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Biziaev N, Sokolova E, Yanvarev DV, Toropygin IY, Shuvalov A, Egorova T, Alkalaeva E. Recognition of 3' nucleotide context and stop codon readthrough are determined during mRNA translation elongation. J Biol Chem 2022; 298:102133. [PMID: 35700825 PMCID: PMC9272376 DOI: 10.1016/j.jbc.2022.102133] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 11/16/2022] Open
Abstract
The nucleotide context surrounding stop codons significantly affects the efficiency of translation termination. In eukaryotes, various 3′ contexts that are unfavorable for translation termination have been described; however, the exact molecular mechanism that mediates their effects remains unknown. In this study, we used a reconstituted mammalian translation system to examine the efficiency of stop codons in different contexts, including several previously described weak 3′ stop codon contexts. We developed an approach to estimate the level of stop codon readthrough in the absence of eukaryotic release factors (eRFs). In this system, the stop codon is recognized by the suppressor or near-cognate tRNAs. We observed that in the absence of eRFs, readthrough occurs in a 3′ nucleotide context-dependent manner, and the main factors determining readthrough efficiency were the type of stop codon and the sequence of the 3′ nucleotides. Moreover, the efficiency of translation termination in weak 3′ contexts was almost equal to that in the tested standard context. Therefore, the ability of eRFs to recognize stop codons and induce peptide release is not affected by mRNA context. We propose that ribosomes or other participants of the elongation cycle can independently recognize certain contexts and increase the readthrough of stop codons. Thus, the efficiency of translation termination is regulated by the 3′ nucleotide context following the stop codon and depends on the concentrations of eRFs and suppressor/near-cognate tRNAs.
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Affiliation(s)
- Nikita Biziaev
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Elizaveta Sokolova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Dmitry V Yanvarev
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Ilya Yu Toropygin
- Orekhovich Research Institute of Biomedical Chemistry, Moscow, 119992, Russia.
| | - Alexey Shuvalov
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Tatiana Egorova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, 117997, Russia.
| | - Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
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Kostryukova LV, Tereshkina YA, Korotkevich EI, Prozorovsky VN, Torkhovskaya TI, Morozevich GE, Toropygin IY, Konstantinov MA, Tikhonova EG. [Targeted drug delivery system for doxorubicin based on a specific peptide and phospholipid nanoparticles]. Biomed Khim 2020; 66:464-468. [PMID: 33372904 DOI: 10.18097/pbmc20206606464] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Doxorubicin is one of the widely known and frequently used chemotherapy drugs for the treatment of various types of cancer, the use of which is difficult due to its high cardiotoxicity. Targeted drug delivery systems are being developed to reduce side effects. One of the promising components as vector molecules (ligands) are NGR-containing peptides that are affinity for the CD13 receptor, which is expressed on the surface of many tumor cells and tumor blood vessels. Previously, a method was developed for preparing a composition of doxorubicin embedded in phospholipid nanoparticles with a targeted fragment in the form of an ultrafine emulsion. The resulting composition was characterized by a small particle size (less than 40 nm) and a high degree of incorporation of doxorubicin (about 93%) into transport nanoparticles. When assessing the penetrating ability and the degree of binding to the surface of fibrosarcoma cells (HT-1080), it was shown that when the composition with the targeted fragment was added to the cells, the level of doxorubicin was almost 2 times higher than that of the liposomal form of doxorubicin, i.e. the drug in the system with the targeted peptide penetrated the cell better. At the same time, on the control line of breast adenocarcinoma cells (MCF-7), which do not express the CD13 receptor on the surface, there was not significant difference in the level of doxorubicin in the cells. The data obtained allow us to draw preliminary conclusions about the prospects of targeted delivery of doxorubicin to tumor cells when using a peptide conjugate containing an NGR motif and the further need for its comprehensive study.
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Affiliation(s)
| | | | | | | | | | | | | | - M A Konstantinov
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Medical University, Moscow, Russia
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Andreeva AM, Vasiliev AS, Toropygin IY, Garina DV, Lamash N, Filippova A. Involvement of apolipoprotein A in maintaining tissue fluid balance in goldfish Carassius auratus. Fish Physiol Biochem 2019; 45:1717-1730. [PMID: 31227941 DOI: 10.1007/s10695-019-00662-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 05/23/2019] [Indexed: 06/09/2023]
Abstract
Mammalian plasma proteins play a key role in maintaining tissue fluid balance because they are retained within capillaries and thus create colloid osmotic pressure. Likewise, fish plasma contain a considerable concentration oligomeric proteins which likely serve a similar role. To elucidate the functions of these oligomeric proteins, we analyzed blood serum (BS) and interstitial fluid (IF) complexes in goldfish from the wild and under experimental conditions using 2D electrophoresis and matrix-assisted laser desorption/ionization (MALDI). We detected protein compounds with MWs ranging from 50 to 155 kDa, organized as oligomeric complexes. The protein compounds consisted of apolipoproteins АроА-I and Аро-14 which are homological to mammalian АроА-I and АроА-II, respectively. The 155-kDa and 50-125-kDa oligomer complexes were located very low-density lipoproteins (LDL) and high-density lipoproteins (HDL) areas on the BS/IF proteomic maps, respectively. The latter resembled mammalian HDL plasma particles by size and contained lipids, so we considered them as HDL particle populations. Investigation of the uniform dissociation/association mechanism for HDL and LDL oligomers in goldfish, from the wild and under critical salinity conditions, showed the "125/110 → 85/60 kDa" reorganization. This was associated with overcoming physiological stress during spawning and under critical salinity conditions. Opposite reorganization "85/60 → 125/110 kDa" was associated with restoration of metabolic processes after stress. The association/dissociation reorganizations promoted equilibration of BS and IF osmolarities in all fish groups. We discuss the connection of these reorganizations with total protein distribution across the capillary wall and salinity, as well as the role of oligomeric apolipoproteins as universal metabolic regulators.
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Affiliation(s)
- Alla M Andreeva
- Ecological Biochemistry Laboratory, Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, House 109, Borok, Nekouzskii Raion, Yaroslavl, Oblast, Russia, 152742.
| | - Alexey S Vasiliev
- Ecological Biochemistry Laboratory, Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, House 109, Borok, Nekouzskii Raion, Yaroslavl, Oblast, Russia, 152742
| | - Ilya Yu Toropygin
- Institute of Biomedical Chemistry, Russian Academy of Sciences, Pogodinskaya Street, House 10, Building 8, Moscow, Russia, 119121
| | - Darina V Garina
- Ecological Biochemistry Laboratory, Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, House 109, Borok, Nekouzskii Raion, Yaroslavl, Oblast, Russia, 152742
| | - Nina Lamash
- Ecological Biochemistry Laboratory, Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, House 109, Borok, Nekouzskii Raion, Yaroslavl, Oblast, Russia, 152742
- National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia, 690041
| | - Alexandra Filippova
- Ecological Biochemistry Laboratory, Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, House 109, Borok, Nekouzskii Raion, Yaroslavl, Oblast, Russia, 152742
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Shishkin SS, Kovalyov LI, Kovalyova MA, Lisitskaya KV, Eremina LS, Ivanov AV, Gerasimov EV, Sadykhov EG, Ulasova NY, Sokolova OS, Toropygin IY, Popov VO. Prostate Cancer Proteomics" Database. Acta Naturae 2010. [DOI: 10.32607/20758251-2010-2-4-95-104] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Gavryushina ES, Bryantseva SA, Nadezhdina ES, Zatsepin TS, Toropygin IY, Pickl-Herk A, Blaas D, Drygin YF. Immunolocalization of Picornavirus RNA in infected cells with antibodies to Tyr-pUp, the covalent linkage unit between VPg and RNA. J Virol Methods 2010; 171:206-11. [PMID: 21056058 DOI: 10.1016/j.jviromet.2010.10.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Revised: 10/20/2010] [Accepted: 10/27/2010] [Indexed: 12/01/2022]
Abstract
The genomic RNA of picornaviruses is attached to a small protein (VPg) via a covalent bond between a tyrosine and a 5'-terminal uridine phosphate. The same structure is present in potyvirus and calicivirus families. VPgs play a key role in initiation of viral replication by acting as primers for RNA synthesis. The model compound [N(Ac),CO(NHMe)]Tyr-(5'P→O)Up-O-(CH(2))(6)NH(2) (mCLU), mimicking this 'covalent linkage unit' (CLU) and containing Tyr-pUp was synthesized in solution following the phosphoramidite scheme and used to raise antibodies for studying picornavirus infection. The antibodies recognized CLU-containing mengovirus RNA and showed minimal cross-reactivity with RNAs lacking CLU. Immunofluorescence staining of cells infected with a human rhinovirus demonstrated co-localization of the signals from anti-mCLU and from anti-VPg antibodies. Efficient synthesis of mCLU and anti-mCLU antibodies might be of great utility for investigating viral replication and identifying yet unknown viral and cellular CLU-containing RNA-protein complexes.
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Affiliation(s)
- Elena S Gavryushina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
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Toropygin IY, Kugaevskaya EV, Mirgorodskaya OA, Elisseeva YE, Kozmin YP, Popov IA, Nikolaev EN, Makarov AA, Kozin SA. The N-domain of angiotensin-converting enzyme specifically hydrolyzes the Arg-5-His-6 bond of Alzheimer's Abeta-(1-16) peptide and its isoAsp-7 analogue with different efficiency as evidenced by quantitative matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 2008; 22:231-239. [PMID: 18085519 DOI: 10.1002/rcm.3357] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Chronic imbalance between production and degradation of the human amyloid-beta peptide (Abeta) is assumed to play an important role in pathogenesis of Alzheimer's disease (AD). Post-translational modifications of Abeta could influence its interactions with specifically cleaving proteases and, therefore, perturb the Abeta homeostasis. The angiotensin-converting enzyme (ACE) was previously shown to degrade non-modified Abeta in vitro and in cells. In the presented work, we investigated the effect of isomerization of Asp-7, a common non-enzymatic age-related modification found in AD-associated Abeta species, on hydrolysis of Abeta by ACE. Two synthetic peptides corresponding to the Abeta region 1-16 with either Asp or isoAsp residues in position 7 were examined as monomeric soluble substrates for the N- as well as for the C-domain of ACE. The use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) coupled with the (18)O-labeled internal standard approach has allowed us to show that (i) the N-domain of ACE (N-ACE), but not the C-domain, selectively cleaves the Arg-5-His-6 bond in both peptides, and that (ii) N-ACE hydrolyzes the isoAsp-7 analogue more efficiently than the non-modified one. Our results demonstrate a new endopeptidase activity of N-ACE as well as high preference of the domain to recognize and hydrolyze the isomerized Abeta species that were earlier suggested to promote AD pathogenesis. The results suggest the need for further analysis of biological effects of isomerized Abeta and its interaction with ACE in AD pathogenesis.
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Affiliation(s)
- Ilya Yu Toropygin
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, 10 Pogodinskaya str., Moscow, Russia
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