites for P1/P2 were critical. In contrast, Stx2A was toxic and depurinated ribosomes in P0ΔAB as in wild type, suggesting that it did not require the P1/P2 binding sites. Depurination of ΔP1, but not P0ΔAB ribosomes increased upon addition of purified P1α/P2βin vitro, and the increase was greater for Stx1 than for Stx2. We conclude that cytoplasmic P proteins stimulate depurination by Stx1 by facilitating the access of the toxin to the ribosome. Although ribosomal stalk is important for Stx1 and Stx2 to depurinate the ribosome, Stx2 is less dependent on the stalk proteins for activity than Stx1 and can depurinate ribosomes with an incomplete stalk better than Stx1.
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Affiliation(s)
- Jia-Chi Chiou
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
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Kolaiti RM, Baier A, Szyszka R, Kouyanou-Koutsoukou S. Isolation of a CK2α subunit and the holoenzyme from the mussel Mytilus galloprovincialis and construction of the CK2α and CK2β cDNAs. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2011; 13:505-516. [PMID: 20922551 DOI: 10.1007/s10126-010-9321-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 09/07/2010] [Indexed: 05/29/2023]
Abstract
Protein kinase CK2 is a ubiquitous, highly pleiotropic, and constitutively active phosphotransferase that phosphorylates mainly serine and threonine residues. CK2 has been studied and characterized in many organisms, from yeast to mammals. The holoenzyme is generally composed of two catalytic (α and/or α') and two regulatory (β) subunits, forming a differently assembled tetramer. The free and catalytically active α/α' subunits can be present in cells under some circumstances. We present here the isolation of a putative catalytic CK2α subunit and holoenzyme from gills of the mussel Mytilus galloprovincialis capable of phosphorylating the purified recombinant ribosomal protein rMgP1. For further analysis of M. galloprovincialis protein kinase CK2, the cDNA molecules of CK2α and CK2β subunits were constructed and cloned into expression vectors, and the recombinant proteins were purified after expression in Escherichia coli. The recombinant MgCK2β subunit and MgP1 were phosphorylated by the purified recombinant MgCK2α subunit. The mussel enzyme presented features typical for CK2: affinity for GTP, inhibition by both heparin and ATP competitive inhibitors (TBBt, TBBz), and sensitivity towards NaCl. Predicted amino acid sequence comparison showed that the M. galloprovincialis MgCK2α and MgCK2β subunits have similar features to their mammalian orthologs.
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Affiliation(s)
- Regina-Maria Kolaiti
- Department of Genetics and Biotechnology, Faculty of Biology, University of Athens, Panepistimiopolis, Athens, 15701, Greece
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N(α)-Acetylation of yeast ribosomal proteins and its effect on protein synthesis. J Proteomics 2010; 74:431-41. [PMID: 21184851 DOI: 10.1016/j.jprot.2010.12.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2010] [Revised: 12/13/2010] [Accepted: 12/15/2010] [Indexed: 01/18/2023]
Abstract
N(α)-Acetyltransferases (NATs) cause the N(α)-acetylation of the majority of eukaryotic proteins during their translation, although the functions of this modification have been largely unexplored. In yeast (Saccharomyces cerevisiae), four NATs have been identified: NatA, NatB, NatC, and NatD. In this study, the N(α)-acetylation status of ribosomal protein was analyzed using NAT mutants combined with two-dimensional difference gel electrophoresis (2D-DIGE) and mass spectrometry (MS). A total of 60 ribosomal proteins were identified, of which 17 were N(α)-acetylated by NatA, and two by NatB. The N(α)-acetylation of two of these, S17 and L23, by NatA was not previously observed. Furthermore, we tested the effect of ribosomal protein N(α)-acetylation on protein synthesis using the purified ribosomes from each NAT mutant. It was found that the protein synthesis activities of ribosomes from NatA and NatB mutants were decreased by 27% and 23%, respectively, as compared to that of the normal strain. Furthermore, we have shown that ribosomal protein N(α)-acetylation by NatA influences translational fidelity in the presence of paromomycin. These results suggest that ribosomal protein N(α)-acetylation is necessary to maintain the ribosome's protein synthesis function.
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Lee KM, Yu CWH, Chan DSB, Chiu TYH, Zhu G, Sze KH, Shaw PC, Wong KB. Solution structure of the dimerization domain of ribosomal protein P2 provides insights for the structural organization of eukaryotic stalk. Nucleic Acids Res 2010; 38:5206-16. [PMID: 20385603 PMCID: PMC2926600 DOI: 10.1093/nar/gkq231] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The lateral stalk of ribosome is responsible for kingdom-specific binding of translation factors and activation of GTP hydrolysis that drives protein synthesis. In eukaryotes, the stalk is composed of acidic ribosomal proteins P0, P1 and P2 that constitute a pentameric P-complex in 1: 2: 2 ratio. We have determined the solution structure of the N-terminal dimerization domain of human P2 (NTD-P2), which provides insights into the structural organization of the eukaryotic stalk. Our structure revealed that eukaryotic stalk protein P2 forms a symmetric homodimer in solution, and is structurally distinct from the bacterial counterpart L12 homodimer. The two subunits of NTD-P2 form extensive hydrophobic interactions in the dimeric interface that buries 2400 Å2 of solvent accessible surface area. We have showed that P1 can dissociate P2 homodimer spontaneously to form a more stable P1/P2 1 : 1 heterodimer. By homology modelling, we identified three exposed polar residues on helix-3 of P2 are substituted by conserved hydrophobic residues in P1. Confirmed by mutagenesis, we showed that these residues on helix-3 of P1 are not involved in the dimerization of P1/P2, but instead play a vital role in anchoring P1/P2 heterodimer to P0. Based on our results, models of the eukaryotic stalk complex were proposed.
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Affiliation(s)
- Ka-Ming Lee
- Department of Biochemistry, Centre for Protein Science and Crystallography, The Chinese University of Hong Kong, Hong Kong, China
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Francisco-Velilla R, Remacha M. In vivo formation of a stable pentameric (P2alpha/P1beta)-P0-(P1alpha/P2beta) ribosomal stalk complex in Saccharomyces cerevisiae. Yeast 2010; 27:693-704. [PMID: 20225338 DOI: 10.1002/yea.1765] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Heterodimers of acidic proteins P1alpha/P2beta and P1beta/P2alpha bind to P0 and are fundamental for the assembly of the ribosomal stalk. However, different inconsistencies are found in the literature regarding additional P protein heterodimer formations and their individual interactions with P0. Using the two-hybrid approach, we have found results that help to clarify these interactions. Thus, we have found that neither P1 nor P2 directly interact with P0 unless the endogenous heterodimer partner is being expressed in the cell. In addition, a P2-free amino end is a requisite in these heterodimers for binding to P0. With regard to the two-hybrid interactions between P1 and P2, the known canonical P1alpha-P2beta and P1beta-P2alpha interactions do not depend on either a free amino end or the presence of endogenous P0, P1 or P2 proteins. Furthermore, the non-canonical P1beta-P2beta pair also behaves similarly, although this interaction is weaker. Interestingly, P1alpha-P2alpha, P1alpha-P1beta and P2alpha-P2beta two-hybrid interactions were also detected, although in these cases the endogenous P proteins were involved. Thus, these positive interactions are the consequence of the interaction between two canonical heterodimers. As the ribosome anchorage protein P0 is also necessary, the results suggest that, in vivo, all five P proteins form a complex, independent of the ribosome, containing the two canonical heterodimers and P0. This complex has been isolated in cells expressing a P0 protein unable to bind to the ribosome.
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Liu CC, Lu TC, Li HH, Wang HX, Liu GF, Ma L, Yang CP, Wang BC. Phosphoproteomic identification and phylogenetic analysis of ribosomal P-proteins in Populus dormant terminal buds. PLANTA 2010; 231:571-581. [PMID: 20072825 DOI: 10.1007/s00425-009-1037-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2009] [Accepted: 10/02/2009] [Indexed: 05/28/2023]
Abstract
To better understand the role that reversible phosphorylation plays in woody plant ribosomal P-protein function, we initiated a phosphoproteomic investigation of P-proteins from Populus dormant terminal buds. Using gel-free (in-solution) protein digestion and phosphopeptide enrichment combined with a nanoUPLC-ESI-MS/MS strategy, we identified six phosphorylation sites on eight P-proteins from Populus dormant terminal buds. Among these, six Ser sites and one Thr site were identified in the highly conserved C-terminal region of eight P-proteins of various P-protein subfamilies, including two P0, two P1, three P2 and one P3 protein. Among these, the Thr site was shown to be novel and has not been identified in any other organisms. Sequence analysis indicated that the phosphothreonine sites identified in the C-terminus of Ptr RPP2A exclusively occurred in woody species of Populus, etc. The identified phosphopeptides shared a common phosphorylation motif of (S/T)XX(D/E) and may be phosphorylated in vivo by casein kinase 2 as suggested by using Scansite analysis. Furthermore, phylogenetic analysis suggested that divergence of P2 also occurred in Populus, including type I and type II. To the best of our knowledge, this is the first systematic phosphoproteomic and phylogenetic analysis of P-proteins in woody plants, the results of which will provide a wealth of resources for future understanding and unraveling of the regulatory mechanisms of Populus P-protein phosphorylation during the maintenance of dormancy.
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Affiliation(s)
- Chang-Cai Liu
- Education Ministry Key Laboratory of Forest Tree Genetic Improvement and Biotechnology, Northeast Forestry University, 26 Hexing Road, 150040 Harbin, People's Republic of China
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Grela P, Krokowski D, Gordiyenko Y, Krowarsch D, Robinson CV, Otlewski J, Grankowski N, Tchórzewski M. Biophysical Properties of the Eukaryotic Ribosomal Stalk. Biochemistry 2010; 49:924-33. [DOI: 10.1021/bi901811s] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Przemysław Grela
- Department of Molecular Biology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - Dawid Krokowski
- Department of Molecular Biology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - Yuliya Gordiyenko
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB21EW, United Kingdom
| | - Daniel Krowarsch
- Laboratory of Protein Engineering, University of Wroclaw, Tamka 2, 50-137 Wroclaw, Poland
| | - Carol V. Robinson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB21EW, United Kingdom
| | - Jacek Otlewski
- Laboratory of Protein Engineering, University of Wroclaw, Tamka 2, 50-137 Wroclaw, Poland
| | - Nikodem Grankowski
- Department of Molecular Biology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - Marek Tchórzewski
- Department of Molecular Biology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
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Briceño V, Camargo H, Remacha M, Santos C, Ballesta JPG. Structural and functional characterization of the amino terminal domain of the yeast ribosomal stalk P1 and P2 proteins. Int J Biochem Cell Biol 2008; 41:1315-22. [PMID: 19084076 DOI: 10.1016/j.biocel.2008.11.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Revised: 11/07/2008] [Accepted: 11/17/2008] [Indexed: 11/17/2022]
Abstract
The essential ribosomal stalk is formed in eukaryotes by a pentamer of two P1-P2 protein heterodimers and the P0 rRNA binding protein. In contrast to the highly stable prokaryotic complex, the P1 and P2 proteins in the eukaryotic stalk undergo a cyclic process of assembly and disassembly during translation that seems to modulate the ribosome activity. To better understand this process, the regions of the Saccharomyces cerevisiae P1alpha and P2beta proteins that are directly involved in heterodimer formation and ribosome binding have been characterized using a series of P1alpha/P2beta chimeras. The region required for a stable interaction with the ribosome is formed by the first three predicted alpha-helices in the N-terminal domain of both proteins. The same region is required for heterodimer formation in P2beta but the third helix is dispensable for this association in P1alpha. It seems, therefore, that stable ribosome binding is more structurally demanding than heterodimerization. A fourth predicted alpha-helix in the N-terminal domain of P1alpha and P2beta appears not to be involved in the assembly process but rather, it contributes to the conformation of the proteins by apparently restricting the mobility of their C-terminal domain and paradoxically, by reducing their activity. In addition, the study of P1/P2 chimeras showed that the C-terminal domains of these two types of protein are functionally identical and that their protein specificity is exclusively determined by their N-terminal domains.
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Affiliation(s)
- Verónica Briceño
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid and Consejo Superior de Investigaciones Científicas, Cantoblanco, Madrid 28049, Spain
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Grela P, Bernadó P, Svergun D, Kwiatowski J, Abramczyk D, Grankowski N, Tchórzewski M. Structural Relationships Among the Ribosomal Stalk Proteins from the Three Domains of Life. J Mol Evol 2008; 67:154-67. [DOI: 10.1007/s00239-008-9132-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2007] [Revised: 05/10/2008] [Accepted: 06/09/2008] [Indexed: 11/30/2022]
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Grela P, Sawa-Makarska J, Gordiyenko Y, Robinson CV, Grankowski N, Tchorzewski M. Structural Properties of the Human Acidic Ribosomal P Proteins Forming the P1-P2 Heterocomplex. J Biochem 2007; 143:169-77. [PMID: 17984123 DOI: 10.1093/jb/mvm207] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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García-Marcos A, Morreale A, Guarinos E, Briones E, Remacha M, Ortiz AR, Ballesta JPG. In vivo assembling of bacterial ribosomal protein L11 into yeast ribosomes makes the particles sensitive to the prokaryotic specific antibiotic thiostrepton. Nucleic Acids Res 2007; 35:7109-17. [PMID: 17940088 PMCID: PMC2175356 DOI: 10.1093/nar/gkm773] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Eukaryotic ribosomal stalk protein L12 and its bacterial orthologue L11 play a central role on ribosomal conformational changes during translocation. Deletion of the two genes encoding L12 in Saccharomyces cerevisiae resulted in a very slow-growth phenotype. Gene RPL12B, but not the RPL12A, cloned in centromeric plasmids fully restored control protein level and the growth rate when expressed in a L12-deprived strain. The same strain has been transformed to express Escherichia coli protein EcL11 under the control of yeast RPL12B promoter. The bacterial protein has been found in similar amounts in washed ribosomes from the transformed yeast strain and from control E. coli cells, however, EcL11 was unable to restore the defective acidic protein stalk composition caused by the absence of ScL12 in the yeast ribosome. Protein EcL11 induced a 10% increase in L12-defective cell growth rate, although the in vitro polymerizing capacity of the EcL11-containing ribosomes is restored in a higher proportion, and, moreover, the particles became partially sensitive to the prokaryotic specific antibiotic thiostrepton. Molecular dynamic simulations using modelled complexes support the correct assembly of bacterial L11 into the yeast ribosome and confirm its direct implication of its CTD in the binding of thiostrepton to ribosomes.
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Affiliation(s)
- Alberto García-Marcos
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid and Consejo Superior de investigaciones Científicas, Cantoblanco, Madrid 28049, Spain
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31
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Krokowski D, Boguszewska A, Abramczyk D, Liljas A, Tchórzewski M, Grankowski N. Yeast ribosomal P0 protein has two separate binding sites for P1/P2 proteins. Mol Microbiol 2006; 60:386-400. [PMID: 16573688 DOI: 10.1111/j.1365-2958.2006.05117.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The ribosome has a distinct lateral protuberance called the stalk; in eukaryotes it is formed by the acidic ribosomal P-proteins which are organized as a pentameric entity described as P0-(P1-P2)(2). Bilateral interactions between P0 and P1/P2 proteins have been studied extensively, however, the region on P0 responsible for the binding of P1/P2 proteins has not been precisely defined. Here we report a study which takes the current knowledge of the P0 - P1/P2 protein interaction beyond the recently published information. Using truncated forms of P0 protein and several in vitro and in vivo approaches, we have defined the region between positions 199 and 258 as the P0 protein fragment responsible for the binding of P1/P2 proteins in the yeast Saccharomyces cerevisiae. We show two short amino acid regions of P0 protein located at positions 199-230 and 231-258, to be responsible for independent binding of two dimers, P1A-P2B and P1B-P2A respectively. In addition, two elements, the sequence spanning amino acids 199-230 and the P1A-P2B dimer were found to be essential for stalk formation, indicating that this process is dependent on a balance between the P1A-P2B dimer and the P0 protein.
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Affiliation(s)
- Dawid Krokowski
- Department of Molecular Biology, Institute of Microbiology and Biotechnology, Maria Curie-Skodowska University, Akademicka 19, 20-033 Lublin, Poland
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Hagiya A, Naganuma T, Maki Y, Ohta J, Tohkairin Y, Shimizu T, Nomura T, Hachimori A, Uchiumi T. A Mode of Assembly of P0, P1, and P2 Proteins at the GTPase-associated Center in Animal Ribosome. J Biol Chem 2005; 280:39193-9. [PMID: 16188884 DOI: 10.1074/jbc.m506050200] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ribosomal P0, P1, and P2 proteins, together with the conserved domain of 28 S rRNA, constitute a major part of the GTPase-associated center in eukaryotic ribosomes. We investigated the mode of assembly in vitro by using various truncation mutants of silkworm P0. When compared with wild type (WT)-P0, the C-terminal truncation mutants CDelta65 and CDelta81 showed markedly reduced binding ability to P1 and P2, which was offset by the addition of an rRNA fragment covering the P0.P1-P2 binding site. The mutant CDelta107 lost the P1/P2 binding activity, whereas it retained the rRNA binding. In contrast, the N-terminal truncation mutants NDelta21-NDelta92 completely lost the rRNA binding, although they retained P1/P2 binding capability, implying an essential role of the N terminus of P0 for rRNA binding. The P0 mutants NDelta6, NDelta14, and CDelta18-CDelta81, together with P1/P2 and eL12, bound to the Escherichia coli core 50 S subunits deficient in L10.L7/L12 complex and L11. Analysis of incorporation of (32)P-labeled P1/P2 into the 50 S subunits with WT-P0 and CDelta81 by sedimentation analysis indicated that WT-P0 bound two copies of P1 and P2, but CDelta81 bound only one copy each. The hybrid ribosome with CDelta81 that appears to contain one P1-P2 heterodimer retained lower but considerable activities dependent on eukaryotic elongation factors. These results suggested that two P1-P2 dimers bind to close but separate regions on the C-terminal half of P0. The results were further confirmed by binding experiments using chimeric P0 mutants in which the C-terminal 81 or 107 amino acids were replaced with the homologous sequences of the archaebacterial P0.
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Affiliation(s)
- Akiko Hagiya
- Institute of High Polymer Research, Faculty of Textile Science and Technology, Shinshu University, Ueda 386-8567, Japan
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33
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Krokowski D, Tchórzewski M, Boguszewska A, Grankowski N. Acquisition of a stable structure by yeast ribosomal P0 protein requires binding of P1A–P2B complex: In vitro formation of the stalk structure. Biochim Biophys Acta Gen Subj 2005; 1724:59-70. [PMID: 15866509 DOI: 10.1016/j.bbagen.2005.03.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2004] [Revised: 03/10/2005] [Accepted: 03/15/2005] [Indexed: 11/22/2022]
Abstract
Saccharomyces cerevisiae ribosomal stalk consists of five proteins: P0 protein, with molecular mass of 34 kDa, and four small, 11 kDa, P1A, P1B, P2A and P2B acidic proteins, which form a pentameric complex P0-(P1A-P2B)/(P1B-P2A). This structure binds to a region of 26S rRNA termed GTPase-associated domain and plays a crucial role in protein synthesis. The consecutive steps leading to the formation of the stalk structure have not been fully elucidated and the function of individual P-proteins in the assembling of the stalk and protein synthesis still remains elusive. We applied an integrated approach in order to examine all the P-proteins with respect to stalk assembly. Several in vitro methods were utilized to mimic protein self-organization in the cell. Our efforts resulted in reconstitution of the whole recombinant stalk in solution as well as on the ribosomal particle. On the basis of our analysis, it can be inferred that the P1A-P2B protein complex may be regarded as the key element in stalk formation, having structural and functional importance, whereas P1B-P2A protein complex is implicated in regulation of stalk function. The mechanism of quaternary structure formation could be described as a sequential co-folding/association reaction of an oligomeric system with P0-(P1A-P2B) protein complex as an essential element in the acquisition of a stable quaternary structure of the ribosomal stalk. On the other hand, the P1B-P2A complex is not involved in the cooperative stalk formation and our results indicate an increased rate of protein synthesis due to the latter protein pair.
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Affiliation(s)
- Dawid Krokowski
- Department of Molecular Biology, Institute of Microbiology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
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Brendel C, Rehbein M, Kreienkamp HJ, Buck F, Richter D, Kindler S. Characterization of Staufen 1 ribonucleoprotein complexes. Biochem J 2004; 384:239-46. [PMID: 15303970 PMCID: PMC1134106 DOI: 10.1042/bj20040812] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2004] [Revised: 07/21/2004] [Accepted: 08/10/2004] [Indexed: 10/26/2022]
Abstract
In Drosophila oocytes and neuroblasts, the double-stranded RNA binding protein Staufen assembles into ribonucleoprotein particles, which mediate cytoplasmic mRNA trafficking and translation. Two different mammalian orthologues also appear to reside in distinct RNA-containing particles. To date, relatively little is known about the molecular composition of Staufen-containing ribonucleoprotein complexes. Here, we have used a novel one-step affinity purification protocol to identify components of Staufen 1-containing particles. Whereas the nucleocytoplasmic RNA-binding protein nucleolin is linked to Staufen in an RNA-dependent manner, the association of protein phosphatase 1, the microtubule-dependent motor protein kinesin and several components of the large and small ribosomal subunits with Staufen ribonucleoprotein complexes is RNA-independent. Notably, all these components do not co-purify with a second RNA-binding protein, hnRNPK (heterogeneous ribonucleoprotein K), demonstrating the high specificity of the purification protocol. Furthermore, pull-down and immunoprecipitation experiments suggest a direct interaction between Staufen 1 and the ribosomal protein P0 in vitro as well as in cells. In cell fractionation and sucrose gradient assays, Staufen co-fractionates with intact ribosomes and polysomes, but not with the isolated 40 S ribosomal subunit. Taken together, these findings imply that, in the cytoplasm of mammalian cells, an association with the ribosomal P-stalk protein P0 recruits Staufen 1 into ribosome-containing ribonucleoprotein particles, which also contain kinesin, protein phosphatase 1 and nucleolin.
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Key Words
- ribonucleoprotein particle
- ribosome
- rna sorting
- rna-binding protein
- translation
- dsrbd, double-stranded rna-binding domain
- ef1α, elongation factor 1α
- (e)gfp, (enhanced) green fluorescent protein
- fmrp, fragile x mental retardation protein 1
- gkap/sapap1, guanylate kinase-associated protein/sap90/psd-95-associated protein
- gst, glutathione s-transferase
- hek, human embryonic kidney
- hnrnp(k/u), heterogeneous ribonucleoprotein k or u respectively
- ip buffer, immunoprecipitation buffer
- pp1, protein phosphatase-1
- (m)rnp, (messenger) ribonucleoprotein particle
- nfar, nuclear factor associated with double-stranded rna
- pabp, poly(a)+-binding protein
- rha, rna helicase a
- rstau, rat staufen
- sstrip, somatostatin receptor-interacting protein
- stau1, staufen 1
- stau2, staufen 2
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Affiliation(s)
- Cornelia Brendel
- Institute for Cell Biochemistry and Clinical Neurobiology, University Hospital Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Monika Rehbein
- Institute for Cell Biochemistry and Clinical Neurobiology, University Hospital Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Hans-Jürgen Kreienkamp
- Institute for Cell Biochemistry and Clinical Neurobiology, University Hospital Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Friedrich Buck
- Institute for Cell Biochemistry and Clinical Neurobiology, University Hospital Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Dietmar Richter
- Institute for Cell Biochemistry and Clinical Neurobiology, University Hospital Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Stefan Kindler
- Institute for Cell Biochemistry and Clinical Neurobiology, University Hospital Hamburg-Eppendorf, D-20246 Hamburg, Germany
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Guarinos E, Santos C, Sánchez A, Qiu DY, Remacha M, Ballesta JPG. Tag-mediated fractionation of yeast ribosome populations proves the monomeric organization of the eukaryotic ribosomal stalk structure. Mol Microbiol 2004; 50:703-12. [PMID: 14617190 DOI: 10.1046/j.1365-2958.2003.03733.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The analysis of the not well understood composition of the stalk, a key ribosomal structure, in eukaryotes having multiple 12 kDa P1/P2 acidic protein components has been approached using these proteins tagged with a histidine tail at the C-terminus. Tagged Saccharomyces cerevisiae ribosomes, which contain two P1 proteins (P1 alpha and P1 beta) and two P2 proteins (P2 alpha and P2 beta), were fractionated by affinity chromatography and their stalk composition was determined. Different yeast strains expressing one or two tagged proteins and containing either a complete or a defective stalk were used. No indication of protein dimers was found in the tested strains. The results are only compatible with a stalk structure containing a single copy of each one of the four 12 kDa proteins per ribosome. Ribosomes having an incomplete stalk are found in wild-type cells. When one of the four proteins is missing, the ribosomes do not carry the three remaining proteins simultaneously, containing only two of them distributed in pairs made of one P1 and one P2. Ribosomes can carry two, one or no acidic protein pairs. The P1 alpha/P2 beta and P1beta/P2 alpha pairs are preferentially found in the ribosome, but they are not essential either for stalk assembly or function.
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Affiliation(s)
- Esther Guarinos
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
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Abramczyk D, Tchórzewski M, Krokowski D, Boguszewska A, Grankowski N. Overexpression, purification and characterization of the acidic ribosomal P-proteins from Candida albicans. Biochim Biophys Acta Gen Subj 2004; 1672:214-23. [PMID: 15182941 DOI: 10.1016/j.bbagen.2004.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2003] [Revised: 04/13/2004] [Accepted: 04/14/2004] [Indexed: 11/28/2022]
Abstract
In all eukaryotic cells, acidic ribosomal P-proteins form a lateral protuberance on the 60S ribosomal subunit-the so-called stalk-structure that plays an important role during protein synthesis. In this work, we report for the first time a full-length cloning of four genes encoding the P-proteins from Candida albicans, their expression in Escherichia coli, purification and characterization of the recombinant proteins. Considerable amino acid sequence similarity was found between the cloned proteins and other known fungal ribosomal P-proteins. On the basis of their phylogenetic relationship and amino acid similarity to their yeast counterparts, the C. albicans P-proteins were named P1A, P1B, P2A and P2B. Using three different approaches, namely: chemical cross-linking method, gel filtration and two-hybrid system, we analyzed mutual interactions among the C. albicans P-proteins. The obtained data showed all the four P-proteins able to form homo-oligomeric complexes. However, the ones found between P1B-P2A and P1A-P2B were dominant forms among the C. albicans P-proteins. Moreover, the strength of interactions between particular proteins was different in these two complexes; the strongest interactions were observed between P1B and P2A proteins, and a significantly weaker one between P1A and P2B proteins.
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Affiliation(s)
- Dariusz Abramczyk
- Department of Molecular Biology, Maria Curie-Skłodowska University, Institute of Microbiology and Biotechnology, Akademicka Street 19, 20-033 Lublin, Poland
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Tchórzewski M, Krokowski D, Rzeski W, Issinger OG, Grankowski N. The subcellular distribution of the human ribosomal "stalk" components: P1, P2 and P0 proteins. Int J Biochem Cell Biol 2003; 35:203-11. [PMID: 12479870 DOI: 10.1016/s1357-2725(02)00133-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ribosomal "stalk" structure is a distinct lateral protuberance located on the large ribosomal subunit in prokaryotic, as well as in eukaryotic cells. In eukaryotes, this ribosomal structure is composed of the acidic ribosomal P proteins, forming two hetero-dimers (P1/P2) attached to the ribosome through the P0 protein. The "stalk" is essential for the ribosome activity, taking part in the interaction with elongation factors. In this report, we have shown that the subcellular distribution of the human P proteins does not fall into standard behavior of regular ribosomal proteins. We have used two approaches to assess the distribution of the P proteins, in vivo experiments with GFP fusion proteins and in vitro one with anti-P protein antibodies. In contrast to standard r-proteins, the P1 and P2 proteins are not actively transported into the nucleus compartment, remaining predominantly in the cytoplasm (the perinuclear compartment). The P0 protein was found in the cytoplasm, as well as in the nucleus; however, the nucleoli were excluded. This protein was scattered around the nuclei, and the distribution might reflect association with the so-called nuclear bodies. This is the first example of r-proteins that are not actively transported into the nucleus; moreover, this might imply that the "stalk" constituents are assembled onto the ribosomal particle at the very last step of ribosomal maturation, which takes part in the cell cytoplasm.
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Affiliation(s)
- Marek Tchórzewski
- Department of Molecular Biology, Institute of Microbiology and Biotechnology, Maria Curie-Sklodowska University, Akademicka Street 19, 20-033, Lublin, Poland
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Abstract
The acidic ribosomal P proteins (pI 3-4) are unique among ribosomal constituents: the only molecules on the ribosomes existing in multiple copies, they form a hetero-oligomeric complex (P1/P2)(2) recognizable as a lateral protuberance on the 60S ribosomal subunit, which is thought to be directly involved in interactions with elongation factors during the course of protein synthesis. The role of P proteins in translation is still vague; however, they might possess two functional roles-the proteins may increase performance of ribosomes and/or change ribosomal specificity toward different subset of mRNAs. Furthermore, there are also indications that P proteins might be involved in transcription and DNA repair. Also, P proteins are important antigens in autoimmune diseases, infections caused by protozoan parasites, and in molds.
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Affiliation(s)
- Marek Tchórzewski
- Department of Molecular Biology, Institute of Microbiology and Biotechnology, Maria Curie-Sklodowska University, Akademicka Street 19, Lublin, Poland.
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Shimizu T, Nakagaki M, Nishi Y, Kobayashi Y, Hachimori A, Uchiumi T. Interaction among silkworm ribosomal proteins P1, P2 and P0 required for functional protein binding to the GTPase-associated domain of 28S rRNA. Nucleic Acids Res 2002; 30:2620-7. [PMID: 12060678 PMCID: PMC117291 DOI: 10.1093/nar/gkf379] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Acidic ribosomal phosphoproteins P0, P1 and P2 were isolated in soluble form from silkworm ribosomes and tested for their interactions with each other and with RNA fragments corresponding to the GTPase-associated domain of residues 1030-1127 (Escherichia coli numbering) in silkworm 28S rRNA in vitro. Mixing of P1 and P2 formed the P1-P2 heterodimer, as demonstrated by gel mobility shift and chemical crosslinking. This heterodimer, but neither P1 or P2 alone, tightly bound to P0 and formed a pentameric complex, presumably as P0(P1-P2)2, assumed from its molecular weight derived from sedimentation analysis. Complex formation strongly stimulated binding of P0 to the GTPase-associated RNA domain. The protein complex and eL12 (E.coli L11-type), which cross-bound to the E.coli equivalent RNA domain, were tested for their function by replacing with the E.coli counterparts L10.L7/L12 complex and L11 on the rRNA domain within the 50S subunits. Both P1 and P2, together with P0 and eL12, were required to activate ribosomes in polyphenylalanine synthesis dependent on eucaryotic elongation factors as well as eEF-2-dependent GTPase activity. The results suggest that formation of the P1-P2 heterodimer is required for subsequent formation of the P0(P1-P2)2 complex and its functional rRNA binding in silkworm ribosomes.
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Affiliation(s)
- Tomomi Shimizu
- Institute of High Polymer Research and Department of Applied Biological Science, Faculty of Textile Science and Technology, Shinshu University, Ueda 386-8567, Japan
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40
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Current awareness on yeast. Yeast 2001; 18:577-84. [PMID: 11284013 DOI: 10.1002/yea.684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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