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Chernova AI, Gubaev RF, Singh A, Sherbina K, Goryunova SV, Martynova EU, Goryunov DV, Boldyrev SV, Vanyushkina AA, Anikanov NA, Stekolshchikova EA, Yushina EA, Demurin YN, Mukhina ZM, Gavrilova VA, Anisimova IN, Karabitsina YI, Alpatieva NV, Chang PL, Khaitovich P, Mazin PV, Nuzhdin SV. Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content. BMC Genomics 2021; 22:505. [PMID: 34225652 PMCID: PMC8256595 DOI: 10.1186/s12864-021-07768-y] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 06/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sunflower is an important oilseed crop domesticated in North America approximately 4000 years ago. During the last century, oil content in sunflower was under strong selection. Further improvement of oil properties achieved by modulating its fatty acid composition is one of the main directions in modern oilseed crop breeding. RESULTS We searched for the genetic basis of fatty acid content variation by genotyping 601 inbred sunflower lines and assessing their lipid and fatty acid composition. Our genome-wide association analysis based on the genotypes for 15,483 SNPs and the concentrations of 23 fatty acids, including minor fatty acids, revealed significant genetic associations for eleven of them. Identified genomic regions included the loci involved in rare fatty acids variation on chromosomes 3 and 14, explaining up to 34.5% of the total variation of docosanoic acid (22:0) in sunflower oil. CONCLUSIONS This is the first large scale implementation of high-throughput lipidomic profiling to sunflower germplasm characterization. This study contributes to the genetic characterization of Russian sunflower collections, which made a substantial contribution to the development of sunflower as the oilseed crop worldwide, and provides new insights into the genetic control of oil composition that can be implemented in future studies.
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Affiliation(s)
- Alina I Chernova
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia. .,LLC "OIL GENE", Skolkovo Innovation Center, Moscow, Russia.
| | - Rim F Gubaev
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia.,LLC "OIL GENE", Skolkovo Innovation Center, Moscow, Russia
| | - Anupam Singh
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Katrina Sherbina
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Svetlana V Goryunova
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia.,Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin st. 3, Moscow, 119991, Russia.,FSBSI Lorch Potato Research Institute, Lorkha Str. 23, Kraskovo, 140051, Russia
| | - Elena U Martynova
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Denis V Goryunov
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia.,MSU A.N. Belozersky Institute of Physico-Chemical Biology, Leninsky Gori 1, Building 40, Moscow, 119992, Russia
| | - Stepan V Boldyrev
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia.,LLC "OIL GENE", Skolkovo Innovation Center, Moscow, Russia
| | - Anna A Vanyushkina
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Nikolay A Anikanov
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Elena A Stekolshchikova
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Ekaterina A Yushina
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia.,FSBSI N P Bochkov Research Center of Medical Genetics, Moskvorechye St.1, Moscow, 115522, Russia
| | - Yakov N Demurin
- Pustovoit All-Russia Research Institute of Oilseed Crops, Filatova St. 17, Krasnodar, 350038, Russia
| | | | - Vera A Gavrilova
- N. I. Vavilov Research Institute of Plant Genetic Resources (VIR), 42 B. Morskaja, St. Petersburg, 190000, Russia
| | - Irina N Anisimova
- N. I. Vavilov Research Institute of Plant Genetic Resources (VIR), 42 B. Morskaja, St. Petersburg, 190000, Russia
| | - Yulia I Karabitsina
- N. I. Vavilov Research Institute of Plant Genetic Resources (VIR), 42 B. Morskaja, St. Petersburg, 190000, Russia
| | - Natalia V Alpatieva
- N. I. Vavilov Research Institute of Plant Genetic Resources (VIR), 42 B. Morskaja, St. Petersburg, 190000, Russia
| | - Peter L Chang
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Philipp Khaitovich
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Pavel V Mazin
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Sergey V Nuzhdin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
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Grafskaia EN, Polina NF, Babenko VV, Kharlampieva DD, Bobrovsky PA, Manuvera VA, Farafonova TE, Anikanov NA, Lazarev VN. Discovery of novel antimicrobial peptides: A transcriptomic study of the sea anemone Cnidopus japonicus. J Bioinform Comput Biol 2018; 16:1840006. [PMID: 29361893 DOI: 10.1142/s0219720018400061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 11/18/2022]
Abstract
As essential conservative component of the innate immune systems of living organisms, antimicrobial peptides (AMPs) could complement pharmaceuticals that increasingly fail to combat various pathogens exhibiting increased resistance to microbial antibiotics. Among the properties of AMPs that suggest their potential as therapeutic agents, diverse peptides in the venoms of various predators demonstrate antimicrobial activity and kill a wide range of microorganisms. To identify potent AMPs, the study reported here involved a transcriptomic profiling of the tentacle secretion of the sea anemone Cnidopus japonicus. An in silico search algorithm designed to discover toxin-like proteins containing AMPs was developed based on the evaluation of the properties and structural peculiarities of amino acid sequences. The algorithm revealed new proteins of the anemone containing antimicrobial candidate sequences, and 10 AMPs verified using high-throughput proteomics were synthesized. The antimicrobial activity of the candidate molecules was experimentally estimated against Gram-positive and -negative bacteria. Ultimately, three peptides exhibited antimicrobial activity against bacterial strains, which suggests that the method can be applied to reveal new AMPs in the venoms of other predators as well.
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Affiliation(s)
- Ekaterina N Grafskaia
- * Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Institutskii per. 9, Dolgoprudny, Moscow 141700, Russia.,† Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a, Malaya Pirogovskaya Street, Moscow 119435, Russia
| | - Nadezhda F Polina
- † Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a, Malaya Pirogovskaya Street, Moscow 119435, Russia
| | - Vladislav V Babenko
- † Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a, Malaya Pirogovskaya Street, Moscow 119435, Russia
| | - Daria D Kharlampieva
- † Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a, Malaya Pirogovskaya Street, Moscow 119435, Russia
| | - Pavel A Bobrovsky
- † Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a, Malaya Pirogovskaya Street, Moscow 119435, Russia
| | - Valentin A Manuvera
- * Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Institutskii per. 9, Dolgoprudny, Moscow 141700, Russia.,† Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a, Malaya Pirogovskaya Street, Moscow 119435, Russia
| | - Tatyana E Farafonova
- ‡ Department of Proteomic Research and Mass Spectrometry, Laboratory of Systems Biology, Institute of Biomedical Chemistry of the Russian Academy of Sciences, 10, Pogodinskaya Street, Moscow 119121, Russia
| | - Nikolay A Anikanov
- † Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a, Malaya Pirogovskaya Street, Moscow 119435, Russia.,§ Department of Peptide and Protein Technologies Laboratory of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic, Chemistry of the Russian Academy of Sciences, 16/10, Miklukho-Maklaya Street, Moscow 117997, Russia
| | - Vassili N Lazarev
- * Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Institutskii per. 9, Dolgoprudny, Moscow 141700, Russia.,† Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a, Malaya Pirogovskaya Street, Moscow 119435, 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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4
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Shender VO, Pavlyukov MS, Ziganshin RH, Arapidi GP, Kovalchuk SI, Anikanov NA, Altukhov IA, Alexeev DG, Butenko IO, Shavarda AL, Khomyakova EB, Evtushenko E, Ashrafyan LA, Antonova IB, Kuznetcov IN, Gorbachev AY, Shakhparonov MI, Govorun VM. Proteome-metabolome profiling of ovarian cancer ascites reveals novel components involved in intercellular communication. Mol Cell Proteomics 2014; 13:3558-71. [PMID: 25271300 DOI: 10.1074/mcp.m114.041194] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Ovarian cancer ascites is a native medium for cancer cells that allows investigation of their secretome in a natural environment. This medium is of interest as a promising source of potential biomarkers, and also as a medium for cell-cell communication. The aim of this study was to elucidate specific features of the malignant ascites metabolome and proteome. In order to omit components of the systemic response to ascites formation, we compared malignant ascites with cirrhosis ascites. Metabolome analysis revealed 41 components that differed significantly between malignant and cirrhosis ascites. Most of the identified cancer-specific metabolites are known to be important signaling molecules. Proteomic analysis identified 2096 and 1855 proteins in the ovarian cancer and cirrhosis ascites, respectively; 424 proteins were specific for the malignant ascites. Functional analysis of the proteome demonstrated that the major differences between cirrhosis and malignant ascites were observed for the cluster of spliceosomal proteins. Additionally, we demonstrate that several splicing RNAs were exclusively detected in malignant ascites, where they probably existed within protein complexes. This result was confirmed in vitro using an ovarian cancer cell line. Identification of spliceosomal proteins and RNAs in an extracellular medium is of particular interest; the finding suggests that they might play a role in the communication between cancer cells. In addition, malignant ascites contains a high number of exosomes that are known to play an important role in signal transduction. Thus our study reveals the specific features of malignant ascites that are associated with its function as a medium of intercellular communication.
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Affiliation(s)
- Victoria O Shender
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str. 16/10, Moscow 117997, Russian Federation;
| | - Marat S Pavlyukov
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str. 16/10, Moscow 117997, Russian Federation
| | - Rustam H Ziganshin
- 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
| | - Sergey I Kovalchuk
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str. 16/10, Moscow 117997, Russian Federation
| | - Nikolay A Anikanov
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str. 16/10, Moscow 117997, Russian Federation
| | - Ilya A Altukhov
- ‖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
| | - Dmitry G Alexeev
- ‖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
| | - Ivan O Butenko
- **Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya str., 1a, Moscow 119435, Russian Federation
| | - Alexey L Shavarda
- ‡‡Research Resource Center molecular and Cell Technologies, Saint-Petersburg State University, Universitetskaya nab. 7-9, Saint-Petersburg 199034, Russian Federation; §§Analytical Phytochemistry Laboratory, Komarov Botanical Institute, Prof. Popov Street 2, Saint-Petersburg 197376, Russia
| | - Elena B Khomyakova
- **Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya str., 1a, Moscow 119435, Russian Federation
| | - Evgeniy Evtushenko
- ¶¶Faculty of Chemistry, Lomonosov Moscow State University, Leninskiye Gory 1-3, Moscow 119991, Russian Federation
| | - Lev A Ashrafyan
- ‖‖Russian Scientific Center of Roentgenoradiology, Profsoyuznaya str. 86, Moscow 117997, Russian Federation
| | - Irina B Antonova
- ‖‖Russian Scientific Center of Roentgenoradiology, Profsoyuznaya str. 86, Moscow 117997, Russian Federation
| | - Igor N Kuznetcov
- ‖‖Russian Scientific Center of Roentgenoradiology, Profsoyuznaya str. 86, Moscow 117997, Russian Federation
| | - Alexey Yu Gorbachev
- **Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya str., 1a, Moscow 119435, Russian Federation
| | - Mikhail I Shakhparonov
- 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; **Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya str., 1a, Moscow 119435, Russian Federation; Kazan Federal University, Kremlyovskaya str. 18, Kazan 420008, Russian Federation
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Skripnikov AI, Anikanov NA, Kazakov VS, Dolgov SV, Ziganshin RK, Govorun VM, Ivanov VT. [Exploration and identification of Physcomitrella patens moss peptides]. Bioorg Khim 2011; 37:108-18. [PMID: 21460886 DOI: 10.1134/s1068162011010158] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In the current study the isolation and identification of Physcomitrella patens (Hedw.) B.S.G. moss peptides are described. Physcomitrella patens moss is actively used in recent years as a model organism to study the biology of plants. Protoplasts, protonemata and gametophores of the moss are demonstrated for the first time to contain diverse small peptides. From gametophores was isolated and identified 58 peptides that are fragments of 14 proteins, and from protonemata - 49 peptides, fragments of 15 proteins. It was found that the protonemata and gametophores Ph. patens, which are the successive stages of development of this plant, significantly different from each other as a peptide composition and the spectrum of the precursor protein of identified peptides. Isolation of protoplasts of the enzymatic destruction of cell wall protonemata accompanied by massive degradation of intracellular proteins, many of whom are proteins of photosynthesis, which is a characteristic response of plants to stress the impact of environmental factors. A total of moss protoplasts were isolated and identified 323 peptides that are fragments of 79 proteins.
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