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Mizgina TO, Chikalovets IV, Bulanova TA, Molchanova VI, Filshtein AP, Ziganshin RH, Rogozhin EA, Shilova NV, Chernikov OV. New l-Rhamnose-Binding Lectin from the Bivalve Glycymeris yessoensis: Purification, Partial Structural Characterization and Antibacterial Activity. Mar Drugs 2023; 22:27. [PMID: 38248652 PMCID: PMC10817417 DOI: 10.3390/md22010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 01/23/2024] Open
Abstract
In this study, a new l-rhamnose-binding lectin (GYL-R) from the hemolymph of bivalve Glycymeris yessoensis was purified using affinity and ion-exchange chromatography and functionally characterized. Lectin antimicrobial activity was examined in different ways. The lectin was inhibited by saccharides possessing the same configuration of hydroxyl groups at C-2 and C-4, such as l-rhamnose, d-galactose, lactose, l-arabinose and raffinose. Using the glycan microarray approach, natural carbohydrate ligands were established for GYL-R as l-Rha and glycans containing the α-Gal residue in the terminal position. The GYL-R molecular mass determined by MALDI-TOF mass spectrometry was 30,415 Da. The hemagglutination activity of the lectin was not affected by metal ions. The lectin was stable up to 75 °C and between pH 4.0 and 12.0. The amino acid sequence of the five GYL-R segments was obtained with nano-ESI MS/MS and contained both YGR and DPC-peptide motifs which are conserved in most of the l-rhamnose-binding lectin carbohydrate recognition domains. Circular dichroism confirmed that GYL is a α/β-protein with a predominance of the random coil. Furthermore, GYL-R was able to bind and suppress the growth of the Gram-negative bacteria E. coli by recognizing lipopolysaccharides. Together, these results suggest that GYL-R is a new member of the RBL family which participates in the self-defense mechanism against bacteria and pathogens with a distinct carbohydrate-binding specificity.
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Affiliation(s)
- Tatyana O. Mizgina
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, Vladivostok 690022, Russia; (I.V.C.); (V.I.M.); (A.P.F.)
| | - Irina V. Chikalovets
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, Vladivostok 690022, Russia; (I.V.C.); (V.I.M.); (A.P.F.)
| | - Tatyana A. Bulanova
- Department of Chemistry and Materials, Far Eastern Federal University, Vladivostok 690950, Russia;
| | - Valentina I. Molchanova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, Vladivostok 690022, Russia; (I.V.C.); (V.I.M.); (A.P.F.)
| | - Alina P. Filshtein
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, Vladivostok 690022, Russia; (I.V.C.); (V.I.M.); (A.P.F.)
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (R.H.Z.); (E.A.R.); (N.V.S.)
| | - Eugene A. Rogozhin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (R.H.Z.); (E.A.R.); (N.V.S.)
| | - Nadezhda V. Shilova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (R.H.Z.); (E.A.R.); (N.V.S.)
| | - Oleg V. Chernikov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, Vladivostok 690022, Russia; (I.V.C.); (V.I.M.); (A.P.F.)
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Pipiya SO, Kudzhaev AM, Mirzoeva NZ, Mokrushina YA, Ziganshin RH, Komlev AS, Petrova PE, Smirnov IV, Gabibov AG, Shamova OV, Terekhov SS. Bioengineering the Antimicrobial Activity of Yeast by Recombinant Thanatin Production. Antibiotics (Basel) 2023; 12:1719. [PMID: 38136753 PMCID: PMC10741026 DOI: 10.3390/antibiotics12121719] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The global spread of antibiotic resistance marks the end of the era of conventional antibiotics. Mankind desires new molecular tools to fight pathogenic bacteria. In this regard, the development of new antimicrobials based on antimicrobial peptides (AMPs) is again of particular interest. AMPs have various mechanisms of action on bacterial cells. Moreover, AMPs have been reported to be efficient in preclinical studies, demonstrating a low level of resistance formation. Thanatin is a small, beta-hairpin antimicrobial peptide with a bacterial-specific mode of action, predetermining its low cytotoxicity toward eukaryotic cells. This makes thanatin an exceptional candidate for new antibiotic development. Here, a microorganism was bioengineered to produce an antimicrobial agent, providing novel opportunities in antibiotic research through the directed creation of biocontrol agents. The constitutive heterologous production of recombinant thanatin (rThan) in the yeast Pichia pastoris endows the latter with antibacterial properties. Optimized expression and purification conditions enable a high production level, yielding up to 20 mg/L of rThan from the culture medium. rThan shows a wide spectrum of activity against pathogenic bacteria, similarly to its chemically synthesized analogue. The designed approach provides new avenues for AMP engineering and creating live biocontrol agents to fight antibiotic resistance.
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Affiliation(s)
- Sofiya O. Pipiya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
| | - Arsen M. Kudzhaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
| | - Nisso Z. Mirzoeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
| | - Yuliana A. Mokrushina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
| | - Alexey S. Komlev
- Institute of Experimental Medicine, WCRC “Center for Personalized Medicine”, Saint-Petersburg 197022, Russia; (A.S.K.); (P.E.P.); (O.V.S.)
| | - Polina E. Petrova
- Institute of Experimental Medicine, WCRC “Center for Personalized Medicine”, Saint-Petersburg 197022, Russia; (A.S.K.); (P.E.P.); (O.V.S.)
| | - Ivan V. Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
- Department of Chemistry, Lomonosov Mscow State University, Moscow 119991, Russia
| | - Alexander G. Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
- Department of Chemistry, Lomonosov Mscow State University, Moscow 119991, Russia
| | - Olga V. Shamova
- Institute of Experimental Medicine, WCRC “Center for Personalized Medicine”, Saint-Petersburg 197022, Russia; (A.S.K.); (P.E.P.); (O.V.S.)
- Department of Biochemistry, Saint Petersburg State University, Saint-Petersburg 199034, Russia
| | - Stanislav S. Terekhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
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Kravchuk OI, Finoshin AD, Mikhailov KV, Ziganshin RH, Adameyko KI, Gornostaev NG, Zhurakovskaya AI, Mikhailov VS, Shagimardanova EI, Lyupina YV. [Characteristics of δ-Aminolevulinic Acid Dehydratase of the Cold-Water Sponge Halisarca dujardinii]. Mol Biol (Mosk) 2023; 57:1085-1097. [PMID: 38062963 DOI: 10.31857/s0026898423060113, edn: qftcto] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/20/2023] [Indexed: 12/18/2023]
Abstract
δ-Aminolevulinic acid dehydratase (ALAD) is a key enzyme of the cytoplasmic heme biosynthesis pathway. The primary structure of the ALAD gene, the multimeric structure of the ALAD/hemB protein, and ALAD expression during the annual reproductive cycle were studied in the cold-water marine sponge Halisarca dujardinii. The results implicated the GATA-1 transcription factor and DNA methylation in regulating ALAD expression. Re-aggregation of sponge cells was accompanied by a decrease in ALAD expression and a change in the cell content of an active ALAD/hemB form. Further study of heme biosynthesis and the role of ALAD/hemB in morphogenesis of basal animals may provide new opportunities for treating pathologies in higher animals.
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Affiliation(s)
- O I Kravchuk
- Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - A D Finoshin
- Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - K V Mikhailov
- Belozersky Institute of Physicochemical Biology, Moscow State University, Moscow, 119992 Russia
- Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051 Russia
| | - R H Ziganshin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
| | - K I Adameyko
- Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - N G Gornostaev
- Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - A I Zhurakovskaya
- Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - V S Mikhailov
- Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - E I Shagimardanova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420012 Russia
| | - Yu V Lyupina
- Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, 119334 Russia
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Averina OV, Kovtun AS, Mavletova DA, Ziganshin RH, Danilenko VN, Mihaylova D, Blazheva D, Slavchev A, Brazkova M, Ibrahim SA, Krastanov A. Oxidative Stress Response of Probiotic Strain Bifidobacterium longum subsp. longum GT15. Foods 2023; 12:3356. [PMID: 37761064 PMCID: PMC10530004 DOI: 10.3390/foods12183356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/01/2023] [Accepted: 09/02/2023] [Indexed: 09/29/2023] Open
Abstract
Bifidobacterium is a predominant and important genus in the bacterial population of the human gut microbiota. Despite the increasing number of studies on the beneficial functionality of bifidobacteria for human health, knowledge about their antioxidant potential is still insufficient. Several in vivo and in vitro studies of Bifidobacterium strains and their cellular components have shown good antioxidant capacity that provided a certain protection of their own and the host's cells. Our work presents the data of transcriptomic, proteomic, and metabolomic analyses of the growing and stationary culture of the probiotic strain B. longum subsp. longum GT15 after exposure to hydrogen peroxide for 2 h and oxygen for 2 and 4 h. The results of the analysis of the sequenced genome of B. longum GT15 showed the presence of 16 gene-encoding proteins with known antioxidant functions. The results of the full transcriptomic analysis demonstrated a more than two-fold increase of levels of transcripts for eleven genes, encoding proteins with antioxidant functions. Proteomic data analysis showed an increased level of more than two times for glutaredoxin and thioredoxin after the exposure to oxygen, which indicates that the thioredoxin-dependent antioxidant system may be the major redox homeostasis system in B. longum bacteria. We also found that the levels of proteins presumably involved in global stress, amino acid metabolism, nucleotide and carbohydrate metabolism, and transport had significantly increased in response to oxidative stress. The metabolic fingerprint analysis also showed good discrimination between cells responding to oxidative stress and the untreated controls. Our results provide a greater understanding of the mechanism of oxidative stress response in B. longum and the factors that contribute to its survival in functional food products.
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Affiliation(s)
- Olga V. Averina
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (A.S.K.); (D.A.M.); (V.N.D.)
| | - Aleksey S. Kovtun
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (A.S.K.); (D.A.M.); (V.N.D.)
| | - Dilara A. Mavletova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (A.S.K.); (D.A.M.); (V.N.D.)
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia;
| | - Valery N. Danilenko
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (A.S.K.); (D.A.M.); (V.N.D.)
| | - Dasha Mihaylova
- Department of Biotechnology, University of Food Technologies, 4002 Plovdiv, Bulgaria; (D.M.); (A.K.)
| | - Denica Blazheva
- Department of Microbiology, University of Food Technologies, 4002 Plovdiv, Bulgaria; (D.B.); (A.S.)
| | - Aleksandar Slavchev
- Department of Microbiology, University of Food Technologies, 4002 Plovdiv, Bulgaria; (D.B.); (A.S.)
| | - Mariya Brazkova
- Department of Biotechnology, University of Food Technologies, 4002 Plovdiv, Bulgaria; (D.M.); (A.K.)
| | - Salam A. Ibrahim
- Food Microbiology and Biotechnology Laboratory, Food and Nutritional Science Program, North Carolina A&T State University, Greensboro, NC 27411-1064, USA;
| | - Albert Krastanov
- Department of Biotechnology, University of Food Technologies, 4002 Plovdiv, Bulgaria; (D.M.); (A.K.)
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Gannesen AV, Ziganshin RH, Ovcharova MA, Nevolina ED, Klimko AI, Martyanov SV, Plakunov VK. Epinephrine Affects Ribosomes, Cell Division, and Catabolic Processes in Micrococcus luteus Skin Strain C01: Revelation of the Conditionally Extensive Hormone Effect Using Orbitrap Mass Spectrometry and Proteomic Analysis. Microorganisms 2023; 11:2181. [PMID: 37764026 PMCID: PMC10535722 DOI: 10.3390/microorganisms11092181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/15/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
In the current study, extensive Orbitrap mass spectrometry analysis was conducted for skin strain Micrococcus luteus C01 planktonic cultures and biofilms after 24 h and 72 h of incubation either in the presence of epinephrine or without any implementations. The investigation revealed the complex and conditionally extensive effect of epinephrine at concentrations closer to normal blood plasma concentrations on both planktonic cultures and biofilms of skin strain M. luteus C01. The concentrations of hundreds of proteins changed during the shift from planktonic growth mode to biofilm and hundreds of proteins were downregulated or upregulated in the presence of epinephrine. Ribosomal, TCA, and cell division proteins appear to be the most altered in their amounts in the presence of the hormone. Potentially, the regulatory mechanism of this process is connected with c-di-GMP and histidine kinases, which were affected by epinephrine in different samples. The phenomenon of epinephrine-based biofilm regulation in M. luteus C01 has wide implications for microbial endocrinology and other research areas.
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Affiliation(s)
- Andrei V. Gannesen
- Federal Research Center “Fundamentals of Biotechnology”, Russian Academy of Sciences, 119071 Moscow, Russia; (M.A.O.); (E.D.N.); (A.I.K.); (S.V.M.); (V.K.P.)
| | - Rustam H. Ziganshin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia;
| | - Maria A. Ovcharova
- Federal Research Center “Fundamentals of Biotechnology”, Russian Academy of Sciences, 119071 Moscow, Russia; (M.A.O.); (E.D.N.); (A.I.K.); (S.V.M.); (V.K.P.)
| | - Ekaterina D. Nevolina
- Federal Research Center “Fundamentals of Biotechnology”, Russian Academy of Sciences, 119071 Moscow, Russia; (M.A.O.); (E.D.N.); (A.I.K.); (S.V.M.); (V.K.P.)
| | - Alena I. Klimko
- Federal Research Center “Fundamentals of Biotechnology”, Russian Academy of Sciences, 119071 Moscow, Russia; (M.A.O.); (E.D.N.); (A.I.K.); (S.V.M.); (V.K.P.)
| | - Sergey V. Martyanov
- Federal Research Center “Fundamentals of Biotechnology”, Russian Academy of Sciences, 119071 Moscow, Russia; (M.A.O.); (E.D.N.); (A.I.K.); (S.V.M.); (V.K.P.)
| | - Vladimir K. Plakunov
- Federal Research Center “Fundamentals of Biotechnology”, Russian Academy of Sciences, 119071 Moscow, Russia; (M.A.O.); (E.D.N.); (A.I.K.); (S.V.M.); (V.K.P.)
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Zavarzina DG, Merkel AY, Klyukina AA, Elizarov IM, Pikhtereva VA, Rusakov VS, Chistyakova NI, Ziganshin RH, Maslov AA, Gavrilov SN. Iron or sulfur respiration-an adaptive choice determining the fitness of a natronophilic bacterium Dethiobacter alkaliphilus in geochemically contrasting environments. Front Microbiol 2023; 14:1108245. [PMID: 37520367 PMCID: PMC10376724 DOI: 10.3389/fmicb.2023.1108245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
Haloalkaliphilic microorganisms are double extremophiles functioning optimally at high salinity and pH. Their typical habitats are soda lakes, geologically ancient yet widespread ecosystems supposed to harbor relict microbial communities. We compared metabolic features and their determinants in two strains of the natronophilic species Dethiobacter alkaliphilus, the only cultured representative of the class "Dethiobacteria" (Bacillota). The strains of D. alkaliphilus were previously isolated from geographically remote Mongolian and Kenyan soda lakes. The type strain AHT1T was described as a facultative chemolithoautotrophic sulfidogen reducing or disproportionating sulfur or thiosulfate, while strain Z-1002 was isolated as a chemolithoautotrophic iron reducer. Here, we uncovered the iron reducing ability of strain AHT1T and the ability of strain Z-1002 for thiosulfate reduction and anaerobic Fe(II) oxidation. Key catabolic processes sustaining the growth of both D. alkaliphilus strains appeared to fit the geochemical settings of two contrasting natural alkaline environments, sulfur-enriched soda lakes and iron-enriched serpentinites. This hypothesis was supported by a meta-analysis of Dethiobacterial genomes and by the enrichment of a novel phylotype from a subsurface alkaline aquifer under Fe(III)-reducing conditions. Genome analysis revealed multiheme c-type cytochromes to be the most probable determinants of iron and sulfur redox transformations in D. alkaliphilus. Phylogeny reconstruction showed that all the respiratory processes in this organism are likely provided by evolutionarily related early forms of unconventional octaheme tetrathionate and sulfite reductases and their structural analogs, OmhA/OcwA Fe(III)-reductases. Several phylogenetically related determinants of anaerobic Fe(II) oxidation were identified in the Z-1002 genome, and the oxidation process was experimentally demonstrated. Proteomic profiling revealed two distinct sets of multiheme cytochromes upregulated in iron(III)- or thiosulfate-respiring cells and the cytochromes peculiar for Fe(II) oxidizing cells. We suggest that maintaining high variation in multiheme cytochromes is an effective adaptive strategy to occupy geochemically contrasting alkaline environments. We propose that sulfur-enriched soda lakes could be secondary habitats for D. alkaliphilus compared to Fe-rich serpentinites, and that the ongoing evolution of Dethiobacterales could retrace the evolutionary path that may have occurred in prokaryotes at a turning point in the biosphere's history, when the intensification of the sulfur cycle outweighed the global significance of the iron cycle.
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Affiliation(s)
- Daria G. Zavarzina
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Yu Merkel
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexandra A. Klyukina
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Ivan M. Elizarov
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Valeria A. Pikhtereva
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A. Maslov
- Faculty of Geology, Lomonosov Moscow State University, Moscow, Russia
| | - Sergey N. Gavrilov
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
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Osipov AV, Cheremnykh EG, Ziganshin RH, Starkov VG, Nguyen TTT, Nguyen KC, Le DT, Hoang AN, Tsetlin VI, Utkin YN. The Potassium Channel Blocker β-Bungarotoxin from the Krait Bungarus multicinctus Venom Manifests Antiprotozoal Activity. Biomedicines 2023; 11:biomedicines11041115. [PMID: 37189733 DOI: 10.3390/biomedicines11041115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/17/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023] Open
Abstract
Protozoal infections are a world-wide problem. The toxicity and somewhat low effectiveness of the existing drugs require the search for new ways of protozoa suppression. Snake venom contains structurally diverse components manifesting antiprotozoal activity; for example, those in cobra venom are cytotoxins. In this work, we aimed to characterize a novel antiprotozoal component(s) in the Bungarus multicinctus krait venom using the ciliate Tetrahymena pyriformis as a model organism. To determine the toxicity of the substances under study, surviving ciliates were registered automatically by an original BioLaT-3.2 instrument. The krait venom was separated by three-step liquid chromatography and the toxicity of the obtained fractions against T. pyriformis was analyzed. As a result, 21 kDa protein toxic to Tetrahymena was isolated and its amino acid sequence was determined by MALDI TOF MS and high-resolution mass spectrometry. It was found that antiprotozoal activity was manifested by β-bungarotoxin (β-Bgt) differing from the known toxins by two amino acid residues. Inactivation of β-Bgt phospholipolytic activity with p-bromophenacyl bromide did not change its antiprotozoal activity. Thus, this is the first demonstration of the antiprotozoal activity of β-Bgt, which is shown to be independent of its phospholipolytic activity.
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Affiliation(s)
- Alexey V Osipov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | | | - Rustam H Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Vladislav G Starkov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | | | - Khoa Cuu Nguyen
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, Ho Chi Minh City 700000, Vietnam
| | - Dung Tien Le
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, Ho Chi Minh City 700000, Vietnam
| | - Anh Ngoc Hoang
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, Ho Chi Minh City 700000, Vietnam
| | - Victor I Tsetlin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Yuri N Utkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
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8
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Petrovskaya LE, Lukashev EP, Lyukmanova EN, Shulepko MA, Kryukova EA, Ziganshin RH, Dolgikh DA, Maksimov EG, Rubin AB, Kirpichnikov MP, Lanyi JK, Balashov SP. Expression of Xanthorhodopsin in Escherichia coli. Protein J 2023:10.1007/s10930-023-10109-5. [DOI: 10.1007/s10930-023-10109-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2023] [Indexed: 04/03/2023]
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9
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Smirnova EV, Rakitina TV, Ziganshin RH, Saratov GA, Arapidi GP, Belogurov AA, Kudriaeva AA. Identification of Myelin Basic Protein Proximity Interactome Using TurboID Labeling Proteomics. Cells 2023; 12:cells12060944. [PMID: 36980286 PMCID: PMC10047773 DOI: 10.3390/cells12060944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Myelin basic protein (MBP) is one of the key structural elements of the myelin sheath and has autoantigenic properties in multiple sclerosis (MS). Its intracellular interaction network is still partially deconvoluted due to the unfolded structure, abnormally basic charge, and specific cellular localization. Here we used the fusion protein of MBP with TurboID, an engineered biotin ligase that uses ATP to convert biotin to reactive biotin-AMP that covalently attaches to nearby proteins, to determine MBP interactome. Despite evident benefits, the proximity labeling proteomics technique generates high background noise, especially in the case of proteins tending to semi-specific interactions. In order to recognize unique MBP partners, we additionally mapped protein interaction networks for deaminated MBP variant and cyclin-dependent kinase inhibitor 1 (p21), mimicking MBP in terms of natively unfolded state, size and basic amino acid clusters. We found that in the plasma membrane region, MBP is colocalized with adhesion proteins occludin and myelin protein zero-like protein 1, solute carrier family transporters ZIP6 and SNAT1, Eph receptors ligand Ephrin-B1, and structural components of the vesicle transport machinery-synaptosomal-associated protein 23 (SNAP23), vesicle-associated membrane protein 3 (VAMP3), protein transport protein hSec23B and cytoplasmic dynein 1 heavy chain 1. We also detected that MBP potentially interacts with proteins involved in Fe2+ and lipid metabolism, namely, ganglioside GM2 activator protein, long-chain-fatty-acid-CoA ligase 4 (ACSL4), NADH-cytochrome b5 reductase 1 (CYB5R1) and metalloreductase STEAP3. Assuming the emerging role of ferroptosis and vesicle cargo docking in the development of autoimmune neurodegeneration, MBP may recruit and regulate the activity of these processes, thus, having a more inclusive role in the integrity of the myelin sheath.
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Affiliation(s)
- Evgeniya V Smirnova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Tatiana V Rakitina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Rustam H Ziganshin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - George A Saratov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Russia
| | - Georgij P Arapidi
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Russia
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Alexey A Belogurov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Department of Biological Chemistry, Evdokimov Moscow State University of Medicine and Dentistry, Ministry of Health of Russian Federation, 127473 Moscow, Russia
| | - Anna A Kudriaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
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10
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Saratov GA, Vladimirov VI, Novoselov AL, Ziganshin RH, Chen G, Baymukhametov TN, Konevega AL, Belogurov AA, Kudriaeva AA. Myelin Basic Protein Fragmentation by Engineered Human Proteasomes with Different Catalytic Phenotypes Revealed Direct Peptide Ligands of MS-Associated and Protective HLA Class I Molecules. Int J Mol Sci 2023; 24:ijms24032091. [PMID: 36768413 PMCID: PMC9917034 DOI: 10.3390/ijms24032091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/17/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023] Open
Abstract
Proteasomes exist in mammalian cells in multiple combinatorial variants due to the diverse regulatory particles and exchange of catalytic subunits. Here, using biotin carboxyl carrier domain of transcarboxylase from Propionibacterium shermanii fused with different proteasome subunits of catalytic and regulatory particles, we report comprehensive characterization of highly homogenous one-step purified human constitutive and immune 20S and 26S/30S proteasomes. Hydrolysis of a multiple sclerosis (MS) autoantigen, myelin basic protein (MBP), by engineered human proteasomes with different catalytic phenotypes, revealed that peptides which may be directly loaded on the HLA class I molecules are produced mainly by immunoproteasomes. We detected at least five MBP immunodominant core regions, namely, LPRHRDTGIL, SLPQKSHGR, QDENPVVHFF, KGRGLSLSRF and GYGGRASDY. All peptides, except QDENPVVHFF, which originates from the encephalitogenic MBP part, were associated with HLA I alleles considered to increase MS risk. Prediction of the affinity of HLA class I to this peptide demonstrated that MS-protective HLA-A*44 and -B*35 molecules are high-affinity binders, whereas MS-associated HLA-A*23, -A*24, -A*26 and -B*51 molecules tend to have moderate to low affinity. The HLA-A*44 molecules may bind QDENPVVHFF and its deamidated form in several registers with unprecedently high affinity, probably linking its distinct protective phenotype with thymic depletion of the repertoire of autoreactive cytotoxic T cells or induction of CD8+ regulatory T cells, specific to the encephalitogenic MBP peptide.
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Affiliation(s)
- George A. Saratov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Russia
| | - Vasiliy I. Vladimirov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Alexey L. Novoselov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Rustam H. Ziganshin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Guo Chen
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, China
| | | | - Andrey L. Konevega
- National Research Center, “Kurchatov Institute”, 123182 Moscow, Russia
- Institute of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre, Kurchatov Institute, 188300 Gatchina, Russia
| | - Alexey A. Belogurov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Department of Biological Chemistry, Ministry of Health of Russian Federation, Evdokimov Moscow State University of Medicine and Dentistry, 127473 Moscow, Russia
- Correspondence: (A.A.B.J.); (A.A.K.); Tel.: +7-495-3352288 (A.A.B.J. & A.A.K.)
| | - Anna A. Kudriaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Correspondence: (A.A.B.J.); (A.A.K.); Tel.: +7-495-3352288 (A.A.B.J. & A.A.K.)
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11
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Petushkov VN, Vavilov MV, Ivanov IA, Ziganshin RH, Rodionova NS, Yampolsky IV, Tsarkova AS, Dubinnyi MA. Deazaflavin cofactor boosts earthworms Henlea bioluminescence. Org Biomol Chem 2023; 21:415-427. [PMID: 36530053 DOI: 10.1039/d2ob01946a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The bioluminescence of Siberian earthworms Henlea sp. was found to be enhanced by two low molecular weight activators, termed ActH and ActS, found in the hot extracts. The fluorescence emission maximum of the activators matches the bioluminescence spectrum that peaks at 464 nm. We purified 4.3 and 8.8 micrograms of ActH and ActS from 200 worms and explored them using orbitrap HRMS with deep fragmentation and 1D/2D NMR equipped with cryoprobes. Their chemical structures were ascertained using chemical shift prediction services, structure elucidation software and database searches. ActH was identified as the riboflavin analoge archaeal cofactor F0, namely 7,8-didemethyl-8-hydroxy-5-deazariboflavin. ActS is a novel compound, namely ActH sulfated at the 3' ribityl hydroxyl. We designed and implemented a new four step synthesis strategy forActH that outperformed previous synthetic approaches. The synthetic ActH was identical to the natural one and activated Henlea sp. bioluminescence. The bioluminescence enhancement factor X was measured at different ActH concentrations and the Michaelis constant Km = 0.22 ± 0.01 μM was obtained by nonlinear regression. At an excess of synthetic ActH, the factor X was saturated at Xmax = 33.3 ± 0.5, thus opening an avenue to further characterisation of the Henlea sp. bioluminescence system. ActH did not produce bioluminescence without the luciferin with an as yet unknown chemical structure. We propose that ActH and the novel sulfated deazariboflavin ActS either emit the light of the Henlea sp. bioluminescence and/or accept hydride(s) donor upon luciferin oxidation.
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Affiliation(s)
- Valentin N Petushkov
- Institute of Biophysics, Krasnoyarsk Research Center, Siberian Branch, Russian Academy of Sciences, Akademgorodok, 660036, Krasnoyarsk, Russia
| | - Matvey V Vavilov
- Shemyakin-Ovchinnikov Institute of bioorganic chemistry, Russian academy of Sciences GSP-7, Miklukho-Maklaya str., 16/10, 117997, Moscow, Russia.
| | - Igor A Ivanov
- Shemyakin-Ovchinnikov Institute of bioorganic chemistry, Russian academy of Sciences GSP-7, Miklukho-Maklaya str., 16/10, 117997, Moscow, Russia.
| | - Rustam H Ziganshin
- Shemyakin-Ovchinnikov Institute of bioorganic chemistry, Russian academy of Sciences GSP-7, Miklukho-Maklaya str., 16/10, 117997, Moscow, Russia.
| | - Natalia S Rodionova
- Institute of Biophysics, Krasnoyarsk Research Center, Siberian Branch, Russian Academy of Sciences, Akademgorodok, 660036, Krasnoyarsk, Russia
| | - Ilia V Yampolsky
- Shemyakin-Ovchinnikov Institute of bioorganic chemistry, Russian academy of Sciences GSP-7, Miklukho-Maklaya str., 16/10, 117997, Moscow, Russia.
| | - Aleksandra S Tsarkova
- Shemyakin-Ovchinnikov Institute of bioorganic chemistry, Russian academy of Sciences GSP-7, Miklukho-Maklaya str., 16/10, 117997, Moscow, Russia. .,Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Maxim A Dubinnyi
- Shemyakin-Ovchinnikov Institute of bioorganic chemistry, Russian academy of Sciences GSP-7, Miklukho-Maklaya str., 16/10, 117997, Moscow, Russia. .,Moscow Institute of Physics and Technology (State University), 9 Institutskiy per., Dolgoprudny, Moscow Region 141700, Russia
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12
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Yampolskaya DS, Kopylova GV, Shchepkin DV, Nabiev SR, Nikitina LV, Walklate J, Ziganshin RH, Bershitsky SY, Geeves MA, Matyushenko AM, Levitsky DI. Pseudo-phosphorylation of essential light chains affects the functioning of skeletal muscle myosin. Biophys Chem 2023; 292:106936. [PMID: 36436358 DOI: 10.1016/j.bpc.2022.106936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/10/2022] [Accepted: 11/18/2022] [Indexed: 11/21/2022]
Abstract
The work aimed to investigate how the phosphorylation of the myosin essential light chain of fast skeletal myosin (LC1) affects the functional properties of the myosin molecule. Using mass-spectrometry, we revealed phosphorylated peptides of LC1 in myosin from different fast skeletal muscles. Mutations S193D and T65D that mimic natural phosphorylation of LC1 were produced, and their effects on functional properties of the entire myosin molecule and isolated myosin head (S1) were studied. We have shown that T65D mutation drastically decreased the sliding velocity of thin filaments in an in vitro motility assay and strongly increased the duration of actin-myosin interaction in optical trap experiments. These effects of T65D mutation in LC1 observed only with the whole myosin but not with S1 were prevented by double T65D/S193D mutation. The T65D and T65D/S193D mutations increased actin-activated ATPase activity of S1 and decreased ADP affinity for the actin-S1 complex. The results indicate that pseudo-phosphorylation of LC1 differently affects the properties of the whole myosin molecule and its isolated head. Also, the results show that phosphorylation of LC1 of skeletal myosin could be one more mechanism of regulation of actin-myosin interaction that needs further investigation.
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Affiliation(s)
- Daria S Yampolskaya
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prosp. 33, Moscow 119071, Russia
| | - Galina V Kopylova
- Institute of Immunology and Physiology of the Russian Academy of Sciences, Yekaterinburg 620049, Russia
| | - Daniil V Shchepkin
- Institute of Immunology and Physiology of the Russian Academy of Sciences, Yekaterinburg 620049, Russia
| | - Salavat R Nabiev
- Institute of Immunology and Physiology of the Russian Academy of Sciences, Yekaterinburg 620049, Russia
| | - Larisa V Nikitina
- Institute of Immunology and Physiology of the Russian Academy of Sciences, Yekaterinburg 620049, Russia
| | - Jonathan Walklate
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, United Kingdom
| | - Rustam H Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Sergey Y Bershitsky
- Institute of Immunology and Physiology of the Russian Academy of Sciences, Yekaterinburg 620049, Russia
| | - Michael A Geeves
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, United Kingdom
| | - Alexander M Matyushenko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prosp. 33, Moscow 119071, Russia
| | - Dmitrii I Levitsky
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prosp. 33, Moscow 119071, Russia.
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13
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Kalebina TS, Kulakovskaya EV, Rekstina VV, Trilisenko LV, Ziganshin RH, Marmiy NV, Esipov DS, Kulakovskaya TV. Effect of Deletions of the Genes Encoding Pho3p and Bgl2p on Polyphosphate Level, Stress Adaptation, and Attachments of These Proteins to Saccharomyces cerevisiae Cell Wall. Biochemistry Moscow 2023; 88:152-161. [PMID: 37068877 DOI: 10.1134/s0006297923010133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Inorganic polyphosphates (polyP), according to literature data, are involved in the regulatory processes of molecular complex of the Saccharomyces cerevisiae cell wall (CW). The aim of the work was to reveal relationship between polyP, acid phosphatase Pho3p, and the major CW protein, glucanosyltransglycosylase Bgl2p, which is the main glucan-remodelling enzyme with amyloid properties. It has been shown that the yeast cells with deletion of the PHO3 gene contain more high molecular alkali-soluble polyP and are also more resistant to exposure to alkali and manganese ions compared to the wild type strain. This suggests that Pho3p is responsible for hydrolysis of the high molecular polyP on the surface of yeast cells, and these polyP belong to the stress resistance factors. The S. cerevisiae strain with deletion of the BGL2 gene is similar to the Δpho3 strain both in the level of high molecular alkali-soluble polyP and in the increased resistance to alkali and manganese. Comparative analysis of the CW proteins demonstrated correlation between the extractability of the acid phosphatase and Bgl2p, and also revealed a change in the mode of Bgl2p attachment to the CW of the strain lacking Pho3p. It has been suggested that Bgl2p and Pho3p are able to form a metabolon or its parts that connects biogenesis of the main structural polymer of the CW, glucan, and catabolism of an important regulatory polymer, polyphosphates.
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Affiliation(s)
- Tatyana S Kalebina
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Ekaterina V Kulakovskaya
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino, 142290, Russia
| | - Valentina V Rekstina
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Ludmila V Trilisenko
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino, 142290, Russia
| | - Rustam H Ziganshin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Natalia V Marmiy
- Institute of Mitoengineering, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Dmitriy S Esipov
- Department of Bioorganic Chemistry, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Tatiana V Kulakovskaya
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino, 142290, Russia
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14
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Gannesen AV, Ziganshin RH, Zdorovenko EL, Klimko AI, Ianutsevich EA, Danilova OA, Tereshina VM, Gorbachevskii MV, Ovcharova MA, Nevolina ED, Martyanov SV, Shashkov AS, Dmitrenok AS, Novikov AA, Zhurina MV, Botchkova EA, Toukach PV, Plakunov VK. Epinephrine extensively changes the biofilm matrix composition in Micrococcus luteus C01 isolated from human skin. Front Microbiol 2022; 13:1003942. [PMID: 36204611 PMCID: PMC9530943 DOI: 10.3389/fmicb.2022.1003942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 08/22/2022] [Indexed: 12/04/2022] Open
Abstract
The importance of the impact of human hormones on commensal microbiota and microbial biofilms is established in lots of studies. In the present investigation, we continued and extended the research of epinephrine effects on the skin commensal Micrococcus luteus C01 and its biofilms, and also the matrix changes during the biofilm growth. Epinephrine in concentration 4.9 × 10-9 M which is close to normal blood plasma level increased the amount of polysaccharides and extracellular DNA in the matrix, changed extensively its protein, lipid and polysaccharide composition. The Ef-Tu factor was one of the most abundant proteins in the matrix and its amount increased in the presence of the hormone. One of the glucose-mannose polysaccharide was absent in the matrix in presence of epinephrine after 24 h of incubation. The matrix phospholipids were also eradicated by the addition of the hormone. Hence, epinephrine has a great impact on the M. luteus biofilms and their matrix composition, and this fact opens wide perspectives for the future research.
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Affiliation(s)
- Andrei V. Gannesen
- Winogradsky Institute of Microbiology, Federal Research Center “Fundamentals of Biotechnology” of Russian Academy of Sciences, Moscow, Russia
| | - Rustam H. Ziganshin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Evelina L. Zdorovenko
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alena I. Klimko
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Elena A. Ianutsevich
- Winogradsky Institute of Microbiology, Federal Research Center “Fundamentals of Biotechnology” of Russian Academy of Sciences, Moscow, Russia
| | - Olga A. Danilova
- Winogradsky Institute of Microbiology, Federal Research Center “Fundamentals of Biotechnology” of Russian Academy of Sciences, Moscow, Russia
| | - Vera M. Tereshina
- Winogradsky Institute of Microbiology, Federal Research Center “Fundamentals of Biotechnology” of Russian Academy of Sciences, Moscow, Russia
| | | | - Maria A. Ovcharova
- Winogradsky Institute of Microbiology, Federal Research Center “Fundamentals of Biotechnology” of Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina D. Nevolina
- Winogradsky Institute of Microbiology, Federal Research Center “Fundamentals of Biotechnology” of Russian Academy of Sciences, Moscow, Russia
| | - Sergey V. Martyanov
- Winogradsky Institute of Microbiology, Federal Research Center “Fundamentals of Biotechnology” of Russian Academy of Sciences, Moscow, Russia
| | - Alexander S. Shashkov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Andrey S. Dmitrenok
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Andrei A. Novikov
- Faculty of Chemical and Environmental Engineering, Gubkin University, Moscow, Russia
| | - Marina V. Zhurina
- Winogradsky Institute of Microbiology, Federal Research Center “Fundamentals of Biotechnology” of Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina A. Botchkova
- Winogradsky Institute of Microbiology, Federal Research Center “Fundamentals of Biotechnology” of Russian Academy of Sciences, Moscow, Russia
- Faculty of Chemical and Environmental Engineering, Gubkin University, Moscow, Russia
| | - Philipp V. Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir K. Plakunov
- Winogradsky Institute of Microbiology, Federal Research Center “Fundamentals of Biotechnology” of Russian Academy of Sciences, Moscow, Russia
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15
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Evsyutina DV, Semashko TA, Galyamina MA, Kovalchuk SI, Ziganshin RH, Ladygina VG, Fisunov GY, Pobeguts OV. Molecular Basis of the Slow Growth of Mycoplasma hominis on Different Energy Sources. Front Cell Infect Microbiol 2022; 12:918557. [PMID: 35873139 PMCID: PMC9301678 DOI: 10.3389/fcimb.2022.918557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/15/2022] [Indexed: 12/05/2022] Open
Abstract
Mycoplasma hominis is an opportunistic urogenital pathogen in vertebrates. It is a non-glycolytic species that produces energy via arginine degradation. Among genital mycoplasmas, M. hominis is the most commonly reported to play a role in systemic infections and can persist in the host for a long time. However, it is unclear how M. hominis proceeds under arginine limitation. The recent metabolic reconstruction of M. hominis has demonstrated its ability to catabolize deoxyribose phosphate to produce ATP. In this study, we cultivated M. hominis on two different energy sources (arginine and thymidine) and demonstrated the differences in growth rate, antibiotic sensitivity, and biofilm formation. Using label-free quantitative proteomics, we compared the proteome of M. hominis under these conditions. A total of 466 proteins were identified from M. hominis, representing approximately 85% of the predicted proteome, while the levels of 94 proteins changed significantly. As expected, we observed changes in the levels of metabolic enzymes. The energy source strongly affects the synthesis of enzymes related to RNA modifications and ribosome assembly. The translocation of lipoproteins and other membrane-associated proteins was also impaired. Our study, the first global characterization of the proteomic switching of M. hominis in arginine-deficiency media, illustrates energy source-dependent control of pathogenicity factors and can help to determine the mechanisms underlying the interaction between the growth rate and fitness of genome-reduced bacteria.
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Affiliation(s)
- Daria V. Evsyutina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency Malaya Pirogovskaya 1a, Moscow, Russia
- Department of Systems and Synthetic Biology, Scientific Research Institute for Systems Biology and Medicine Nauchniy proezd 18, Moscow, Russia
- *Correspondence: Daria V. Evsyutina,
| | - Tatiana A. Semashko
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency Malaya Pirogovskaya 1a, Moscow, Russia
- Department of Systems and Synthetic Biology, Scientific Research Institute for Systems Biology and Medicine Nauchniy proezd 18, Moscow, Russia
| | - Maria A. Galyamina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency Malaya Pirogovskaya 1a, Moscow, Russia
| | - Sergey I. Kovalchuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10, Moscow, Russia
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10, Moscow, Russia
| | - Valentina G. Ladygina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency Malaya Pirogovskaya 1a, Moscow, Russia
| | - Gleb Y. Fisunov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency Malaya Pirogovskaya 1a, Moscow, Russia
- Department of Systems and Synthetic Biology, Scientific Research Institute for Systems Biology and Medicine Nauchniy proezd 18, Moscow, Russia
| | - Olga V. Pobeguts
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency Malaya Pirogovskaya 1a, Moscow, Russia
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16
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Chetverina D, Vorobyeva NE, Mazina MY, Fab LV, Lomaev D, Golovnina A, Mogila V, Georgiev P, Ziganshin RH, Erokhin M. Comparative interactome analysis of the PRE DNA-binding factors: purification of the Combgap-, Zeste-, Psq-, and Adf1-associated proteins. Cell Mol Life Sci 2022; 79:353. [PMID: 35676368 PMCID: PMC11072172 DOI: 10.1007/s00018-022-04383-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 04/14/2022] [Accepted: 05/08/2022] [Indexed: 01/08/2023]
Abstract
The Polycomb group (PcG) and Trithorax group (TrxG) proteins are key epigenetic regulators controlling the silenced and active states of genes in multicellular organisms, respectively. In Drosophila, PcG/TrxG proteins are recruited to the chromatin via binding to specific DNA sequences termed polycomb response elements (PREs). While precise mechanisms of the PcG/TrxG protein recruitment remain unknown, the important role is suggested to belong to sequence-specific DNA-binding factors. At the same time, it was demonstrated that the PRE DNA-binding proteins are not exclusively localized to PREs but can bind other DNA regulatory elements, including enhancers, promoters, and boundaries. To gain an insight into the PRE DNA-binding protein regulatory network, here, using ChIP-seq and immuno-affinity purification coupled to the high-throughput mass spectrometry, we searched for differences in abundance of the Combgap, Zeste, Psq, and Adf1 PRE DNA-binding proteins. While there were no conspicuous differences in co-localization of these proteins with other functional transcription factors, we show that Combgap and Zeste are more tightly associated with the Polycomb repressive complex 1 (PRC1), while Psq interacts strongly with the TrxG proteins, including the BAP SWI/SNF complex. The Adf1 interactome contained Mediator subunits as the top interactors. In addition, Combgap efficiently interacted with AGO2, NELF, and TFIID. Combgap, Psq, and Adf1 have architectural proteins in their networks. We further investigated the existence of direct interactions between different PRE DNA-binding proteins and demonstrated that Combgap-Adf1, Psq-Dsp1, and Pho-Spps can interact in the yeast two-hybrid assay. Overall, our data suggest that Combgap, Psq, Zeste, and Adf1 are associated with the protein complexes implicated in different regulatory activities and indicate their potential multifunctional role in the regulation of transcription.
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Affiliation(s)
- Darya Chetverina
- Group of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow, 119334, Russia.
| | - Nadezhda E Vorobyeva
- Group of Dynamics of Transcriptional Complexes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Marina Yu Mazina
- Group of Hormone-Dependent Transcriptional Regulation, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Lika V Fab
- Group of Chromatin Biology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow, 119334, Russia
| | - Dmitry Lomaev
- Group of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow, 119334, Russia
| | - Alexandra Golovnina
- Group of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow, 119334, Russia
| | - Vladic Mogila
- Department of Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow, 119334, Russia
| | - Pavel Georgiev
- Department of Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow, 119334, Russia
| | - Rustam H Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Maksim Erokhin
- Group of Chromatin Biology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow, 119334, Russia.
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17
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Levitsky LI, Kuznetsova KG, Kliuchnikova AA, Ilina IY, Goncharov AO, Lobas AA, Ivanov MV, Lazarev VN, Ziganshin RH, Gorshkov MV, Moshkovskii SA. Validating Amino Acid Variants in Proteogenomics Using Sequence Coverage by Multiple Reads. J Proteome Res 2022; 21:1438-1448. [PMID: 35536917 DOI: 10.1021/acs.jproteome.2c00033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Mass spectrometry-based proteome analysis implies matching the mass spectra of proteolytic peptides to amino acid sequences predicted from genomic sequences. Reliability of peptide variant identification in proteogenomic studies is often lacking. We propose a way to interpret shotgun proteomics results, specifically in the data-dependent acquisition mode, as protein sequence coverage by multiple reads as it is done in nucleic acid sequencing for calling of single nucleotide variants. Multiple reads for each sequence position could be provided by overlapping distinct peptides, thus confirming the presence of certain amino acid residues in the overlapping stretch with a lower false discovery rate. Overlapping distinct peptides originate from miscleaved tryptic peptides in combination with their properly cleaved counterparts and from peptides generated by multiple proteases after the same specimen is subject to parallel digestion and analyzed separately. We illustrate this approach using publicly available multiprotease data sets and our own data generated for the HEK-293 cell line digests obtained using trypsin, LysC, and GluC proteases. Totally, up to 30% of the whole proteome was covered by tryptic peptides with up to 7% covered twofold and more. The proteogenomic analysis of the HEK-293 cell line revealed 36 single amino acid variants, seven of which were supported by multiple reads.
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Affiliation(s)
- Lev I Levitsky
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 38, bld. 2, Leninsky Prospect, Moscow 119334, Russia
| | - Ksenia G Kuznetsova
- Federal Research and Clinical Center of Physical-Chemical Medicine, 1a, Malaya Pirogovskaya, Moscow 119435, Russia
| | - Anna A Kliuchnikova
- Federal Research and Clinical Center of Physical-Chemical Medicine, 1a, Malaya Pirogovskaya, Moscow 119435, Russia.,Pirogov Russian National Research Medical University, 1, Ostrovityanova, Moscow 117997, Russia
| | - Irina Y Ilina
- Federal Research and Clinical Center of Physical-Chemical Medicine, 1a, Malaya Pirogovskaya, Moscow 119435, Russia
| | - Anton O Goncharov
- Federal Research and Clinical Center of Physical-Chemical Medicine, 1a, Malaya Pirogovskaya, Moscow 119435, Russia.,Pirogov Russian National Research Medical University, 1, Ostrovityanova, Moscow 117997, Russia
| | - Anna A Lobas
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 38, bld. 2, Leninsky Prospect, Moscow 119334, Russia
| | - Mark V Ivanov
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 38, bld. 2, Leninsky Prospect, Moscow 119334, Russia
| | - Vassili N Lazarev
- Federal Research and Clinical Center of Physical-Chemical Medicine, 1a, Malaya Pirogovskaya, Moscow 119435, Russia.,Moscow Institute of Physics and Technology (State University), 9, Institutskiy per., Dolgoprudny, Moscow Region 141701, Russia
| | - Rustam H Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya, Moscow 117997, Russia
| | - Mikhail V Gorshkov
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 38, bld. 2, Leninsky Prospect, Moscow 119334, Russia
| | - Sergei A Moshkovskii
- Federal Research and Clinical Center of Physical-Chemical Medicine, 1a, Malaya Pirogovskaya, Moscow 119435, Russia.,Pirogov Russian National Research Medical University, 1, Ostrovityanova, Moscow 117997, Russia
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18
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Kasheverov IE, Kuzmenkov AI, Kudryavtsev DS, Chudetskiy IS, Shelukhina IV, Barykin EP, Ivanov IA, Siniavin AE, Ziganshin RH, Baranov MS, Tsetlin VI, Vassilevski AA, Utkin YN. Snake Toxins Labeled by Green Fluorescent Protein or Its Synthetic Chromophore are New Probes for Nicotinic acetylcholine Receptors. Front Mol Biosci 2021; 8:753283. [PMID: 34926576 PMCID: PMC8671107 DOI: 10.3389/fmolb.2021.753283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 08/04/2021] [Accepted: 11/10/2021] [Indexed: 11/25/2022] Open
Abstract
Fluorescence can be exploited to monitor intermolecular interactions in real time and at a resolution up to a single molecule. It is a method of choice to study ligand-receptor interactions. However, at least one of the interacting molecules should possess good fluorescence characteristics, which can be achieved by the introduction of a fluorescent label. Gene constructs with green fluorescent protein (GFP) are widely used to follow the expression of the respective fusion proteins and monitor their function. Recently, a small synthetic analogue of GFP chromophore (p-HOBDI-BF2) was successfully used for tagging DNA molecules, so we decided to test its applicability as a potential fluorescent label for proteins and peptides. This was done on α-cobratoxin (α-CbTx), a three-finger protein used as a molecular marker of muscle-type, neuronal α7 and α9/α10 nicotinic acetylcholine receptors (nAChRs), as well as on azemiopsin, a linear peptide neurotoxin selectively inhibiting muscle-type nAChRs. An activated N-hydroxysuccinimide ester of p-HOBDI-BF2 was prepared and utilized for toxin labeling. For comparison we used a recombinant α-CbTx fused with a full-length GFP prepared by expression of a chimeric gene. The structure of modified toxins was confirmed by mass spectrometry and their activity was characterized by competition with iodinated α-bungarotoxin in radioligand assay with respective receptor preparations, as well as by thermophoresis. With the tested protein and peptide neurotoxins, introduction of the synthetic GFP chromophore induced considerably lower decrease in their affinity for the receptors as compared with full-length GFP attachment. The obtained fluorescent derivatives were used for nAChR visualization in tissue slices and cell cultures.
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Affiliation(s)
- Igor E Kasheverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexey I Kuzmenkov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Denis S Kudryavtsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ivan S Chudetskiy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Irina V Shelukhina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Evgeny P Barykin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Igor A Ivanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Andrei E Siniavin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Rustam H Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail S Baranov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Victor I Tsetlin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander A Vassilevski
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Moscow Region, Russia
| | - Yuri N Utkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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19
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Anashkina AA, Petrushanko IY, Ziganshin RH, Orlov YL, Nekrasov AN. Entropy Analysis of Protein Sequences Reveals a Hierarchical Organization. Entropy (Basel) 2021; 23:1647. [PMID: 34945953 PMCID: PMC8700119 DOI: 10.3390/e23121647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/28/2021] [Accepted: 12/04/2021] [Indexed: 11/16/2022]
Abstract
BACKGROUND Analyzing the local sequence content in proteins, earlier we found that amino acid residue frequencies differ on various distances between amino acid positions in the sequence, assuming the existence of structural units. METHODS We used informational entropy of protein sequences to find that the structural unit of proteins is a block of adjacent amino acid residues-"information unit". The ANIS (ANalysis of Informational Structure) method uses these information units for revealing hierarchically organized Elements of the Information Structure (ELIS) in amino acid sequences. RESULTS The developed mathematical apparatus gives stable results on the structural unit description even with a significant variation in the parameters. The optimal length of the information unit is five, and the number of allowed substitutions is one. Examples of the application of the method for the design of protein molecules, intermolecular interactions analysis, and the study of the mechanisms of functioning of protein molecular machines are given. CONCLUSIONS ANIS method makes it possible not only to analyze native proteins but also to design artificial polypeptide chains with a given spatial organization and, possibly, function.
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Affiliation(s)
- Anastasia A. Anashkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov St. 32, 119991 Moscow, Russia;
| | - Irina Yu. Petrushanko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov St. 32, 119991 Moscow, Russia;
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997 Moscow, Russia; (R.H.Z.); (A.N.N.)
| | - Yuriy L. Orlov
- The Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Trubetskaya 8-2, 119991 Moscow, Russia;
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia (RUDN University), Miklukho-Maklaya Str. 6, 117198 Moscow, Russia
| | - Alexei N. Nekrasov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997 Moscow, Russia; (R.H.Z.); (A.N.N.)
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20
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Purtov KV, Petushkov VN, Rodionova NS, Chepurnykh TV, Kozhemyako VB, Zagitova RI, Shcheglov AS, Ziganshin RH, Tsarkova AS. Similarities and differences between the Chaetopterus variopedatus polychaete luciferases depending on the type of habitat. BRSMU 2021. [DOI: 10.24075/brsmu.2021.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The marine polychaete Chaetopterus variopedatus (Renier) (family Chaetopteridae) is a cosmopolitan species complex, consisting of distinct populations/ subspecies. The worms release glowing (460 nm) clouds of mucus when disturbed, and their parapodia often glow brightly. Currently, it is still unclear how exactly the bioluminescence system of these polychaetes functions. It has been previously assumed that the C. variopedatus luciferase may be used for detection of ferroptosis, the recently explored pathway of programmed cell death, resulting from accumulation of the ferrous ions. This study was aimed to extract and characterize the C. variopedatus luciferases, as well as to compare luciferases obtained from C. variopedatus of different populations. When extracting the enzyme responsible for bioluminescence from the frozen samples of Brazilian C. variopedatus using the improved method, two active luciferases, L1 and L2, were obtained. We assumed that one of the listed above luciferases was responsible for luminescence of the mucus and the other luciferase was responsible for luminescence in parapodia, and used the method for the distinct samples of mucus and parapodia of the living Far Eastern C. variopedatus. However, mucus of the latter turned out to be non-glowing. It is shown that luciferase L2 is responsible for luminescence in the parapodia of the C. variopedatus polychaete, since this luciferase has been found in the total biomass of Brazilian polychaetes and parapodia of Far Eastern polychaetes. Luminescence of the Brazilian C. variopedatus mucus is attributed to the functioning of luciferase L1, which is lacking in the mucus of the Far Eastern subspecies. The range of luciferase isoforms in polychaetes C. variopedatus depends on the place of origin.
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Affiliation(s)
- KV Purtov
- Institute of Biophysics, Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences
| | - VN Petushkov
- Institute of Biophysics, Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences
| | - NS Rodionova
- Institute of Biophysics, Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences
| | - TV Chepurnykh
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - VB Kozhemyako
- Pacific State Medical University, Vladivostok, Russia
| | - RI Zagitova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - AS Shcheglov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - RH Ziganshin
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - AS Tsarkova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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21
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Mizgina TO, Chikalovets IV, Molchanova VI, Ziganshin RH, Chernikov OV. Identification and Characterization of a Novel Lectin from the Clam Glycymeris yessoensis and Its Functional Characterization under Microbial Stimulation and Environmental Stress. Mar Drugs 2021; 19:474. [PMID: 34564136 PMCID: PMC8466245 DOI: 10.3390/md19090474] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 12/20/2022] Open
Abstract
Lectin from the bivalve Glycymeris yessoensis (GYL) was purified by affinity chromatography on porcine stomach mucin-Sepharose. GYL is a dimeric protein with a molecular mass of 36 kDa, as established by SDS-PAGE and MALDI-TOF analysis, consisting of 18 kDa subunits linked by a disulfide bridge. According to circular dichroism data, GYL is a β/α-protein with the predominance of β-structure. GYL preferentially agglutinates enzyme-treated rabbit erythrocytes and recognizes glycoproteins containing O-glycosidically linked glycans, such as porcine stomach mucin (PSM), fetuin, thyroglobulin, and ovalbumin. The amino acid sequences of five segments of GYL were acquired via mass spectrometry. The sequences have no homology with other known lectins. GYL is Ca2+-dependent and stable over a range above a pH of 8 and temperatures up to 20 °C for 30 min. GYL is a pattern recognition receptor, as it binds common pathogen-associated molecular patterns, such as peptidoglycan, LPS, β-1,3-glucan and mannan. GYL possesses a broad microbial-binding spectrum, including Gram-positive (Bacillus subtilis, Staphylococcus aureus) and Gram-negative bacteria (Escherichia coli, Vibrio proteolyticus), but not the fungus Candida albicans. Expression levels of GYL in the hemolymph were significantly upregulated after bacterial challenge by V. proteolyticus plus environmental stress (diesel fuel). Results indicate that GYL is probably a new member of the C-type lectin family, and may be involved in the immune response of G. yessoensis to bacterial attack.
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Affiliation(s)
- Tatyana O. Mizgina
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, 690022 Vladivostok, Russia; (I.V.C.); (V.I.M.)
- School of Natural Sciences, Far Eastern Federal University, 690950 Vladivostok, Russia
| | - Irina V. Chikalovets
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, 690022 Vladivostok, Russia; (I.V.C.); (V.I.M.)
- School of Natural Sciences, Far Eastern Federal University, 690950 Vladivostok, Russia
| | - Valentina I. Molchanova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, 690022 Vladivostok, Russia; (I.V.C.); (V.I.M.)
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia;
| | - Oleg V. Chernikov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, 690022 Vladivostok, Russia; (I.V.C.); (V.I.M.)
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22
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Petrovskaya LE, Ziganshin RH, Kryukova EA, Zlobinov AV, Gapizov SS, Shingarova LN, Mironov VA, Lomakina GY, Dolgikh DA, Kirpichnikov MP. Increased Synthesis of a Magnesium Transporter MgtA During Recombinant Autotransporter Expression in Escherichia coli. Appl Biochem Biotechnol 2021; 193:3672-3703. [PMID: 34351586 DOI: 10.1007/s12010-021-03634-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/19/2021] [Indexed: 12/01/2022]
Abstract
Overproduction of the membrane proteins in Escherichia coli cells is a common approach to obtain sufficient material for their functional and structural studies. However, the efficiency of this process can be limited by toxic effects which decrease the viability of the host and lead to low yield of the product. During the expression of the esterase autotransporter AT877 from Psychrobacter cryohalolentis K5T, we observed significant growth inhibition of the C41(DE3) cells in comparison with the same cells producing other recombinant proteins. Induction of AT877 synthesis also resulted in the elevated expression of a magnesium transporter MgtA and decreased ATP content of the cells. To characterize the response to overexpression of the autotransporter in bacterial cells, we performed a comparative analysis of their proteomic profile by mass spectrometry. According to the obtained data, E. coli cells which synthesize AT877 experience complex stress condition presumably associated with secretion apparatus overloading and improper localization of the recombinant protein. Several response pathways were shown to be activated by AT877 overproduction including Cpx, PhoP/PhoQ, Psp, and σE The obtained results open new opportunities for optimization of the recombinant membrane protein expression in E. coli for structural studies and biotechnological applications.
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Affiliation(s)
- Lada E Petrovskaya
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia.
| | - Rustam H Ziganshin
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
| | - Elena A Kryukova
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
- Emanuel Institute of Biochemical Physics, Kosygina str., 4, Moscow, 119334, Russia
| | - Alexander V Zlobinov
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
| | - Sultan Sh Gapizov
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
- Emanuel Institute of Biochemical Physics, Kosygina str., 4, Moscow, 119334, Russia
- Department of Biology, M. V. Lomonosov Moscow State University, Leninskie gory, 1, Moscow, 119234, Russia
| | - Lyudmila N Shingarova
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
| | - Vasiliy A Mironov
- Roche Diagnostics Rus LLC, Letnikovskaya str. 2/2, Moscow, 115114, Russia
| | - Galina Yu Lomakina
- Department of Chemistry, M. V. Lomonosov Moscow State University, Leninskie Gory, 1/3, Moscow, 119991, Russia
- Bauman Moscow State Technical University, Baumanskaya 2-ya, 5/1, Moscow, 105005, Russia
| | - Dmitriy A Dolgikh
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
- Emanuel Institute of Biochemical Physics, Kosygina str., 4, Moscow, 119334, Russia
- Department of Biology, M. V. Lomonosov Moscow State University, Leninskie gory, 1, Moscow, 119234, Russia
| | - Mikhail P Kirpichnikov
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
- Department of Biology, M. V. Lomonosov Moscow State University, Leninskie gory, 1, Moscow, 119234, Russia
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23
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Nekrasov AN, Kozmin YP, Kozyrev SV, Ziganshin RH, de Brevern AG, Anashkina AA. Hierarchical Structure of Protein Sequence. Int J Mol Sci 2021; 22:8339. [PMID: 34361104 PMCID: PMC8348890 DOI: 10.3390/ijms22158339] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 11/28/2022] Open
Abstract
Most non-communicable diseases are associated with dysfunction of proteins or protein complexes. The relationship between sequence and structure has been analyzed for a long time, and the analysis of the sequences organization in domains and motifs remains an actual research area. Here, we propose a mathematical method for revealing the hierarchical organization of protein sequences. The method is based on the pentapeptide as a unit of protein sequences. Employing the frequency of occurrence of pentapeptides in sequences of natural proteins and a special mathematical approach, this method revealed a hierarchical structure in the protein sequence. The method was applied to 24,647 non-homologous protein sequences with sizes ranging from 50 to 400 residues from the NRDB90 database. Statistical analysis of the branching points of the graphs revealed 11 characteristic values of y (the width of the inscribed function), showing the relationship of these multiple fragments of the sequences. Several examples illustrate how fragments of the protein spatial structure correspond to the elements of the hierarchical structure of the protein sequence. This methodology provides a promising basis for a mathematically-based classification of the elements of the spatial organization of proteins. Elements of the hierarchical structure of different levels of the hierarchy can be used to solve biotechnological and medical problems.
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Affiliation(s)
- Alexei N. Nekrasov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997 Moscow, Russia; (A.N.N.); (Y.P.K.); (R.H.Z.)
| | - Yuri P. Kozmin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997 Moscow, Russia; (A.N.N.); (Y.P.K.); (R.H.Z.)
| | - Sergey V. Kozyrev
- Steklov Mathematical Institute and of Russian Academy of Sciences, 8 Gubkina St., 119991 Moscow, Russia;
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997 Moscow, Russia; (A.N.N.); (Y.P.K.); (R.H.Z.)
| | - Alexandre G. de Brevern
- INSERM UMR S-1134, DSIMB, Univ. Paris, INTS, Lab. of Excellence GR-Ex 6, rue Alexandre Cabanel, CEDEX 15, 75739 Paris, France;
| | - Anastasia A. Anashkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov St. 32, 119991 Moscow, Russia
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Bogdanov IV, Finkina EI, Melnikova DN, Ziganshin RH, Ovchinnikova TV. Investigation of Sensitization Potential of the Soybean Allergen Gly m 4 by Using Caco-2/Immune Cells Co-Culture Model. Nutrients 2021; 13:nu13062058. [PMID: 34208504 PMCID: PMC8234232 DOI: 10.3390/nu13062058] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/07/2021] [Accepted: 06/12/2021] [Indexed: 11/23/2022] Open
Abstract
The soybean allergen Gly m 4 is known to cause severe allergic reactions including anaphylaxis, unlike other Bet v 1 homologues, which induce mainly local allergic reactions. In the present study, we aimed to investigate whether the food Bet v 1 homologue Gly m 4 can be a sensitizer of the immune system. Susceptibility to gastrointestinal digestion was assessed in vitro. Transport through intestinal epithelium was estimated using the Caco-2 monolayer. Cytokine response of different immunocompetent cells was evaluated by using Caco-2/Immune cells co-culture model. Absolute levels of 48 cytokines were measured by multiplex xMAP technology. It was shown that Gly m 4 can cross the epithelial barrier with a moderate rate and then induce production of IL-4 by mature dendritic cells in vitro. Although Gly m 4 was shown to be susceptible to gastrointestinal enzymes, some of its proteolytic fragments can selectively cross the epithelial barrier and induce production of Th2-polarizing IL-5, IL-10, and IL-13, which may point at the presence of the T-cell epitope among the crossed fragments. Our current data indicate that Gly m 4 can potentially be a sensitizer of the immune system, and intercommunication between immunocompetent and epithelial cells may play a key role in the sensitization process.
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Ovchinnikova LA, Terekhov SS, Ziganshin RH, Bagrov DV, Filimonova IN, Zalevsky AO, Lomakin YA. Reprogramming Extracellular Vesicles for Protein Therapeutics Delivery. Pharmaceutics 2021; 13:768. [PMID: 34064144 PMCID: PMC8224366 DOI: 10.3390/pharmaceutics13060768] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/07/2021] [Accepted: 05/17/2021] [Indexed: 02/06/2023] Open
Abstract
Delivering protein therapeutics specifically into target cells and tissues is a promising avenue in medicine. Advancing this process will significantly enhance the efficiency of the designed drugs. In this regard, natural membrane-based systems are of particular interest. Extracellular vesicles (EVs), being the bilayer lipid particles secreted by almost all types of cells, have several principal advantages: biocompatibility, carrier stability, and blood-brain barrier penetrability, which make them a perspective tool for protein therapeutic delivery. Here, we evaluate the engineered genetically encoded EVs produced by a human cell line, which allow efficient cargo loading. In the devised system, the protein of interest is captured by self-assembling structures, i.e., "enveloped protein nanocages" (EPN). In their turn, EPNs are encapsulated in fusogenic EVs by the overexpression of vesicular stomatitis virus G protein (VSV-G). The proteomic profiles of different engineered EVs were determined for a comprehensive evaluation of their therapeutic potential. EVs loading mediated by bio-safe Fos-Jun heterodimerization demonstrates an increased efficacy of active cargo loading and delivery into target cells. Our results emphasize the outstanding technological and biomedical potential of the engineered EV systems, including their application in adoptive cell transfer and targeted cell reprogramming.
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Affiliation(s)
- Leyla A. Ovchinnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (L.A.O.); (S.S.T.); (R.H.Z.); (I.N.F.); (A.O.Z.)
| | - Stanislav S. Terekhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (L.A.O.); (S.S.T.); (R.H.Z.); (I.N.F.); (A.O.Z.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (L.A.O.); (S.S.T.); (R.H.Z.); (I.N.F.); (A.O.Z.)
| | - Dmitriy V. Bagrov
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia;
| | - Ioanna N. Filimonova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (L.A.O.); (S.S.T.); (R.H.Z.); (I.N.F.); (A.O.Z.)
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics, Technology (National Research University), 141701 Dolgoprudny, Russia
| | - Arthur O. Zalevsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (L.A.O.); (S.S.T.); (R.H.Z.); (I.N.F.); (A.O.Z.)
| | - Yakov A. Lomakin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (L.A.O.); (S.S.T.); (R.H.Z.); (I.N.F.); (A.O.Z.)
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Pletneva NV, Maksimov EG, Protasova EA, Mamontova AV, Simonyan TR, Ziganshin RH, Lukyanov KA, Muslinkina L, Pletnev S, Bogdanov AM, Pletnev VZ. Amino acid residue at the 165th position tunes EYFP chromophore maturation. A structure-based design. Comput Struct Biotechnol J 2021; 19:2950-2959. [PMID: 34136094 PMCID: PMC8163865 DOI: 10.1016/j.csbj.2021.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 02/19/2021] [Revised: 05/06/2021] [Accepted: 05/09/2021] [Indexed: 01/07/2023] Open
Abstract
For the whole GFP family, a few cases, when a single mutation in the chromophore environment strongly inhibits maturation, were described. Here we study EYFP-F165G - a variant of the enhanced yellow fluorescent protein - obtained by a single F165G replacement, and demonstrated multiple fluorescent states represented by the minor emission peaks in blue and yellow ranges (~470 and ~530 nm), and the major peak at ~330 nm. The latter has been assigned to tryptophan fluorescence, quenched due to excitation energy transfer to the mature chromophore in the parental EYFP protein. EYFP-F165G crystal structure revealed two general independent routes of post-translational chemistry, resulting in two main states of the polypeptide chain with the intact chromophore forming triad (~85%) and mature chromophore (~15%). Our experiments thus highlighted important stereochemical role of the 165th position strongly affecting spectral characteristics of the protein. On the basis of the determined EYFP-F165G three-dimensional structure, new variants with ~ 2-fold improved brightness were engineered.
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Key Words
- Ala (A), alanine
- Arg (R), arginine
- Asn (R), asparagine
- Chromophore maturation
- DTT, dithiothreitol
- EC, extinction coefficient
- EET, excitation energy transfer
- EGFP, enhanced green fluorescent protein
- ESET, excited-state electron transfer
- EYFP
- EYFP, enhanced yellow fluorescent protein
- Excitation energy transfer
- FLIM, fluorescence lifetime imaging microscopy
- FP, fluorescent protein
- FQY, fluorescence quantum yield
- FRET, Förster resonance energy transfer
- FTIR, Fourier-transform infrared (spectroscopy
- Femtosecond spectroscopy
- Fluorescent proteins
- GFP, green fluorescent protein
- GYG, glycine-tyrosine-glycine
- Gln (Q), glutamine
- Glu (E), glutamic acid
- Gly (G), glycine
- His (H), histidine
- IVA-cloning, in vivo assembly cloning
- Leu (L), leucine
- PBS, phosphate buffered saline
- PCR, polymerase chain reaction
- Phe (F), phenylalanine
- REACh, resonance energy-accepting chromoprotein
- Ser (S), serine
- Structure-guided mutagenesis
- Trp (W), tryptophan
- Tryptophan fluorescence
- Tyr (Y), tyrosine
- Val (V), valine
- X-ray structure
- avGFP, Aequorea victoria green fluorescent protein
- sfGFP, superfolder GFP
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Affiliation(s)
- Nadya V. Pletneva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Eugene G. Maksimov
- Faculty of Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Elena A. Protasova
- Faculty of Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Anastasia V. Mamontova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Tatiana R. Simonyan
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Konstantin A. Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Liya Muslinkina
- Structural Biology Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sergei Pletnev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexey M. Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia,Corresponding authors at: Depatment of biophotonics (both), Laboratory of genetically encoded molecular tools ( A.M.B.), Laboratory of of X-ray study ( V.Z.P.).
| | - Vladimir Z. Pletnev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia,Corresponding authors at: Depatment of biophotonics (both), Laboratory of genetically encoded molecular tools ( A.M.B.), Laboratory of of X-ray study ( V.Z.P.).
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27
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Evtushenko NA, Beilin AK, Dashinimaev EB, Ziganshin RH, Kosykh AV, Perfilov MM, Rippa AL, Alpeeva EV, Vasiliev AV, Vorotelyak EA, Gurskaya NG. hTERT-Driven Immortalization of RDEB Fibroblast and Keratinocyte Cell Lines Followed by Cre-Mediated Transgene Elimination. Int J Mol Sci 2021; 22:3809. [PMID: 33916959 PMCID: PMC8067634 DOI: 10.3390/ijms22083809] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/29/2021] [Accepted: 04/03/2021] [Indexed: 12/20/2022] Open
Abstract
The recessive form of dystrophic epidermolysis bullosa (RDEB) is a crippling disease caused by impairments in the junctions of the dermis and the basement membrane of the epidermis. Using ectopic expression of hTERT/hTERT + BMI-1 in primary cells, we developed expansible cultures of RDEB fibroblasts and keratinocytes. We showed that they display the properties of their founders, including morphology, contraction ability and expression of the respective specific markers including reduced secretion of type VII collagen (C7). The immortalized keratinocytes retained normal stratification in 3D skin equivalents. The comparison of secreted protein patterns from immortalized RDEB and healthy keratinocytes revealed the differences in the contents of the extracellular matrix that were earlier observed specifically for RDEB. We demonstrated the possibility to reverse the genotype of immortalized cells to the state closer to the progenitors by the Cre-dependent hTERT switch off. Increased β-galactosidase activity and reduced proliferation of fibroblasts were shown after splitting out of transgenes. We anticipate our cell lines to be tractable models for studying RDEB from the level of single-cell changes to the evaluation of 3D skin equivalents. Our approach permits the creation of standardized and expandable models of RDEB that can be compared with the models based on primary cell cultures.
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Affiliation(s)
- Nadezhda A. Evtushenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia; (N.A.E.); (A.K.B.); (E.B.D.); (A.V.K.)
| | - Arkadii K. Beilin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia; (N.A.E.); (A.K.B.); (E.B.D.); (A.V.K.)
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 26 Vavilova Str., 119334 Moscow, Russia; (A.L.R.); (E.V.A.); (A.V.V.); (E.A.V.)
| | - Erdem B. Dashinimaev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia; (N.A.E.); (A.K.B.); (E.B.D.); (A.V.K.)
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 26 Vavilova Str., 119334 Moscow, Russia; (A.L.R.); (E.V.A.); (A.V.V.); (E.A.V.)
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (R.H.Z.); (M.M.P.)
| | - Anastasiya V. Kosykh
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia; (N.A.E.); (A.K.B.); (E.B.D.); (A.V.K.)
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 26 Vavilova Str., 119334 Moscow, Russia; (A.L.R.); (E.V.A.); (A.V.V.); (E.A.V.)
| | - Maxim M. Perfilov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (R.H.Z.); (M.M.P.)
| | - Alexandra L. Rippa
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 26 Vavilova Str., 119334 Moscow, Russia; (A.L.R.); (E.V.A.); (A.V.V.); (E.A.V.)
| | - Elena V. Alpeeva
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 26 Vavilova Str., 119334 Moscow, Russia; (A.L.R.); (E.V.A.); (A.V.V.); (E.A.V.)
| | - Andrey V. Vasiliev
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 26 Vavilova Str., 119334 Moscow, Russia; (A.L.R.); (E.V.A.); (A.V.V.); (E.A.V.)
| | - Ekaterina A. Vorotelyak
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 26 Vavilova Str., 119334 Moscow, Russia; (A.L.R.); (E.V.A.); (A.V.V.); (E.A.V.)
| | - Nadya G. Gurskaya
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia; (N.A.E.); (A.K.B.); (E.B.D.); (A.V.K.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (R.H.Z.); (M.M.P.)
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28
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Kudriaeva AA, Livneh I, Baranov MS, Ziganshin RH, Tupikin AE, Zaitseva SO, Kabilov MR, Ciechanover A, Belogurov AA. In-depth characterization of ubiquitin turnover in mammalian cells by fluorescence tracking. Cell Chem Biol 2021; 28:1192-1205.e9. [PMID: 33675681 DOI: 10.1016/j.chembiol.2021.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/29/2020] [Accepted: 02/11/2021] [Indexed: 01/01/2023]
Abstract
Despite almost 40 years having passed from the initial discovery of ubiquitin (Ub), fundamental questions related to its intracellular metabolism are still enigmatic. Here we utilized fluorescent tracking for monitoring ubiquitin turnover in mammalian cells, resulting in obtaining qualitatively new data. In the present study we report (1) short Ub half-life estimated as 4 h; (2) for a median of six Ub molecules per substrate as a dynamic equilibrium between Ub ligases and deubiquitinated enzymes (DUBs); (3) loss on average of one Ub molecule per four acts of engagement of polyubiquitinated substrate by the proteasome; (4) direct correlation between incorporation of Ub into the distinct type of chains and Ub half-life; and (5) critical influence of the single lysine residue K27 on the stability of the whole Ub molecule. Concluding, our data provide a comprehensive understanding of ubiquitin-proteasome system dynamics on the previously unreachable state of the art.
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Affiliation(s)
- Anna A Kudriaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation
| | - Ido Livneh
- Technion Integrated Cancer Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, 3109602 Haifa, Israel
| | - Mikhail S Baranov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation; Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russian Federation
| | - Rustam H Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation
| | - Alexey E Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentieva 8, 630090 Novosibirsk, Russian Federation
| | - Snizhana O Zaitseva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentieva 8, 630090 Novosibirsk, Russian Federation
| | - Aaron Ciechanover
- Technion Integrated Cancer Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, 3109602 Haifa, Israel
| | - Alexey A Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation; Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russian Federation.
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29
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Ziganshin RH, Berezina NY, Alexandrov PL, Ryabinin VV, Buzhilova AP. Optimization of Method for Human Sex Determination Using Peptidome Analysis of Teeth Enamel from Teeth of Different Biological Generation, Archeological Age, and Degrees of Taphonomic Preservation. Biochemistry (Mosc) 2021; 85:614-622. [PMID: 32571191 DOI: 10.1134/s0006297920050107] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Determination of biological sex to human remains is a fundamental requirement in anthropological, archeological, and forensic anthropological studies. Sex determination based on morphological criteria is significantly limited in the cases of juvenile remains and adult skeletons in a poor state of preservation. Regular attempts have been made to use alternative techniques to resolve this issue, including analysis of tooth enamel peptides by liquid chromatography/mass spectrometry. Optimization of this method involving acid etching of tooth enamel for 10 min followed by desalting of the products of etching on SDB-RPS StageTips microcolumns and analysis of desalted sample (1/3) by liquid chromatography/mass spectrometry allowed reliable sex determination to fossil remains within a wide range of archeological and biological ages without destructing analyzed teeth. Increasing the duration of enamel etching ensured a 2 to 3-fold increase in the total number of identified peptides and, more importantly, in the number of identified fragments of amelogenin Y isoform specific for male teeth, which facilitated reliable sex determination of fossil remains. The suggested technique was tested with 8 permanent and 15 deciduous teeth of different archaeological age and different degree of preservation. Two amelogenin Y-specific peptide sequences were identified. One of these peptides [SM(+15.99)IRPPYS)] was found in all male-derived samples without exception; the other peptide [IRPPYSS(+79.97)], which contained phosphorylated Ser66 residue, was found only in the enamel from deciduous teeth, which suggests that phosphorylation of Ser66 plays a role in the enamel formation in deciduous teeth.
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Affiliation(s)
- R H Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - N Ya Berezina
- Anuchin Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, 125009, Russia
| | - P L Alexandrov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - V V Ryabinin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - A P Buzhilova
- Anuchin Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, 125009, Russia
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30
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Albakova Z, Siam MKS, Sacitharan PK, Ziganshin RH, Ryazantsev DY, Sapozhnikov AM. Extracellular heat shock proteins and cancer: New perspectives. Transl Oncol 2020; 14:100995. [PMID: 33338880 PMCID: PMC7749402 DOI: 10.1016/j.tranon.2020.100995] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [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: 10/09/2020] [Revised: 11/08/2020] [Accepted: 12/07/2020] [Indexed: 02/07/2023] Open
Abstract
High expression of extracellular heat shock proteins (HSPs) indicates highly aggressive tumors. HSP profiling of extracellular vesicles (EVs) derived from various biological fluids and released by immune cells may open new perspectives for an identification of diagnostic, prognostic and predictive biomarkers of cancer. Identification of specific microRNAs targeting HSPs in EVs may be a promising strategy for the discovery of novel biomarkers of cancer.
Heat shock proteins (HSPs) are a large family of molecular chaperones aberrantly expressed in cancer. The expression of HSPs in tumor cells has been shown to be implicated in the regulation of apoptosis, immune responses, angiogenesis and metastasis. Given that extracellular vesicles (EVs) can serve as potential source for the discovery of clinically useful biomarkers and therapeutic targets, it is of particular interest to study proteomic profiling of HSPs in EVs derived from various biological fluids of cancer patients. Furthermore, a divergent expression of circulating microRNAs (miRNAs) in patient samples has opened new opportunities in exploiting miRNAs as diagnostic tools. Herein, we address the current literature on the expression of extracellular HSPs with particular interest in HSPs in EVs derived from various biological fluids of cancer patients and different types of immune cells as promising targets for identification of clinical biomarkers of cancer. We also discuss the emerging role of miRNAs in HSP regulation for the discovery of blood-based biomarkers of cancer. We outline the importance of understanding relationships between various HSP networks and co-chaperones and propose the model for identification of HSP signatures in cancer. Elucidating the role of HSPs in EVs from the proteomic and miRNAs perspectives may provide new opportunities for the discovery of novel biomarkers of cancer.
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Affiliation(s)
- Zarema Albakova
- Department of Biology, Lomonosov Moscow State University, 199192 Moscow, Russia.
| | | | - Pradeep Kumar Sacitharan
- The Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom; Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Rustam H Ziganshin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
| | - Dmitriy Y Ryazantsev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
| | - Alexander M Sapozhnikov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
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31
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Rekstina VV, Sabirzyanova TA, Sabirzyanov FA, Adzhubei AA, Tkachev YV, Kudryashova IB, Snalina NE, Bykova AA, Alessenko AV, Ziganshin RH, Kuznetsov SA, Kalebina TS. The Post-Translational Modifications, Localization, and Mode of Attachment of Non-Covalently Bound Glucanosyltransglycosylases of Yeast Cell Wall as a Key to Understanding their Functioning. Int J Mol Sci 2020; 21:ijms21218304. [PMID: 33167499 PMCID: PMC7663962 DOI: 10.3390/ijms21218304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/26/2020] [Accepted: 10/30/2020] [Indexed: 01/27/2023] Open
Abstract
Glucan linked to proteins is a natural mega-glycoconjugate (mGC) playing the central role as a structural component of a yeast cell wall (CW). Regulation of functioning of non-covalently bound glucanosyltransglycosylases (ncGTGs) that have to remodel mGC to provide CW extension is poorly understood. We demonstrate that the main ncGTGs Bgl2 and Scw4 have phosphorylated and glutathionylated residues and are represented in CW as different pools of molecules having various firmness of attachment. Identified pools contain Bgl2 molecules with unmodified peptides, but differ from each other in the presence and combination of modified ones, as well as in the presence or absence of other CW proteins. Correlation of Bgl2 distribution among pools and its N-glycosylation was not found. Glutathione affects Bgl2 conformation, probably resulting in the mode of its attachment and enzymatic activity. Bgl2 from the pool of unmodified and monophosphorylated molecules demonstrates the ability to fibrillate after isolation from CW. Revealing of Bgl2 microcompartments and their mosaic arrangement summarized with the results obtained give the evidence that the functioning of ncGTGs in CW can be controlled by reversible post-translational modifications and facilitated due to their compact localization. The hypothetical scheme of distribution of Bgl2 inside CW is represented.
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Affiliation(s)
- Valentina V. Rekstina
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (V.V.R.); (T.A.S.); (F.A.S.); (I.B.K.); (A.A.B.)
| | - Tatyana A. Sabirzyanova
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (V.V.R.); (T.A.S.); (F.A.S.); (I.B.K.); (A.A.B.)
| | - Fanis A. Sabirzyanov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (V.V.R.); (T.A.S.); (F.A.S.); (I.B.K.); (A.A.B.)
| | - Alexei A. Adzhubei
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (A.A.A.); (Y.V.T.)
| | - Yaroslav V. Tkachev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (A.A.A.); (Y.V.T.)
| | - Irina B. Kudryashova
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (V.V.R.); (T.A.S.); (F.A.S.); (I.B.K.); (A.A.B.)
| | - Natalia E. Snalina
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia; (N.E.S.); (A.V.A.)
| | - Anastasia A. Bykova
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (V.V.R.); (T.A.S.); (F.A.S.); (I.B.K.); (A.A.B.)
| | - Alice V. Alessenko
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia; (N.E.S.); (A.V.A.)
| | - Rustam H. Ziganshin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia;
| | - Sergei A. Kuznetsov
- Institute of Biological Sciences, University of Rostock, 18059 Rostock, Germany;
| | - Tatyana S. Kalebina
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (V.V.R.); (T.A.S.); (F.A.S.); (I.B.K.); (A.A.B.)
- Correspondence: ; Tel.: +7-(495)-939-50-75
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Semashko TA, Evsyutina DV, Ladygina VG, Zubov AI, Rakovskaya IV, Kovalchuk SI, Ziganshin RH, Pobeguts OV. Data on proteome of Mycoplasma hominis cultivated with arginine or thymidine as a carbon source. Data Brief 2020; 31:106034. [PMID: 32760766 PMCID: PMC7390850 DOI: 10.1016/j.dib.2020.106034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 05/06/2020] [Revised: 07/08/2020] [Accepted: 07/13/2020] [Indexed: 11/28/2022] Open
Abstract
Mycoplasma hominis is an opportunistic bacterium that can cause acute and chronic infections of the urogenital tract. This bacterium, like all other Mycoplasma species, is characterized by the reduced genome size, and, consequently, reduction of the main metabolic pathways. M. hominis cells cannot effectively use glucose as a carbon and energy source. Therefore, the main pathway of energy metabolism is the arginine dihydrolase pathway. However, several bacteria can use nucleosides as the sole energy source. Biochemical studies using Salmonella typhimurium have shown that three enzymes (thymidine phosphorylase, phosphopentose mutase and deoxyribose-phosphate aldolase) are involved in the thymidine catabolic pathway. All these enzymes are present in M. hominis. For understanding changes in the energy metabolism of M. hominis we performed shotgun proteome analysis of M. hominis cells in liquid medium with arginine or thymidine as a carbon source. LC-MS analysis was performed with an Ultimate 3000 Nano LC System (Thermo Fisher Scientific) coupled to a Q Exactive HF benchtop Orbitrap mass spectrometer (Thermo Fisher Scientific) via a nanoelectrospray source (Thermo Fisher Scientific). Data are available via ProteomeXchange with identifier PXD018714 (https://www.ebi.ac.uk/pride/archive/projects/PXD018714).
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Affiliation(s)
- Tatiana A Semashko
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Daria V Evsyutina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Valentina G Ladygina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Aleksandr I Zubov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Irina V Rakovskaya
- Gamaleya National Research Center of Epidemiology and Microbiology, Moscow, Russia
| | | | | | - Olga V Pobeguts
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
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Babenko VV, Ziganshin RH, Weise C, Dyachenko I, Shaykhutdinova E, Murashev AN, Zhmak M, Starkov V, Hoang AN, Tsetlin V, Utkin Y. Novel Bradykinin-Potentiating Peptides and Three-Finger Toxins from Viper Venom: Combined NGS Venom Gland Transcriptomics and Quantitative Venom Proteomics of the Azemiops feae Viper. Biomedicines 2020; 8:biomedicines8080249. [PMID: 32731454 PMCID: PMC7460416 DOI: 10.3390/biomedicines8080249] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 06/29/2020] [Revised: 07/24/2020] [Accepted: 07/24/2020] [Indexed: 01/22/2023] Open
Abstract
Feae's viper Azemipos feae belongs to the Azemiopinae subfamily of the Viperidae family. The effects of Viperidae venoms are mostly coagulopathic with limited neurotoxicity manifested by phospholipases A2. From A. feae venom, we have earlier isolated azemiopsin, a novel neurotoxin inhibiting the nicotinic acetylcholine receptor. To characterize other A. feae toxins, we applied label-free quantitative proteomics, which revealed 120 unique proteins, the most abundant being serine proteinases and phospholipases A2. In total, toxins representing 14 families were identified, among which bradykinin-potentiating peptides with unique amino acid sequences possessed biological activity in vivo. The proteomic analysis revealed also basal (commonly known as non-conventional) three-finger toxins belonging to the group of those possessing neurotoxic activity. This is the first indication of the presence of three-finger neurotoxins in viper venom. In parallel, the transcriptomic analysis of venom gland performed by Illumina next-generation sequencing further revealed 206 putative venom transcripts. Together, the study unveiled the venom proteome and venom gland transciptome of A. feae, which in general resemble those of other snakes from the Viperidae family. However, new toxins not found earlier in viper venom and including three-finger toxins and unusual bradykinin-potentiating peptides were discovered.
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Affiliation(s)
- Vladislav V. Babenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia;
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (R.H.Z.); (M.Z.); (V.S.); (V.T.)
| | - Christoph Weise
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany;
| | - Igor Dyachenko
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, 142290 Moscow Region, Russia; (I.D.); (E.S.); (A.N.M.)
| | - Elvira Shaykhutdinova
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, 142290 Moscow Region, Russia; (I.D.); (E.S.); (A.N.M.)
| | - Arkady N. Murashev
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, 142290 Moscow Region, Russia; (I.D.); (E.S.); (A.N.M.)
| | - Maxim Zhmak
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (R.H.Z.); (M.Z.); (V.S.); (V.T.)
| | - Vladislav Starkov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (R.H.Z.); (M.Z.); (V.S.); (V.T.)
| | - Anh Ngoc Hoang
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, Ho Chi Minh City 700000, Vietnam;
| | - Victor Tsetlin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (R.H.Z.); (M.Z.); (V.S.); (V.T.)
| | - Yuri Utkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (R.H.Z.); (M.Z.); (V.S.); (V.T.)
- Correspondence: or ; Tel.: +7-495-336-6522
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Kryukova EV, Vulfius CA, Ziganshin RH, Andreeva TV, Starkov VG, Tsetlin VI, Utkin YN. Snake C-type lectin-like proteins inhibit nicotinic acetylcholine receptors. J Venom Res 2020; 10:23-29. [PMID: 33024544 PMCID: PMC7512478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 10/26/2022]
Abstract
Venoms of viperid snakes affect mostly hemostasis, while C-type lectin-like proteins (CTLPs), one of the main components of viperid venoms, act as anticoagulants, procoagulants, or agonists/antagonists of platelet activation. However, we have shown earlier that CTLPs from the saw-scaled viper Echis multisquamatus, called emunarecins EM1 and EM2, were able to inhibit nicotinic acetylcholine receptors (nAChRs) in neurons of a pond snail (Lymnaea stagnalis). Here we analysed the structure of the emunarecins by mass spectrometry and report that EM1 and EM2 inhibit fluorescent α-bungarotoxin binding to both muscle-type nAChRs from Torpedo californica and human neuronal α7 nAChRs. EM1 at 23µM and EM2 at 9µM almost completely prevented fluorecsent α-bungarotoxin binding to muscle-type nAChRs. Interaction with human neuronal α7 nAChR was weaker; EM1 at the concentration of 23µM blocked the α-bungarotoxin binding only by about 40% and EM2 at 9µM by about 20%. The efficiency of the EM2 interaction with nAChRs was comparable to that of a non-conventional toxin, WTX, from Naja kaouthia cobra venom. Together with the data obtained earlier, these results show that CTLPs may represent new nAChR ligands.
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Affiliation(s)
- Elena V Kryukova
- 1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Catherine A Vulfius
- 2Institute of Cell Biophysics Russian Academy of Sciences, 3 Institutskaya Street, Pushchino Moscow region, 142290, Russia
| | - Rustam H Ziganshin
- 1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Tatyana V Andreeva
- 1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Vladislav G Starkov
- 1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Victor I Tsetlin
- 1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Yuri N Utkin
- 1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117997, Russia,*Correspondence to: Yuri Utkin, E-mail: ; , Tel/Fax: +74953366522
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Kuleshina ON, Kruykova EV, Cheremnykh EG, Kozlov LV, Andreeva TV, Starkov VG, Osipov AV, Ziganshin RH, Tsetlin VI, Utkin YN. Screening Snake Venoms for Toxicity to Tetrahymena Pyriformis Revealed Anti-Protozoan Activity of Cobra Cytotoxins. Toxins (Basel) 2020; 12:toxins12050325. [PMID: 32429047 PMCID: PMC7290292 DOI: 10.3390/toxins12050325] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 12/11/2022] Open
Abstract
Snake venoms possess lethal activities against different organisms, ranging from bacteria to higher vertebrates. Several venoms were shown to be active against protozoa, however, data about the anti-protozoan activity of cobra and viper venoms are very scarce. We tested the effects of venoms from several snake species on the ciliate Tetrahymena pyriformis. The venoms tested induced T. pyriformis immobilization, followed by death, the most pronounced effect being observed for cobra Naja sumatrana venom. The active polypeptides were isolated from this venom by a combination of gel-filtration, ion exchange and reversed-phase HPLC and analyzed by mass spectrometry. It was found that these were cytotoxins of the three-finger toxin family. The cytotoxins from several cobra species were tested and manifested toxicity for infusorians. Light microscopy revealed that, because of the cytotoxin action, the infusorians’ morphology was changed greatly, from teardrop-like to an almost spherical shape, this alteration being accompanied by a leakage of cell contents. Fluorescence microscopy showed that the fluorescently labelled cytotoxin 2 from cobra N. oxiana was localized mainly at the membrane of killed infusorians, indicating that cytotoxins may kill T. pyriformis by causing membrane rupture. This work is the first evidence of the antiprotozoal activity of cobra venom cytotoxins, as demonstrated by the example of the ciliate T. pyriformis.
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Affiliation(s)
- Olga N. Kuleshina
- Gabrichevsky Research Institute of Epidemiology and Microbiology, ul. Admirala Makarova 10, Moscow 125212, Russia;
| | - Elena V. Kruykova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, ul. Miklukho-Maklaya 16/10, Moscow 117997, Russia; (E.V.K.); (T.V.A.); (V.G.S.); (A.V.O.); (R.H.Z.); (V.I.T.)
| | - Elena G. Cheremnykh
- Mental Health Research Centre, Kashirskoye shosse, 34, Moscow 115522, Russia;
| | - Leonid V. Kozlov
- Gabrichevsky Research Institute of Epidemiology and Microbiology, ul. Admirala Makarova 10, Moscow 125212, Russia;
| | - Tatyana V. Andreeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, ul. Miklukho-Maklaya 16/10, Moscow 117997, Russia; (E.V.K.); (T.V.A.); (V.G.S.); (A.V.O.); (R.H.Z.); (V.I.T.)
| | - Vladislav G. Starkov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, ul. Miklukho-Maklaya 16/10, Moscow 117997, Russia; (E.V.K.); (T.V.A.); (V.G.S.); (A.V.O.); (R.H.Z.); (V.I.T.)
| | - Alexey V. Osipov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, ul. Miklukho-Maklaya 16/10, Moscow 117997, Russia; (E.V.K.); (T.V.A.); (V.G.S.); (A.V.O.); (R.H.Z.); (V.I.T.)
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, ul. Miklukho-Maklaya 16/10, Moscow 117997, Russia; (E.V.K.); (T.V.A.); (V.G.S.); (A.V.O.); (R.H.Z.); (V.I.T.)
| | - Victor I. Tsetlin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, ul. Miklukho-Maklaya 16/10, Moscow 117997, Russia; (E.V.K.); (T.V.A.); (V.G.S.); (A.V.O.); (R.H.Z.); (V.I.T.)
| | - Yuri N. Utkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, ul. Miklukho-Maklaya 16/10, Moscow 117997, Russia; (E.V.K.); (T.V.A.); (V.G.S.); (A.V.O.); (R.H.Z.); (V.I.T.)
- Correspondence: or ; Tel.: +7-495-3366522
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Zayulina KS, Kochetkova TV, Piunova UE, Ziganshin RH, Podosokorskaya OA, Kublanov IV. Novel Hyperthermophilic Crenarchaeon Thermofilum adornatum sp. nov. Uses GH1, GH3, and Two Novel Glycosidases for Cellulose Hydrolysis. Front Microbiol 2020; 10:2972. [PMID: 31998263 PMCID: PMC6965361 DOI: 10.3389/fmicb.2019.02972] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 11/05/2019] [Accepted: 12/10/2019] [Indexed: 01/16/2023] Open
Abstract
A novel hyperthermophilic, anaerobic filamentous archaeon, Thermofilum adornatum strain 1910bT, is capable of growing with cellulose as its sole carbon and energy source. This strain was isolated from a terrestrial hot spring in Kamchatka, Russia. The isolate 1910bT grew optimally at a temperature of 80°C and a pH of 5.5-6.0, producing cell-bound inducible cellulases. During genome analysis, genes, encoding various glycosidases (GHs) involved in oligo- and polysaccharide hydrolysis and genes for the fermentation of sugars were identified. No homologs of currently known cellulase families were found among the GHs encoded by the 1910bT genome, suggesting that novel proteins are involved. To figure this out, a proteomic analysis of cells grown on cellulose or pyruvate (as a control) was performed. Both in-depth genomic and proteomic analyses revealed four proteins (Cel25, Cel30, Cel40, and Cel45) that were the most likely to be involved in the cellulose hydrolysis in this archaeon. Two of these proteins (Cel30 and Cel45) were hypothetical according to genome analysis, while the other two (Cel25 and Cel40) have GH3 and GH1 domains, respectively. The respective genes were heterologously expressed in Escherichia coli BL21 (DE3), and enzymatic activities of recombinant proteins were measured with carboxymethyl cellulose (CMC), Avicel and cellobiose as substrates. It was revealed that the Cel30 and Cel25 proteins were likely exoglucanases with side beta-glucosidase and endoglucanase activities, that Cel40 was a multifunctional glucanase capable of hydrolyzing beta-1,4-glucosides of various lengths, and that Cel45 was an endoglucanase with side exoglucanase activity. Taking into account that the cellulolytic activity of T. adornatum 1910bT surface protein fractions was inducible, that recombinant Cel25 and Cel30 were much less active than Cel40 and Cel45, and that their gene expressions were (almost) non-induced by CMC, we suggest that Cel40 and Cel45 play a major role in the degradation of cellulose, while Cel25 and Cel30 act only as accessory enzymes.
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Affiliation(s)
- Kseniya S. Zayulina
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana V. Kochetkova
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Ulyana E. Piunova
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Olga A. Podosokorskaya
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya V. Kublanov
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
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Rekstina VV, Bykova AA, Ziganshin RH, Kalebina TS. GPI-Modified Proteins Non-covalently Attached to Saccharomyces cerevisiae Yeast Cell Wall. Biochemistry (Mosc) 2019; 84:1513-1520. [PMID: 31870255 DOI: 10.1134/s0006297919120101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Yeast cell wall GPI-anchored proteins lack the lipid part of the anchor and are covalently bound to the high-molecular-weight polysaccharides glucan and/or chitin through the mannose residues. They perform many functions, including participation in the cell wall molecular ensemble formation and providing cell resistance to stress. In this work, we identified a pool of GPI-modified proteins firmly bound to the cell wall by non-covalent interactions with the high-molecular-weight structural polysaccharides. We believe that the detected proteins are intermediate forms in the processing of the cell wall GPI-proteins, since they had already lost the lipid part of the GPI anchor and are absent in the lipoprotein fraction extracted according to Folch, but were not yet incorporated into the cell wall by the covalent binding to high-molecular-weight polysaccharides because they could be extracted into water by heating of delipidized cell walls. This group of previously unknown proteins might be present in the cell wall in a form of lipid-associated microcompartments represented by transport vesicles recently found in yeast. GPI-modified proteins non-covalently attached to the high-molecular-weight polysaccharides were found in the cell walls of both the parent strain and yeast devoid of glucanosyltransglycosylase Bgl2, which indicates that the pathway of their incorporation into the cell wall is independent on this enzyme.
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Affiliation(s)
- V V Rekstina
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia
| | - A A Bykova
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia
| | - R H Ziganshin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - T S Kalebina
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia.
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Tran TV, Siniavin AE, Hoang AN, Le MTT, Pham CD, Phung TV, Nguyen KC, Ziganshin RH, Tsetlin VI, Weng CF, Utkin YN. Phospholipase A 2 from krait Bungarus fasciatus venom induces human cancer cell death in vitro. PeerJ 2019; 7:e8055. [PMID: 31824756 PMCID: PMC6896944 DOI: 10.7717/peerj.8055] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 04/12/2019] [Accepted: 10/17/2019] [Indexed: 02/06/2023] Open
Abstract
Background Snake venoms are the complex mixtures of different compounds manifesting a wide array of biological activities. The venoms of kraits (genus Bungarus, family Elapidae) induce mainly neurological symptoms; however, these venoms show a cytotoxicity against cancer cells as well. This study was conducted to identify in Bungarus fasciatus venom an active compound(s) exerting cytotoxic effects toward MCF7 human breast cancer cells and A549 human lung cancer cells. Methods The crude venom of B. fasciatus was separated by gel-filtration on Superdex HR 75 column and reversed phase HPLC on C18 column. The fractions obtained were screened for cytotoxic effect against MCF7, A549, and HK2 cell lines using colorimetric assay with the tetrazolium dye MTT- 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide. The primary structure of active protein was established by ultra high resolution LC-MS/MS. The molecular mechanism of the isolated protein action on MCF7 cells was elucidated by flow cytometry. Results MTT cell viability assays of cancer cells incubated with fractions isolated from B. fasciatus venom revealed a protein with molecular mass of about 13 kDa possessing significant cytotoxicity. This protein manifested the dose and time dependent cytotoxicity for MCF7 and A549 cell lines while showed no toxic effect on human normal kidney HK2 cells. In MCF7, flow cytometry analysis revealed a decrease in the proportion of Ki-67 positive cells. As Ki-67 protein is a cellular marker for proliferation, its decline indicates the reduction in the proliferation of MCF7 cells treated with the protein. Flow cytometry analysis of MCF7 cells stained with propidium iodide and Annexin V conjugated with allophycocyanin showed that a probable mechanism of cell death is apoptosis. Mass spectrometric studies showed that the cytotoxic protein was phospholipase A2. The amino acid sequence of this enzyme earlier was deduced from cloned cDNA, and in this work it was isolated from the venom as a protein for the first time. It is also the first krait phospholipase A2 manifesting the cytotoxicity for cancer cells.
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Affiliation(s)
- Thien V Tran
- Tra Vinh University, Tra Vinh City, Vietnam.,Graduate University of Science and Technology VAST, Hanoi, Vietnam
| | - Andrei E Siniavin
- Laboratory of Molecular Toxinology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russian Federation
| | - Anh N Hoang
- Graduate University of Science and Technology VAST, Hanoi, Vietnam.,Institute of Applied Materials Science VAST, Ho Chi Minh City, Vietnam
| | - My T T Le
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Chuong D Pham
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Trung V Phung
- Center for Research and Technology Transfer VAST, Ho Chi Minh City, Vietnam
| | - Khoa C Nguyen
- Graduate University of Science and Technology VAST, Hanoi, Vietnam.,Institute of Applied Materials Science VAST, Ho Chi Minh City, Vietnam
| | - Rustam H Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russian Federation
| | - Victor I Tsetlin
- Department of Molecular Neuroimmune Signalling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russian Federation
| | - Ching-Feng Weng
- Department of Life Science and Institute of Biotechnology, National Dong Hwa University, Shoufeng, Hualien, Taiwan
| | - Yuri N Utkin
- Laboratory of Molecular Toxinology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russian Federation
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Kryukova EV, Potapenko AS, Andreeva TV, Ivanov IA, Ryabinin VV, Ziganshin RH, Starkov VG, Ayvazyan NM, Tsetlin VI, Utkin YN. Dimeric Disintegrins from the Steppe Viper V. ursinii Venom. DOKL BIOCHEM BIOPHYS 2019; 488:338-341. [PMID: 31768855 DOI: 10.1134/s1607672919050132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Indexed: 11/22/2022]
Abstract
Four dimeric disintegrins were isolated from the venom of the steppe viper V. ursinii using liquid chromatography. Disintegrins prevented adhesion of MCF7 cells to fibronectin, which indicates their interaction with integrin receptors of the αVβ1 type. According to mass spectrometry data, the molar masses of disintegrins are about 14 kDa. The method of peptide mapping established the structure of a new heterodimeric disintegrin weighing 13 995.5 Da and shows that it belongs to the class of RGD/KGD-containing disintegrins.
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Affiliation(s)
- E V Kryukova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia.
| | - A S Potapenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
| | - T V Andreeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
| | - I A Ivanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
| | - V V Ryabinin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
| | - R H Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
| | - V G Starkov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
| | - N M Ayvazyan
- Orbeli Institute of Physiology, National Academy of Sciences of the Republic of Armenia, 0019, Yerevan, Armenia
| | - V I Tsetlin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
| | - Yu N Utkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
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40
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Alekseeva MG, Boyko KM, Nikolaeva AY, Mavletova DA, Rudakova NN, Zakharevich NV, Korzhenevskiy DA, Ziganshin RH, Popov VO, Danilenko VN. Identification, functional and structural characterization of novel aminoglycoside phosphotransferase APH(3″)-Id from Streptomyces rimosus subsp. rimosus ATCC 10970. Arch Biochem Biophys 2019; 671:111-122. [DOI: 10.1016/j.abb.2019.06.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 06/21/2019] [Accepted: 06/22/2019] [Indexed: 01/03/2023]
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Kostin NN, Bobik TV, Shurdova EM, Ziganshin RH, Surina EA, Shagin DA, Shagina IA, Knorre VD, Isaev VA, Rudenskaya GN, Gabibov AG, Smirnov IV. Cloning and characterization of serpin from red king crab Paralithodes camtschaticus. Fish Shellfish Immunol 2018; 81:99-107. [PMID: 30006043 DOI: 10.1016/j.fsi.2018.07.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 03/14/2018] [Revised: 06/28/2018] [Accepted: 07/09/2018] [Indexed: 06/08/2023]
Abstract
Serpins are a family of serine protease inhibitors that are involved in numerous physiological processes and are known to regulate innate immunity pathways. To advance our understanding of their role in P. camtschaticus, a commercially significant species, we cloned and characterized a serpin from this species, designated serpin PC, that has anticoagulant and anticomplement effects on human blood. We found that serpin PC is a secreted protein with a typical serpin-like primary structure that is similar to other known crustacean serpins. Recombinant serpin PC was found to have inhibitory activity against R/K-specific bovine cationic trypsin. The reaction proceeds through the formation of a stable covalent complex of peptidase with P1 residue R383 of serpin PC. This interaction is characterized by a relatively high overall inhibition constant kass=(2.3 ± 0.7) × 106 M-1s-1 and an SI of 4.7 ± 0.8. Protein localization by western blotting showed that serpin PC is present in the muscles and, to a lesser extent, the heart, whereas it is transcribed predominantly in hemocytes and the heart. Through peptidase activity profiling of hemocytes and plasma, we found that serpin PC inhibits at least two R/K-specific activities and showed that it inhibits phenoloxidase (PO) activity induction in hemocytes.
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Affiliation(s)
- N N Kostin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - T V Bobik
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - E M Shurdova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - R H Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - E A Surina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - D A Shagin
- Central Research Institute of Epidemiology, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | - I A Shagina
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - V D Knorre
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - V A Isaev
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - G N Rudenskaya
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - A G Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - I V Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
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Sidorenko SV, Ziganshin RH, Luneva OG, Deev LI, Alekseeva NV, Maksimov GV, Grygorczyk R, Orlov SN. Proteomics-based identification of hypoxia-sensitive membrane-bound proteins in rat erythrocytes. J Proteomics 2018; 184:25-33. [DOI: 10.1016/j.jprot.2018.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 06/01/2018] [Accepted: 06/11/2018] [Indexed: 12/25/2022]
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Dergousova EA, Petrushanko IY, Klimanova EA, Mitkevich VA, Ziganshin RH, Lopina OD, Makarov AA. [Enhancement of Na,K-ATPase Activity as a Result of Removal of Redox Modifications from Cysteine Residues of the al Subunit: the Effect of Reducing Agents]. Mol Biol (Mosk) 2018; 52:289-293. [PMID: 29695697 DOI: 10.7868/s002689841802012x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 12/06/2016] [Indexed: 11/23/2022]
Abstract
Na,K-ATPase is a transmembrane enzyme that creates a gradient of sodium and potassium, which is necessary for the viability of animal cells. The activity of Na,K-ATPase depends on the redox status of the cell, decreasing with oxidative stress and hypoxia. Previously, we have shown that the key role in the redox sensitivity of Na,K-ATPase is played by the regulatory glutathionylation of cysteine residues of the catalytic alpha subunit, which leads to the inhibition of the enzyme. In this study, the effect of reducing agents (DTT, ME, TCEP) on the level of glutathionylation of the alpha subunit of Na,K-ATPase from rabbit kidneys and the enzyme activity has been evaluated. We have found that the reducing agents partially deglutathionylate the protein, which leads to its activation. It was impossible to completely remove glutathionylation from the native rabbit kidney protein. The treatment of a partially denatured protein on the PVDF membrane with reducing agents (TCEP, NaBH4) also does not lead to the complete deglutathionylation of the protein. The obtained data indicate that Na,K-ATPase isolated from rabbit kidneys has both regulatory and basal glutathionylation, which appears to play an important role in the redox regulation of the function of Na, K-ATPase in mammalian tissues.
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Affiliation(s)
- E A Dergousova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia.,Faculty of Biology, Moscow State University, Moscow, 119991 Russia
| | - I Yu Petrushanko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - E A Klimanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia.,Faculty of Biology, Moscow State University, Moscow, 119991 Russia
| | - V A Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - R H Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
| | - O D Lopina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia.,Faculty of Biology, Moscow State University, Moscow, 119991 Russia
| | - A A Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia.,
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Dergousova EA, Petrushanko IY, Klimanova EA, Mitkevich VA, Ziganshin RH, Lopina OD, Makarov AA. Effect of Reduction of Redox Modifications of Cys-Residues in the Na,K-ATPase α1-Subunit on Its Activity. Biomolecules 2017; 7:E18. [PMID: 28230807 PMCID: PMC5372730 DOI: 10.3390/biom7010018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 02/03/2017] [Accepted: 02/06/2017] [Indexed: 01/01/2023] Open
Abstract
Sodium-potassium adenosine triphosphatase (Na,K-ATPase) creates a gradient of sodium and potassium ions necessary for the viability of animal cells, and it is extremely sensitive to intracellular redox status. Earlier we found that regulatory glutathionylation determines Na,K-ATPase redox sensitivity but the role of basal glutathionylation and other redox modifications of cysteine residues is not clear. The purpose of this study was to detect oxidized, nitrosylated, or glutathionylated cysteine residues in Na,K-ATPase, evaluate the possibility of removing these modifications and assess their influence on the enzyme activity. To this aim, we have detected such modifications in the Na,K-ATPase α1-subunit purified from duck salt glands and tried to eliminate them by chemical reducing agents and the glutaredoxin1/glutathione reductase enzyme system. Detection of cysteine modifications was performed using mass spectrometry and Western blot analysis. We have found that purified Na,K-ATPase α1-subunit contains glutathionylated, nitrosylated, and oxidized cysteines. Chemical reducing agents partially eliminate these modifications that leads to the slight increase of the enzyme activity. Enzyme system glutaredoxin/glutathione reductase, unlike chemical reducing agents, produces significant increase of the enzyme activity. At the same time, the enzyme system deglutathionylates native Na,K-ATPase to a lesser degree than chemical reducing agents. This suggests that the enzymatic reducing system glutaredoxin/glutathione reductase specifically affects glutathionylation of the regulatory cysteine residues of Na,K-ATPase α1-subunit.
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Affiliation(s)
- Elena A Dergousova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov St, 32, Moscow 119991, Russia.
- Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory, 1/12, Moscow 119234, Russia.
| | - Irina Yu Petrushanko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov St, 32, Moscow 119991, Russia.
| | - Elizaveta A Klimanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov St, 32, Moscow 119991, Russia.
- Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory, 1/12, Moscow 119234, Russia.
| | - Vladimir A Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov St, 32, Moscow 119991, Russia.
| | - Rustam H Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, Moscow 117997, Russia.
| | - Olga D Lopina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov St, 32, Moscow 119991, Russia.
- Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory, 1/12, Moscow 119234, Russia.
| | - Alexander A Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov St, 32, Moscow 119991, Russia.
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Belogurov AA, Ivanova OM, Lomakin YA, Ziganshin RH, Vaskina MI, Knorre VD, Klimova EA, Gabibov AG, Ivanov VT, Govorun VM. Mediators and Biomarkers of Inflammation in Meningitis: Cytokine and Peptidome Profiling of Cerebrospinal Fluid. Biochemistry (Mosc) 2017; 81:1293-1302. [PMID: 27914455 DOI: 10.1134/s0006297916110079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Differential diagnosis of bacterial and viral meningitis is an urgent problem of the modern clinical medicine. Early and accurate detection of meningitis etiology largely determines the strategy of its treatment and significantly increases the likelihood of a favorable outcome for the patient. In the present work, we analyzed the peptidome and cytokine profiles of cerebrospinal fluid (CSF) of 17 patients with meningitis of bacterial and viral etiology and of 20 neurologically healthy controls. In addition to the identified peptides (potential biomarkers), we found significant differences in the cytokine status of the CSF of the patients. We found that cut-off of 100 pg/ml of IL-1β, TNF, and GM-CSF levels discriminates bacterial and viral meningitis with 100% specificity and selectivity. We demonstrated for the first time the reduction in the level of two cytokines, IL-13 and GM-CSF, in the CSF of patients with viral meningitis in comparison with the controls. The decrease in GM-CSF level in the CSF of patients with viral meningitis can be explained by a disproportionate increase in the levels of cytokines IL-10, IFN-γ, and IL-4, which inhibit the GM-CSF expression, whereas IL-1, IL-6, and TNF activate it. These observations suggest an additional approach for differential diagnosis of bacterial and viral meningitis based on the normalized ratio IL-10/IL-1β and IL-10/TNF > 1, as well as on the ratio IFN-γ/IL-1β and IFN-γ/TNF < 0.1. Our findings extend the panel of promising clinical and diagnostic biomarkers of viral and bacterial meningitis and reveal opposite changes in the cytokine expression in meningitis due to compensatory action of pro- and antiinflammatory factors.
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Affiliation(s)
- A A Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia.
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Ziganshin RH, Ivanova OM, Lomakin YA, Belogurov AA, Kovalchuk SI, Azarkin IV, Arapidi GP, Anikanov NA, Shender VO, Piradov MA, Suponeva NA, Vorobyeva AA, Gabibov AG, Ivanov VT, Govorun VM. The Pathogenesis of the Demyelinating Form of Guillain-Barre Syndrome (GBS): Proteo-peptidomic and Immunological Profiling of Physiological Fluids. Mol Cell Proteomics 2016; 15:2366-78. [PMID: 27143409 PMCID: PMC4937510 DOI: 10.1074/mcp.m115.056036] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 04/27/2016] [Indexed: 01/06/2023] Open
Abstract
Acute inflammatory demyelinating polyneuropathy (AIDP) - the main form of Guillain-Barre syndrome-is a rare and severe disorder of the peripheral nervous system with an unknown etiology. One of the hallmarks of the AIDP pathogenesis is a significantly elevated cerebrospinal fluid (CSF) protein level. In this paper CSF peptidome and proteome in AIDP were analyzed and compared with multiple sclerosis and control patients. A total protein concentration increase was shown to be because of even changes in all proteins rather than some specific response, supporting the hypothesis of protein leakage from blood through the blood-nerve barrier. The elevated CSF protein level in AIDP was complemented by activization of protein degradation and much higher peptidome diversity. Because of the studies of the acute motor axonal form, Guillain-Barre syndrome as a whole is thought to be associated with autoimmune response against neurospecific molecules. Thus, in AIDP, autoantibodies against cell adhesion proteins localized at Ranvier's nodes were suggested as possible targets in AIDP. Indeed, AIDP CSF peptidome analysis revealed cell adhesion proteins degradation, however no reliable dependence on the corresponding autoantibodies levels was found. Proteome analysis revealed overrepresentation of Gene Ontology groups related to responses to bacteria and virus infections, which were earlier suggested as possible AIDP triggers. Immunoglobulin blood serum analysis against most common neuronal viruses did not reveal any specific pathogen; however, AIDP patients were more immunopositive in average and often had polyinfections. Cytokine analysis of both AIDP CSF and blood did not show a systemic adaptive immune response or general inflammation, whereas innate immunity cytokines were up-regulated. To supplement the widely-accepted though still unproven autoimmunity-based AIDP mechanism we propose a hypothesis of the primary peripheral nervous system damaging initiated as an innate immunity-associated local inflammation following neurotropic viruses egress, whereas the autoantibody production might be an optional complementary secondary process.
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Affiliation(s)
- Rustam H Ziganshin
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str., 16/10, Moscow 117997, Russian Federation;
| | - Olga M Ivanova
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str., 16/10, Moscow 117997, Russian Federation
| | - Yakov A Lomakin
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str., 16/10, Moscow 117997, Russian Federation
| | - Alexey A Belogurov
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str., 16/10, Moscow 117997, Russian Federation
| | - Sergey I Kovalchuk
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str., 16/10, Moscow 117997, Russian Federation
| | - Igor V Azarkin
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str., 16/10, Moscow 117997, Russian Federation
| | - Georgij P Arapidi
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str., 16/10, Moscow 117997, Russian Federation; §Moscow Institute of Physics and Technology, Institutskiy pereulok 9, Dolgoprudny 141700, Russian Federation
| | - Nikolay A Anikanov
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str., 16/10, Moscow 117997, Russian Federation
| | - Victoria O Shender
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str., 16/10, Moscow 117997, Russian Federation
| | - Mikhail A Piradov
- ¶Research Center of Neurology, Volokolamskoye highway, 80, Moscow 125367, Russian Federation
| | - Natalia A Suponeva
- ¶Research Center of Neurology, Volokolamskoye highway, 80, Moscow 125367, Russian Federation
| | - Anna A Vorobyeva
- ¶Research Center of Neurology, Volokolamskoye highway, 80, Moscow 125367, Russian Federation
| | - Alexander G Gabibov
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str., 16/10, Moscow 117997, Russian Federation
| | - Vadim T Ivanov
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str., 16/10, Moscow 117997, Russian Federation
| | - Vadim M Govorun
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str., 16/10, Moscow 117997, Russian Federation; §Moscow Institute of Physics and Technology, Institutskiy pereulok 9, Dolgoprudny 141700, Russian Federation; ‖Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya str., 1a, Moscow 119435, Russian Federation
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Kovalchuk SI, Ziganshin RH, Starkov VG, Tsetlin VI, Utkin YN. Quantitative Proteomic Analysis of Venoms from Russian Vipers of Pelias Group: Phospholipases A₂ are the Main Venom Components. Toxins (Basel) 2016; 8:105. [PMID: 27077884 PMCID: PMC4848631 DOI: 10.3390/toxins8040105] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/28/2016] [Accepted: 04/05/2016] [Indexed: 02/06/2023] Open
Abstract
Venoms of most Russian viper species are poorly characterized. Here, by quantitative chromato-mass-spectrometry, we analyzed protein and peptide compositions of venoms from four Vipera species (V. kaznakovi, V. renardi, V. orlovi and V. nikolskii) inhabiting different regions of Russia. In all these species, the main components were phospholipases A2, their content ranging from 24% in V. orlovi to 65% in V. nikolskii. Altogether, enzyme content in venom of V. nikolskii reached ~85%. Among the non-enzymatic proteins, the most abundant were disintegrins (14%) in the V. renardi venom, C-type lectin like (12.5%) in V. kaznakovi, cysteine-rich venom proteins (12%) in V. orlovi and venom endothelial growth factors (8%) in V. nikolskii. In total, 210 proteins and 512 endogenous peptides were identified in the four viper venoms. They represented 14 snake venom protein families, most of which were found in the venoms of Vipera snakes previously. However, phospholipase B and nucleotide degrading enzymes were reported here for the first time. Compositions of V. kaznakovi and V. orlovi venoms were described for the first time and showed the greatest similarity among the four venoms studied, which probably reflected close relationship between these species within the “kaznakovi” complex.
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Affiliation(s)
- Sergey I Kovalchuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia.
| | - Rustam H Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia.
| | - Vladislav G Starkov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia.
| | - Victor I Tsetlin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia.
| | - Yuri N Utkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia.
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Utkin YN, Kasheverov IE, Kudryavtsev DS, Andreeva TV, Starkov VG, Ziganshin RH, Kuznetsov DV, Anh HN, Thao NTT, Khoa NC, Tsetlin VI. Nonconventional three-finger toxin BMLCL from krait Bungarus multicinctus venom with high affinity interacts with nicotinic acetylcholine receptors. DOKL BIOCHEM BIOPHYS 2015; 464:294-7. [PMID: 26518551 DOI: 10.1134/s1607672915050099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Indexed: 12/16/2022]
Abstract
Nonconventional three-finger toxin BMLCL was isolated from B. multicinctus venom, and its interaction with different subtypes of nicotinic acetylcholine receptor (nAChR) was studied. It was found that BMLCL is able to interact with high efficiency with both α7 and muscle type nAChRs.
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Affiliation(s)
- Yu N Utkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia. .,The National University of Science and Technology MISiS, Moscow, Russia.
| | - I E Kasheverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia.,Syneuro Ltd., Moscow, Russia
| | - D S Kudryavtsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia.,Syneuro Ltd., Moscow, Russia
| | - T V Andreeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - V G Starkov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - R H Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - D V Kuznetsov
- The National University of Science and Technology MISiS, Moscow, Russia
| | - Hoang Ngoc Anh
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Thanh Thao
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, Ho Chi Minh City, Vietnam
| | - Nguyen Cuu Khoa
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, Ho Chi Minh City, Vietnam
| | - V I Tsetlin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia
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Pletnev VZ, Pletneva NV, Sarkisyan KS, Mishin AS, Lukyanov KA, Goryacheva EA, Ziganshin RH, Dauter Z, Pletnev S. Structure of the green fluorescent protein NowGFP with an anionic tryptophan-based chromophore. Acta Crystallogr D Biol Crystallogr 2015; 71:1699-707. [PMID: 26249350 PMCID: PMC4528802 DOI: 10.1107/s1399004715010159] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 05/26/2015] [Indexed: 11/11/2022]
Abstract
A green-emitting fluorescent variant, NowGFP, with a tryptophan-based chromophore (Thr65-Trp66-Gly67) was recently developed from the cyan mCerulean by introducing 18 point mutations. NowGFP is characterized by bright green fluorescence at physiological and higher pH and by weak cyan fluorescence at low pH. Illumination with blue light induces irreversible photoconversion of NowGFP from a green-emitting to a cyan-emitting form. Here, the X-ray structures of intact NowGFP at pH 9.0 and pH 4.8 and of its photoconverted variant, NowGFP_conv, are reported at 1.35, 1.18 and 2.5 Å resolution, respectively. The structure of NowGFP at pH 9.0 suggests the anionic state of Trp66 of the chromophore to be the primary cause of its green fluorescence. At both examined pH values Trp66 predominantly adopted a cis conformation; only ∼ 20% of the trans conformation was observed at pH 4.8. It was shown that Lys61, which adopts two distinct pH-dependent conformations, is a key residue playing a central role in chromophore ionization. At high pH the side chain of Lys61 forms two hydrogen bonds, one to the indole N atom of Trp66 and the other to the carboxyl group of the catalytic Glu222, enabling an indirect noncovalent connection between them that in turn promotes Trp66 deprotonation. At low pH, the side chain of Lys61 is directed away from Trp66 and forms a hydrogen bond to Gln207. It has been shown that photoconversion of NowGFP is accompanied by decomposition of Lys61, with a predominant cleavage of its side chain at the C(γ)-C(δ) bond. Lys61, Glu222, Thr203 and Ser205 form a local hydrogen-bond network connected to the indole ring of the chromophore Trp66; mutation of any of these residues dramatically affects the spectral properties of NowGFP. On the other hand, an Ala150Val replacement in the vicinity of the chromophore indole ring resulted in a new advanced variant with a 2.5-fold improved photostability.
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Affiliation(s)
- Vladimir Z. Pletnev
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, GSP-7, Moscow, Russian Federation
| | - Nadya V. Pletneva
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, GSP-7, Moscow, Russian Federation
| | - Karen S. Sarkisyan
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, GSP-7, Moscow, Russian Federation
| | - Alexander S. Mishin
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, GSP-7, Moscow, Russian Federation
| | - Konstantin A. Lukyanov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, GSP-7, Moscow, Russian Federation
| | - Ekaterina A. Goryacheva
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, GSP-7, Moscow, Russian Federation
| | - Rustam H. Ziganshin
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, GSP-7, Moscow, Russian Federation
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, IL 60439, USA
| | - Sergei Pletnev
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, IL 60439, USA
- Basic Research Program, Leidos Biomedical Research Inc., Argonne, IL 60439, USA
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Fesenko IA, Arapidi GP, Skripnikov AY, Alexeev DG, Kostryukova ES, Manolov AI, Altukhov IA, Khazigaleeva RA, Seredina AV, Kovalchuk SI, Ziganshin RH, Zgoda VG, Novikova SE, Semashko TA, Slizhikova DK, Ptushenko VV, Gorbachev AY, Govorun VM, Ivanov VT. Specific pools of endogenous peptides are present in gametophore, protonema, and protoplast cells of the moss Physcomitrella patens. BMC Plant Biol 2015; 15:87. [PMID: 25848929 PMCID: PMC4365561 DOI: 10.1186/s12870-015-0468-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [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: 12/08/2014] [Accepted: 02/26/2015] [Indexed: 05/27/2023]
Abstract
BACKGROUND Protein degradation is a basic cell process that operates in general protein turnover or to produce bioactive peptides. However, very little is known about the qualitative and quantitative composition of a plant cell peptidome, the actual result of this degradation. In this study we comprehensively analyzed a plant cell peptidome and systematically analyzed the peptide generation process. RESULTS We thoroughly analyzed native peptide pools of Physcomitrella patens moss in two developmental stages as well as in protoplasts. Peptidomic analysis was supplemented by transcriptional profiling and quantitative analysis of precursor proteins. In total, over 20,000 unique endogenous peptides, ranging in size from 5 to 78 amino acid residues, were identified. We showed that in both the protonema and protoplast states, plastid proteins served as the main source of peptides and that their major fraction formed outside of chloroplasts. However, in general, the composition of peptide pools was very different between these cell types. In gametophores, stress-related proteins, e.g., late embryogenesis abundant proteins, were among the most productive precursors. The Driselase-mediated protonema conversion to protoplasts led to a peptide generation "burst", with a several-fold increase in the number of components in the latter. Degradation of plastid proteins in protoplasts was accompanied by suppression of photosynthetic activity. CONCLUSION We suggest that peptide pools in plant cells are not merely a product of waste protein degradation, but may serve as important functional components for plant metabolism. We assume that the peptide "burst" is a form of biotic stress response that might produce peptides with antimicrobial activity from originally functional proteins. Potential functions of peptides in different developmental stages are discussed.
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Affiliation(s)
- Igor A Fesenko
- />Department of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10, Miklukho-Maklaya, GSP-7, Moscow, 117997 Russian Federation
| | - Georgij P Arapidi
- />Department of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10, Miklukho-Maklaya, GSP-7, Moscow, 117997 Russian Federation
- />Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, 141700 Russian Federation
| | - Alexander Yu Skripnikov
- />Department of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10, Miklukho-Maklaya, GSP-7, Moscow, 117997 Russian Federation
- />Biology Department, Lomonosov Moscow State University, Moscow, 199234 Russian Federation
| | - Dmitry G Alexeev
- />Research Institute of Physical-Chemical Medicine, Federal Medical & Biological Agency, 1a, Malaya Pirogovskaya, Moscow, 119992 Russian Federation
- />Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, 141700 Russian Federation
| | - Elena S Kostryukova
- />Research Institute of Physical-Chemical Medicine, Federal Medical & Biological Agency, 1a, Malaya Pirogovskaya, Moscow, 119992 Russian Federation
| | - Alexander I Manolov
- />Research Institute of Physical-Chemical Medicine, Federal Medical & Biological Agency, 1a, Malaya Pirogovskaya, Moscow, 119992 Russian Federation
- />Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, 141700 Russian Federation
| | - Ilya A Altukhov
- />Research Institute of Physical-Chemical Medicine, Federal Medical & Biological Agency, 1a, Malaya Pirogovskaya, Moscow, 119992 Russian Federation
- />Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, 141700 Russian Federation
| | - Regina A Khazigaleeva
- />Department of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10, Miklukho-Maklaya, GSP-7, Moscow, 117997 Russian Federation
| | - Anna V Seredina
- />Department of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10, Miklukho-Maklaya, GSP-7, Moscow, 117997 Russian Federation
| | - Sergey I Kovalchuk
- />Department of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10, Miklukho-Maklaya, GSP-7, Moscow, 117997 Russian Federation
- />Research Institute of Physical-Chemical Medicine, Federal Medical & Biological Agency, 1a, Malaya Pirogovskaya, Moscow, 119992 Russian Federation
| | - Rustam H Ziganshin
- />Department of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10, Miklukho-Maklaya, GSP-7, Moscow, 117997 Russian Federation
| | - Viktor G Zgoda
- />Institute of Biomedical Chemistry RAMS im. V.N. Orehovicha, 10, Pogodinskaya Street, Moscow, 119121 Russian Federation
| | - Svetlana E Novikova
- />Institute of Biomedical Chemistry RAMS im. V.N. Orehovicha, 10, Pogodinskaya Street, Moscow, 119121 Russian Federation
| | - Tatiana A Semashko
- />Research Institute of Physical-Chemical Medicine, Federal Medical & Biological Agency, 1a, Malaya Pirogovskaya, Moscow, 119992 Russian Federation
| | - Darya K Slizhikova
- />Department of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10, Miklukho-Maklaya, GSP-7, Moscow, 117997 Russian Federation
| | - Vasilij V Ptushenko
- />A. N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskye Gory, House 1, Building 40, Moscow, 119992 Russian Federation
| | - Alexey Y Gorbachev
- />Research Institute of Physical-Chemical Medicine, Federal Medical & Biological Agency, 1a, Malaya Pirogovskaya, Moscow, 119992 Russian Federation
| | - Vadim M Govorun
- />Department of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10, Miklukho-Maklaya, GSP-7, Moscow, 117997 Russian Federation
- />Research Institute of Physical-Chemical Medicine, Federal Medical & Biological Agency, 1a, Malaya Pirogovskaya, Moscow, 119992 Russian Federation
- />Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, 141700 Russian Federation
| | - Vadim T Ivanov
- />Department of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10, Miklukho-Maklaya, GSP-7, Moscow, 117997 Russian Federation
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