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Dyrkheeva NS, Zakharenko AL, Malakhova AA, Okorokova LS, Shtokalo DN, Medvedev SP, Tupikin AA, Kabilov MR, Lavrik OI. Transcriptomic analysis of HEK293A cells with a CRISPR/Cas9-mediated TDP1 knockout. Biochim Biophys Acta Gen Subj 2024; 1868:130616. [PMID: 38621596 DOI: 10.1016/j.bbagen.2024.130616] [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: 12/25/2023] [Revised: 03/21/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a human DNA repair protein. It is a member of the phospholipase D family based on structural similarity. TDP1 is a key enzyme of the repair of stalled topoisomerase 1 (TOP1)-DNA complexes. Previously, with the CRISPR/Cas9 method, we obtained HEK293A cells with a homozygous knockout of the TDP1 gene and used the TDP1 knockout cells as a cellular model for studying mechanisms of action of an anticancer therapy. In the present work, we hypothesized that the TDP1 knockout would alter the expression of DNA repair-related genes. By transcriptomic analysis, we investigated for the first time the effect of the TDP1 gene knockout on genes' expression changes in the human HEK293A cell line. We obtained original data implying a role of TDP1 in other processes besides the repair of the DNA-TOP1 complex. Differentially expressed gene analysis revealed that TDP1 may participate in cell adhesion and communication, spermatogenesis, mitochondrial function, neurodegeneration, a cytokine response, and the MAPK signaling pathway.
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Affiliation(s)
- Nadezhda S Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Alexandra L Zakharenko
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Anastasia A Malakhova
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; Federal research center Institute of Cytology and Genetics, SB RAS, 10 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | | | - Dmitry N Shtokalo
- AcademGene LLC, 6 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; A.P. Ershov Institute of Informatics Systems, SB RAS, 6 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Sergey P Medvedev
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; Federal research center Institute of Cytology and Genetics, SB RAS, 10 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Alexey A Tupikin
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
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Tian Y, Babaylova ES, Gopanenko AV, Tupikin AE, Kabilov MR, Malygin AA. Deficiency of the ribosomal protein uS10 (RPS20) reorganizes human cells translatome according to the abundance, CDS length and GC content of mRNAs. Open Biol 2024; 14:230366. [PMID: 38290548 PMCID: PMC10827436 DOI: 10.1098/rsob.230366] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/02/2024] [Indexed: 02/01/2024] Open
Abstract
Ribosomal protein uS10, a product of the RPS20 gene, is an essential constituent of the small (40S) subunit of the human ribosome. Disruptive mutations in its gene are associated with a predisposition to hereditary colorectal carcinoma. Here, using HEK293T cells, we show that a deficiency of this protein leads to a decrease in the level of ribosomes (ribosomal shortage). RNA sequencing of the total and polysome-associated mRNA samples reveals hundreds of genes differentially expressed in the transcriptome (t)DEGs and translatome (p)DEGs under conditions of uS10 deficiency. We demonstrate that the (t)DEG and (p)DEG sets partially overlap, determine genes with altered translational efficiency (TE) and identify cellular processes affected by uS10 deficiency-induced ribosomal shortage. We reveal that translated mRNAs of upregulated (p)DEGs and genes with altered TE in uS10-deficient cells are generally more abundant and that their GC contents are significantly lower than those of the respective downregulated sets. We also observed that upregulated (p)DEGs have longer coding sequences. Based on our findings, we propose a combinatorial model describing the process of reorganization of mRNA translation under conditions of ribosomal shortage. Our results reveal rules according to which ribosomal shortage reorganizes the transcriptome and translatome repertoires of actively proliferating cells.
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Affiliation(s)
- Yueming Tian
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Elena S. Babaylova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Alexander V. Gopanenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Alexey E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Alexey A. Malygin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
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Melekhina EN, Belykh ES, Kanev VA, Taskaeva AA, Tarabukin DV, Zinovyeva AN, Velegzhaninov IO, Rasova EE, Baturina OA, Kabilov MR, Markarova MY. Soil Microbiome in Conditions of Oil Pollution of Subarctic Ecosystems. Microorganisms 2023; 12:80. [PMID: 38257907 PMCID: PMC10820038 DOI: 10.3390/microorganisms12010080] [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: 10/24/2023] [Revised: 12/25/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
The present study aimed to investigate the recovery of soil quality and the bacterial and fungal communities following various recultivation methods in areas contaminated with oil. Oil spills are known to have severe impacts on ecosystems; thus, the restoration of contaminated soils has become a significant challenge nowadays. The study was conducted in the forest-tundra zone of the European North-East, where 39 soil samples from five oil-contaminated sites and reference sites were subjected to metagenomic analyses. The contaminated sites were treated with different biopreparations, and the recovery of soil quality and microbial communities were analyzed. The analysis of bacteria and fungi communities was carried out using 16S rDNA and ITS metabarcoding. It was found that 68% of bacterial OTUs and 64% of fungal OTUs were unique to the reference plot and not registered in any of the recultivated plots. However, the species diversity of recultivated sites was similar, with 50-80% of bacterial OTUs and 44-60% of fungal OTUs being common to all sites. New data obtained through soil metabarcoding confirm our earlier conclusions about the effectiveness of using biopreparations with indigenous oil-oxidizing micro-organisms also with mineral fertilizers, and herbaceous plant seeds for soil remediation. It is possible that the characteristics of microbial communities will be informative in the bioindication of soils reclaimed after oil pollution.
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Affiliation(s)
- Elena N. Melekhina
- Institute of Biology, Komi Scientifc Center, Ural Branch of Russian Academy of Sciences (IB FRC Komi SC UB RAS), Kommunisticheskaya 28, 167982 Syktyvkar, Russia; (E.S.B.); (V.A.K.); (A.A.T.); (D.V.T.); (A.N.Z.); (I.O.V.); (E.E.R.); (M.Y.M.)
| | - Elena S. Belykh
- Institute of Biology, Komi Scientifc Center, Ural Branch of Russian Academy of Sciences (IB FRC Komi SC UB RAS), Kommunisticheskaya 28, 167982 Syktyvkar, Russia; (E.S.B.); (V.A.K.); (A.A.T.); (D.V.T.); (A.N.Z.); (I.O.V.); (E.E.R.); (M.Y.M.)
| | - Vladimir A. Kanev
- Institute of Biology, Komi Scientifc Center, Ural Branch of Russian Academy of Sciences (IB FRC Komi SC UB RAS), Kommunisticheskaya 28, 167982 Syktyvkar, Russia; (E.S.B.); (V.A.K.); (A.A.T.); (D.V.T.); (A.N.Z.); (I.O.V.); (E.E.R.); (M.Y.M.)
| | - Anastasia A. Taskaeva
- Institute of Biology, Komi Scientifc Center, Ural Branch of Russian Academy of Sciences (IB FRC Komi SC UB RAS), Kommunisticheskaya 28, 167982 Syktyvkar, Russia; (E.S.B.); (V.A.K.); (A.A.T.); (D.V.T.); (A.N.Z.); (I.O.V.); (E.E.R.); (M.Y.M.)
| | - Dmitry V. Tarabukin
- Institute of Biology, Komi Scientifc Center, Ural Branch of Russian Academy of Sciences (IB FRC Komi SC UB RAS), Kommunisticheskaya 28, 167982 Syktyvkar, Russia; (E.S.B.); (V.A.K.); (A.A.T.); (D.V.T.); (A.N.Z.); (I.O.V.); (E.E.R.); (M.Y.M.)
| | - Aurika N. Zinovyeva
- Institute of Biology, Komi Scientifc Center, Ural Branch of Russian Academy of Sciences (IB FRC Komi SC UB RAS), Kommunisticheskaya 28, 167982 Syktyvkar, Russia; (E.S.B.); (V.A.K.); (A.A.T.); (D.V.T.); (A.N.Z.); (I.O.V.); (E.E.R.); (M.Y.M.)
| | - Ilya O. Velegzhaninov
- Institute of Biology, Komi Scientifc Center, Ural Branch of Russian Academy of Sciences (IB FRC Komi SC UB RAS), Kommunisticheskaya 28, 167982 Syktyvkar, Russia; (E.S.B.); (V.A.K.); (A.A.T.); (D.V.T.); (A.N.Z.); (I.O.V.); (E.E.R.); (M.Y.M.)
| | - Elena E. Rasova
- Institute of Biology, Komi Scientifc Center, Ural Branch of Russian Academy of Sciences (IB FRC Komi SC UB RAS), Kommunisticheskaya 28, 167982 Syktyvkar, Russia; (E.S.B.); (V.A.K.); (A.A.T.); (D.V.T.); (A.N.Z.); (I.O.V.); (E.E.R.); (M.Y.M.)
| | - Olga A. Baturina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), Lavrentieva 8, 630090 Novosibirsk, Russia; (O.A.B.); (M.R.K.)
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), Lavrentieva 8, 630090 Novosibirsk, Russia; (O.A.B.); (M.R.K.)
| | - Maria Yu. Markarova
- Institute of Biology, Komi Scientifc Center, Ural Branch of Russian Academy of Sciences (IB FRC Komi SC UB RAS), Kommunisticheskaya 28, 167982 Syktyvkar, Russia; (E.S.B.); (V.A.K.); (A.A.T.); (D.V.T.); (A.N.Z.); (I.O.V.); (E.E.R.); (M.Y.M.)
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Maslennikova VS, Tsvetkova VP, Shelikhova EV, Selyuk MP, Alikina TY, Kabilov MR, Dubovskiy IM. Bacillus subtilis and Bacillus amyloliquefaciens Mix Suppresses Rhizoctonia Disease and Improves Rhizosphere Microbiome, Growth and Yield of Potato ( Solanum tuberosum L.). J Fungi (Basel) 2023; 9:1142. [PMID: 38132743 PMCID: PMC10744094 DOI: 10.3390/jof9121142] [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: 10/14/2023] [Revised: 11/14/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023] Open
Abstract
Black scurf and stem canker caused by Rhizoctonia solani is a significant disease problem of potatoes. Currently, chemical methods are the primary means of controlling this pathogen. This study sought to explore an alternative approach by harnessing the biocontrol potential of a bacterial mix of Bacillus subtilis and Bacillus amyloliquefaciens against black scurf, and to determine their effect on rhizosphere microorganisms of soil microbiota. This study showed that these bacteria demonstrate antagonistic activity against Rhizoctonia solani. Reduced damage to potato plants during the growing season in Siberia was observed. The index of disease development decreased from 40.9% to 12.0%. The treatment of tubers with this mix of bacteria also led to a change in the composition of the rhizosphere microbiota (according to CFU, 16S and ITS sequencing). This effect was accompanied by a positive change in plant physiological parameters (spectrophotometric analysis). The concentration of chlorophyll in potatoes with the bacterial mix treatment increased by 1.3 fold (p ≤ 0.001), and of carotenoids by 1.2 fold (p ≤ 0.01) compared with the control. After bacterial mix treatment, the length of the aerial parts of plants was 1.3 fold higher (p ≤ 0.001), and the number of stems 1.4 fold higher (p ≤ 0.05). The yield of potatoes was increased by 8.2 t/ha, while the large tuber fraction was increased by 16% (p ≤ 0.05). The bacteria mix of Bacillus subtilis and Bacillus amyloliquefaciens suppressed the plant pathogenic fungus Rhizoctonia solani, and simultaneously enhanced the physiological parameters of potato plants. This treatment can be used to enhance the yield/quality of potato tubers under field conditions.
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Affiliation(s)
- Vladislava S. Maslennikova
- Laboratory of Biological Plant Protection and Biotechnology, Novosibirsk State Agrarian University, Dobrolubova Str. 160, 630039 Novosibirsk, Russia; (V.S.M.)
- Laboratory of Biotechnology of Microorganisms and Plants, Tomsk State University, 634050 Tomsk, Russia
| | - Vera P. Tsvetkova
- Laboratory of Biological Plant Protection and Biotechnology, Novosibirsk State Agrarian University, Dobrolubova Str. 160, 630039 Novosibirsk, Russia; (V.S.M.)
| | - Evgenia V. Shelikhova
- Laboratory of Biological Plant Protection and Biotechnology, Novosibirsk State Agrarian University, Dobrolubova Str. 160, 630039 Novosibirsk, Russia; (V.S.M.)
- Laboratory of Biotechnology of Microorganisms and Plants, Tomsk State University, 634050 Tomsk, Russia
| | - Marina P. Selyuk
- Laboratory of Biological Plant Protection and Biotechnology, Novosibirsk State Agrarian University, Dobrolubova Str. 160, 630039 Novosibirsk, Russia; (V.S.M.)
| | - Tatyana Y. Alikina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Ivan M. Dubovskiy
- Laboratory of Biological Plant Protection and Biotechnology, Novosibirsk State Agrarian University, Dobrolubova Str. 160, 630039 Novosibirsk, Russia; (V.S.M.)
- Laboratory of Biotechnology of Microorganisms and Plants, Tomsk State University, 634050 Tomsk, Russia
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Polenogova OV, Klementeva TN, Kabilov MR, Alikina TY, Krivopalov AV, Kruykova NA, Glupov VV. A Diet with Amikacin Changes the Bacteriobiome and the Physiological State of Galleria mellonella and Causes Its Resistance to Bacillus thuringiensis. Insects 2023; 14:889. [PMID: 37999088 PMCID: PMC10672437 DOI: 10.3390/insects14110889] [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] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023]
Abstract
Environmental pollution with antibiotics can cause antibiotic resistance in microorganisms, including the intestinal microbiota of various insects. The effects of low-dose aminoglycoside antibiotic (amikacin) on the resident gut microbiota of Galleria mellonella, its digestion, its physiological parameters, and the resistance of this species to bacteria Bacillus thuringiensis were investigated. Here, 16S rDNA analysis revealed that the number of non-dominant Enterococcus mundtii bacteria in the eighteenth generation of the wax moth treated with amikacin was increased 73 fold compared to E. faecalis, the dominant bacteria in the native line of the wax moth. These changes were accompanied by increased activity of acidic protease and glutathione-S-transferase in the midgut tissues of larvae. Ultra-thin section electron microscopy detected no changes in the structure of the midgut tissues. In addition, reduced pupa weight and resistance of larvae to B. thuringiensis were observed in the eighteenth generation of the wax moth reared on a diet with amikacin. We suggest that long-term cultivation of wax moth larvae on an artificial diet with an antibiotic leads to its adaptation due to changes in both the gut microbiota community and the physiological state of the insect organism.
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Affiliation(s)
- Olga V. Polenogova
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630091, Russia; (T.N.K.); (A.V.K.); (N.A.K.); (V.V.G.)
| | - Tatyana N. Klementeva
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630091, Russia; (T.N.K.); (A.V.K.); (N.A.K.); (V.V.G.)
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (M.R.K.); (T.Y.A.)
| | - Tatyana Y. Alikina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (M.R.K.); (T.Y.A.)
| | - Anton V. Krivopalov
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630091, Russia; (T.N.K.); (A.V.K.); (N.A.K.); (V.V.G.)
| | - Natalya A. Kruykova
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630091, Russia; (T.N.K.); (A.V.K.); (N.A.K.); (V.V.G.)
| | - Viktor V. Glupov
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630091, Russia; (T.N.K.); (A.V.K.); (N.A.K.); (V.V.G.)
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Kravtsova LS, Peretolchina TE, Triboy TI, Nebesnykh IA, Tupikin AE, Kabilov MR. A study of macroinvertebrate communities in Bolshiye Koty Bay of Lake Baikal using DNA metabarcoding. Vavilovskii Zhurnal Genet Selektsii 2023; 27:694-702. [PMID: 38213463 PMCID: PMC10782034 DOI: 10.18699/vjgb-23-80] [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: 02/20/2023] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 01/13/2024] Open
Abstract
The diversity of macroinvertebrates, the structure of their communities in Bolshiye Koty Bay (Lake Baikal) was studied by a DNA metabarcoding approach using an Illumina MiSeq system. Internal primer mlCOIintF in combination with jgHCO2198 of the Folmer fragment of the COI gene were used for macroinvertebrate metabarcoding. A total of 118009 reads of the COI gene fragment (at least 313 bp in length) were obtained. The correlation of the Spearman coefficient (S = 0.6, p<0.05) with the abundance of macroinvertebrates in the samples before DNA extraction showed that the number of reads can serve as an indirect characteristic of the abundance of a species (operational taxonomic unit, OTU). 115 OTUs belonging to the higher taxa of macroinvertebrates were identified: Porifera, 1; Platyhelminthes, 3; Annelida, 38; Arthropoda, 55; Mollusca, 18. At a high level of resolution (with homology with GenBank reference sequences ≥ 95 %, coverage ≥ 90 %), 46 taxa of macroinvertebrates comprising three communities were registered: one dominated by molluscs (Choanomphalus conf. maacki) and two dominated by chironomids (Orthocladius gregarius Linev., Sergentia baicalensis Tshern.). Communities are characterized by low species diversity according to Shannon (from 0.7 to 1.2 bits), high concentration of dominance according to Simpson (from 0.5 to 0.7) and low evenness according to Pielou (from 0.3 to 0.4). Dominants and subdominants in the communities account for 91 to 96 % of COI gene fragment reads. The spatial distribution of the dominant species identified in the communities is influenced by the geomorphological features of the bottom and the composition of sediments in the area studied. The approach proposed for studying the structure of macroinvertebrate communities based on DNA metabarcoding and next generation sequencing can be recommended for express assessment of the state of aquatic ecosystems in the monitoring.
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Affiliation(s)
- L S Kravtsova
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - T E Peretolchina
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - T I Triboy
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - I A Nebesnykh
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - A E Tupikin
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - M R Kabilov
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Pavlova ON, Tupikin AE, Chernitsyna SM, Bukin YS, Lomakina AV, Pogodaeva TV, Nikonova AA, Bukin SV, Zemskaya TI, Kabilov MR. Description and Genomic Analysis of the First Facultatively Lithoautotrophic, Thermophilic Bacteria of the Genus Thermaerobacter Isolated from Low-temperature Sediments of Lake Baikal. Microb Ecol 2023; 86:1604-1619. [PMID: 36717392 DOI: 10.1007/s00248-023-02182-1] [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] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Members of the genus Thermaerobacter belong to the phylum Firmicutes and all isolates characterised to date are strictly aerobic and thermophilic. They were isolated from a mud sample of the Challenger Deep in the Mariana Trench, hydrothermal vents, and silt compost. A novel thermophilic, facultatively lithoautotrophic bacteria of the genus Thermaerobacter, strain PB12/4term (=VKM B-3151T), with a metabolism that is uncharacteristic of the type species, was isolated from low-temperature surface sediments near the Posolsk Bank methane seep, Lake Baikal, Russia. The new strain grows with molecular hydrogen as electron donor, elemental sulfur, and thiosulfate as electron acceptors, and CO2/[Formula: see text] as carbon source. The genome of strain PB12/4term consists of one chromosome with a total length of 2.820.915 bp and the G+C content of the genomic DNA was 72.2%. The phylogenomic reconstruction based on 120 conserved bacterial single-copy proteins revealed that strain PB12/4term belongs to the genus Thermaerobacter within in the class Thermaerobacteria, phylum Firmicutes_E. The strain PB12/4term is closely related to Thermaerobacter subterraneus DSM 13965 (ANI=95.08%, AF=0.91) and Thermaerobacter marianensis DSM 12885 (ANI=84.98%, AF=0.77). Genomic and experimental data confirm the ability of the Thermaerobacter PB12/4term pure culture to facultatively lithotrophic growth, which is provided by the presence of [NiFe]hydrogenase enzymes that are absent in T. marianensis DSM 12885 and T. subterraneus DSM 13965. The data obtained on the physiological and biochemical differences of strain PB12/4term provide a deeper insight into the species diversity and functional activity of the genus Thermaerobacter.
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Affiliation(s)
- O N Pavlova
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia.
| | - A E Tupikin
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - S M Chernitsyna
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - Y S Bukin
- Laboratory of Genosystematics, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - A V Lomakina
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - T V Pogodaeva
- Laboratory of Hydrochemistry and Atmosphere Chemistry, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - A A Nikonova
- Laboratory of Chromatography, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - S V Bukin
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - T I Zemskaya
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - M R Kabilov
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
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Naumova NB, Barsukov PA, Baturina OA, Kabilov MR. Soil Alveolata diversity in the undisturbed steppe and wheat agrocenoses under different tillage. Vavilovskii Zhurnal Genet Selektsii 2023; 27:703-711. [PMID: 38023813 PMCID: PMC10643539 DOI: 10.18699/vjgb-23-81] [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: 03/29/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 12/01/2023] Open
Abstract
Microeukaryotes are vital for maintaining soil quality and ecosystem functioning, however, their communities are less studied than bacterial and fungal ones, especially by high throughput sequencing techniques. Alveolates are important members of soil microbial communities, being consumers and/or prey for other microorganisms. We studied alveolate diversity in soil under the undisturbed steppe (US) and cropped for wheat using two tillage practices (conventional, CT, and no-till, NT) by amplifying the ITS2 marker with ITS3_KYO2/ITS4 primers and sequencing amplicons using Illumina MiSeq. A total of 198 Alveolata OTUs were identified, with 158 OTUs attributed to the Ciliophora phylum, containing five classes: Litostomatea, Spirotrichea and Oligohymenophorea, Nassophorea and Phyllopharyngea. Litostomatea and Phyllopharyngea were more abundant in US as compared with CT and NT. The observed OTU richness was higher in US than in CT and NT. The β-biodiversity of soil ciliates also very distinctly differentiated the US field from CT and NT. In the US, Nassophorea and Spirotrichea correlated positively with sand and negatively with clay, silt and SOM contents. This is the first report about soil ciliates diversity in Siberia as assessed by metabarcoding technique. The revealed clear effect of land use on the relative abundance of some taxa and a lack of tillage effect suggest the importance of the quantity and quality of plant material input for shaping the prey for ciliates. The ITS-metabarcoding technique was used for the first time in the research of ciliates diversity; further studies, embracing diverse aspects of soil ciliates by combining -omics methodology with the traditional one, are needed to get a better insight on the ecological roles of the main ciliate taxa in the complex soil system.
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Affiliation(s)
- N B Naumova
- Institute of Soil Science and Agrochemistry of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - P A Barsukov
- Institute of Soil Science and Agrochemistry of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - O A Baturina
- Institute of Soil Science and Agrochemistry of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - M R Kabilov
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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9
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Kiselev IS, Kulakova OG, Baturina OA, Kabilov MR, Boyko AN, Favorova OO. [DNA Methylation Profile of CD14+ Monocytes Changes in Primary Progressive Multiple Sclerosis]. Mol Biol (Mosk) 2023; 57:819-826. [PMID: 37752647 DOI: 10.31857/s002689842305004x, edn: gvhyat] [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: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 09/28/2023]
Abstract
Multiple sclerosis (MS) is a chronic autoimmune inflammatory and neurodegenerative disease of the central nervous system, which is characterized by significant clinical heterogeneity. Primary progressive MS (PPMS) develops in 10-15% of patients. Unlike the most common relapsing-remitting form of MS, PPMS involves steady progress of neurodegeneration and, as a consequence, a persistent gradual increase in neurological symptoms. The peculiarities of epigenetic regulation of gene expression may be one of the reasons for the differences in the pathogenesis of the two MS forms. DNA methylation is one of the key epigenetic mechanisms, which remains almost unexplored in different cell populations of PPMS patients. The goal of this work was to identify differential methylation profiles of the CpG sites in the CD14+ monocyte DNA, which characterize PPMS. A genome-wide analysis of DNA methylation in PPMS patients and healthy individuals has identified 169 differentially methylated positions (DMPs), 90.5% of which were hypermethylated in PPMS patients. More than half of all DMPs are located in/near known genes and within CpG islands and their neighboring regions, which indicates their high functional significance. We have found six differentially methylated regions (DMRs) in the OR2L13, CAT, LCLAT1, HOXA5, RNF39, and CRTAC1 genes involved in inflammation and neurodegeneration, which indicates active epigenetic regulation of their expression.
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Affiliation(s)
- I S Kiselev
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
| | - O G Kulakova
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
| | - O A Baturina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - M R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - A N Boyko
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
- Federal Center for Brain and Neurotechnology, Federal Medical-Biological Agency, Moscow, 117997 Russia
| | - O O Favorova
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
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10
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Chertkova E, Kabilov MR, Yaroslavtseva O, Polenogova O, Kosman E, Sidorenko D, Alikina T, Noskov Y, Krivopalov A, Glupov VV, Kryukov VY. Links between Soil Bacteriobiomes and Fungistasis toward Fungi Infecting the Colorado Potato Beetle. Microorganisms 2023; 11:microorganisms11040943. [PMID: 37110366 PMCID: PMC10141481 DOI: 10.3390/microorganisms11040943] [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] [Received: 03/13/2023] [Revised: 04/02/2023] [Accepted: 04/02/2023] [Indexed: 04/07/2023] Open
Abstract
Entomopathogenic fungi can be inhibited by different soil microorganisms, but the effect of a soil microbiota on fungal growth, survival, and infectivity toward insects is insufficiently understood. We investigated the level of fungistasis toward Metarhizium robertsii and Beauveria bassiana in soils of conventional potato fields and kitchen potato gardens. Agar diffusion methods, 16S rDNA metabarcoding, bacterial DNA quantification, and assays of Leptinotarsa decemlineata survival in soils inoculated with fungal conidia were used. Soils of kitchen gardens showed stronger fungistasis toward M. robertsii and B. bassiana and at the same time the highest density of the fungi compared to soils of conventional fields. The fungistasis level depended on the quantity of bacterial DNA and relative abundance of Bacillus, Streptomyces, and some Proteobacteria, whose abundance levels were the highest in kitchen garden soils. Cultivable isolates of bacilli exhibited antagonism to both fungi in vitro. Assays involving inoculation of nonsterile soils with B. bassiana conidia showed trends toward elevated mortality of L. decemlineata in highly fungistatic soils compared to low-fungistasis ones. Introduction of antagonistic bacilli into sterile soil did not significantly change infectivity of B. bassiana toward the insect. The results support the idea that entomopathogenic fungi can infect insects within a hypogean habitat despite high abundance and diversity of soil antagonistic bacteria.
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Affiliation(s)
- Ekaterina Chertkova
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630091, Russia
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Olga Yaroslavtseva
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630091, Russia
| | - Olga Polenogova
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630091, Russia
| | - Elena Kosman
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630091, Russia
| | - Darya Sidorenko
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630091, Russia
| | - Tatyana Alikina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Yury Noskov
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630091, Russia
| | - Anton Krivopalov
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630091, Russia
| | - Viktor V. Glupov
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630091, Russia
| | - Vadim Yu. Kryukov
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630091, Russia
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11
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Zolotenkova EA, Gopanenko AV, Tupikin AE, Kabilov MR, Malygin AA. Mutation at the Site of Hydroxylation in the Ribosomal Protein uL15 (RPL27a) Causes Specific Changes in the Repertoire of mRNAs Translated in Mammalian Cells. Int J Mol Sci 2023; 24:ijms24076173. [PMID: 37047141 PMCID: PMC10094517 DOI: 10.3390/ijms24076173] [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: 02/21/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 04/14/2023] Open
Abstract
Ribosomal protein uL15 (RPL27a) carries a specific modification, hydroxylation, at the His39 residue, which neighbors the CCA terminus of the E-site-bound tRNA at the mammalian ribosome. Under hypoxia, the level of hydroxylation of this protein decreases. We transiently transfected HEK293T cells with constructs expressing wild-type uL15 or mutated uL15 (His39Ala) incapable of hydroxylation, and demonstrated that ribosomes containing both proteins are competent in translation. By applying RNA-seq to the total cellular and polysome-associated mRNAs, we identified differentially expressed genes (DEGs) in cells containing exogenous uL15 or its mutant form. Analyzing mRNA features of up- and down-regulated DEGs, we found an increase in the level of more abundant mRNAs and shorter CDSs in cells with uL15 mutant for both translated and total cellular mRNAs. The level of longer and rarer mRNAs, on the contrary, decreased. Our data show how ribosome heterogeneity can change the composition of the translatome and transcriptome, depending on the properties of the translated mRNAs.
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Affiliation(s)
- Elizaveta A Zolotenkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Alexander V Gopanenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Alexey E Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Alexey A Malygin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
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12
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Dyrkheeva NS, Malakhova AA, Zakharenko AL, Okorokova LS, Shtokalo DN, Pavlova SV, Medvedev SP, Zakian SM, Nushtaeva AA, Tupikin AE, Kabilov MR, Khodyreva SN, Luzina OA, Salakhutdinov NF, Lavrik OI. Transcriptomic Analysis of CRISPR/Cas9-Mediated PARP1-Knockout Cells under the Influence of Topotecan and TDP1 Inhibitor. Int J Mol Sci 2023; 24:ijms24065148. [PMID: 36982223 PMCID: PMC10049738 DOI: 10.3390/ijms24065148] [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: 02/08/2023] [Revised: 03/04/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
Topoisomerase 1 (TOP1) is an enzyme that regulates DNA topology and is essential for replication, recombination, and other processes. The normal TOP1 catalytic cycle involves the formation of a short-lived covalent complex with the 3' end of DNA (TOP1 cleavage complex, TOP1cc), which can be stabilized, resulting in cell death. This fact substantiates the effectiveness of anticancer drugs-TOP1 poisons, such as topotecan, that block the relegation of DNA and fix TOP1cc. Tyrosyl-DNA phosphodiesterase 1 (TDP1) is able to eliminate TOP1cc. Thus, TDP1 interferes with the action of topotecan. Poly(ADP-ribose) polymerase 1 (PARP1) is a key regulator of many processes in the cell, such as maintaining the integrity of the genome, regulation of the cell cycle, cell death, and others. PARP1 also controls the repair of TOP1cc. We performed a transcriptomic analysis of wild type and PARP1 knockout HEK293A cells treated with topotecan and TDP1 inhibitor OL9-119 alone and in combination. The largest number of differentially expressed genes (DEGs, about 4000 both up- and down-regulated genes) was found in knockout cells. Topotecan and OL9-119 treatment elicited significantly fewer DEGs in WT cells and negligible DEGs in PARP1-KO cells. A significant part of the changes caused by PARP1-KO affected the synthesis and processing of proteins. Differences under the action of treatment with TOP1 or TDP1 inhibitors alone were found in the signaling pathways for the development of cancer, DNA repair, and the proteasome. The drug combination resulted in DEGs in the ribosome, proteasome, spliceosome, and oxidative phosphorylation pathways.
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Affiliation(s)
- Nadezhda S Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Anastasia A Malakhova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
- Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Aleksandra L Zakharenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | | | - Dmitriy N Shtokalo
- AcademGene LLC, 6 Lavrentyeva Ave., 630090 Novosibirsk, Russia
- A.P. Ershov Institute of Informatics Systems SB RAS, 6 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Sophia V Pavlova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
- Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Sergey P Medvedev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
- Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Suren M Zakian
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
- Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Anna A Nushtaeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Alexey E Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Svetlana N Khodyreva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Olga A Luzina
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Nariman F Salakhutdinov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
- Department of Molecular Biology and Biotechnology, Novosibirsk State University, 630090 Novosibirsk, Russia
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13
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Zakharenko AL, Malakhova AA, Dyrkheeva NS, Okorokova LS, Medvedev SP, Zakian SM, Kabilov MR, Tupikin AA, Lavrik OI. PARP1 Gene Knockout Suppresses Expression of DNA Base Excision Repair Genes. DOKL BIOCHEM BIOPHYS 2023; 508:6-11. [PMID: 36653586 PMCID: PMC10042944 DOI: 10.1134/s1607672922700028] [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: 11/21/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 01/20/2023]
Abstract
The effect of PARP1 knockout in HEK293 cells on the gene expression of DNA base excision repair (BER) proteins was studied. It was shown that the expression of all differentially expressed genes (DEGs) of BER was reduced by knockout. The expression of the DNA glycosylase gene NEIL1, which is considered to be one of the common "hubs" for binding BER proteins, has changed the most. The expression of genes of auxiliary subunits of DNA polymerases δ and ε is also significantly reduced. The PARP1 gene knockout cell line obtained is an adequate cell model for studying the activity of the BER process in the absence of PARP1 and testing drugs aimed at inhibiting repair processes. It has been found for the first time that knockout of the PARP1 gene results in a significant change in the level of expression of proteins responsible for ribosome biogenesis and the functioning of the proteasome.
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Affiliation(s)
- A L Zakharenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Malakhova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Meshalkin National Medical Research Center of the Ministry of Health of the Russian Federation, Novosibirsk, Russia
| | - N S Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | | | - S P Medvedev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Meshalkin National Medical Research Center of the Ministry of Health of the Russian Federation, Novosibirsk, Russia
| | - S M Zakian
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Meshalkin National Medical Research Center of the Ministry of Health of the Russian Federation, Novosibirsk, Russia
| | - M R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - O I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
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14
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Kiselev IS, Kulakova OG, Baturina OA, Kabilov MR, Boyko AN, Favorova OO. [A comparison of DNA methylation profiles of blood mononuclear cells in patients with multiple sclerosis in remission and relapse]. Zh Nevrol Psikhiatr Im S S Korsakova 2023; 123:60-64. [PMID: 37560835 DOI: 10.17116/jnevro202312307260] [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] [Indexed: 08/11/2023]
Abstract
OBJECTIVE To study the whole-genome DNA methylation profiles of peripheral blood mononuclear blood cells (PBMCs) of patients with relapsing-remitting multiple sclerosis (RRMS) in remission and relapse in order to assess the contribution of this epigenetic mechanism of gene expression regulation to the activity of the pathological process. MATERIAL AND METHODS Eight patients with RRMS in remission and 6 patients in relapse were included in the study. Methylation levels of DNA CpG sites in PBMCs were analyzed using Infinium HumanMethylation450 BeadChip DNA microarrays. RESULTS Seven differentially methylated positions (DMPs) were identified, of which 3 were hypermethylated (cg02981003, cg18486102, cg19533582) and 4 were hypomethylated (cg16814680, cg1964802, cg18584440, cg08291996) during RRMS relapse. Five DMPs are located in protein-coding genes (GPR123, FAIM2, BTNL2, ZNF8, ASAP2), one in microRNA gene (MIR548N), and one in an intergenic region. For all identified DMPs, we observed a change in DNA methylation levels of more than 20% (range 20.2-57.5%). Hierarchical clustering of DNA samples on the heatmap shows their clear aggregation into separate clusters corresponding to RRMS patients in the stages of relapse and remission. CONCLUSION For the first time it was shown that during relapse and remission of RRMS there are differences in the DNA methylation profile that allow discrimination between these clinical stages. These data indicate the involvement of the epigenetic mechanism of DNA methylation in the activation of the pathological process in RRMS.
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Affiliation(s)
- I S Kiselev
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - O G Kulakova
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - O A Baturina
- Institute of Chemical Biology and Fundamental Medicine - Genomics Core Facility, Novosibirsk, Russia
| | - M R Kabilov
- Institute of Chemical Biology and Fundamental Medicine - Genomics Core Facility, Novosibirsk, Russia
| | - A N Boyko
- Pirogov Russian National Research Medical University, Moscow, Russia
- Federal Center of Brain Research and Neurotechnologies of the Federal Medical Biological Agency, Moscow, Russia
| | - O O Favorova
- Pirogov Russian National Research Medical University, Moscow, Russia
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15
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Komarova ES, Slesarchuk AN, Rubtsova MP, Osterman IA, Tupikin AE, Pyshnyi DV, Dontsova OA, Kabilov MR, Sergiev PV. Flow-Seq Evaluation of Translation Driven by a Set of Natural Escherichia coli 5'-UTR of Variable Length. Int J Mol Sci 2022; 23:ijms232012293. [PMID: 36293163 PMCID: PMC9604319 DOI: 10.3390/ijms232012293] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/25/2022] Open
Abstract
Flow-seq is a method that combines fluorescently activated cell sorting and next-generation sequencing to deduce a large amount of data about translation efficiency from a single experiment. Here, we constructed a library of fluorescent protein-based reporters preceded by a set of 648 natural 5'-untranslated regions (5'-UTRs) of Escherichia coli genes. Usually, Flow-seq libraries are constructed using uniform-length sequence elements, in contrast to natural situations, where functional elements are of heterogenous lengths. Here, we demonstrated that a 5'-UTR library of variable length could be created and analyzed with Flow-seq. In line with previous Flow-seq experiments with randomized 5'-UTRs, we observed the influence of an RNA secondary structure and Shine-Dalgarno sequences on translation efficiency; however, the variability of these parameters for natural 5'-UTRs in our library was smaller in comparison with randomized libraries. In line with this, we only observed a 30-fold difference in translation efficiency between the best and worst bins sorted with this factor. The results correlated with those obtained with ribosome profiling.
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Affiliation(s)
- Ekaterina S. Komarova
- Institute of Functional Genomics, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Anna N. Slesarchuk
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Maria P. Rubtsova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ilya A. Osterman
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143025 Moscow, Russia
| | - Alexey E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Dmitry V. Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Olga A. Dontsova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143025 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 119992 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Correspondence: (M.R.K.); (P.V.S.)
| | - Petr V. Sergiev
- Institute of Functional Genomics, Lomonosov Moscow State University, 119992 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143025 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Correspondence: (M.R.K.); (P.V.S.)
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16
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Kossinova OA, Gopanenko AV, Babaylova ES, Tupikin AE, Kabilov MR, Malygin AA, Karpova GG. Reorganization of the Landscape of Translated mRNAs in NSUN2-Deficient Cells and Specific Features of NSUN2 Target mRNAs. Int J Mol Sci 2022; 23:ijms23179740. [PMID: 36077143 PMCID: PMC9456143 DOI: 10.3390/ijms23179740] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
The RNA cytosine C5 methyltransferase NSUN2 has a variety of RNA substrates and plays an important role in mRNA metabolism. NSUN2 binds to specific sequences enriched in exosomal mRNAs, suggesting its possible involvement in the sorting of mRNAs into exosomes. We applied the photoactivatable.4-thiouridine-enhanced cross-linking and immunoprecipitation assay involving high-throughput RNA sequencing (RNA-seq) to HEK293T cells to determine NSUN2 mRNA targets. NSUN2 cross-linking sites were found in more than one hundred relatively abundant mRNAs with a high GC content and a pronounced secondary structure. Then, utilizing RNA-seq for the total and polysome-associated mRNA from HEK293T cells with and without the knockdown of NSUN2, we identified differentially expressed genes, as well as genes with altered translational efficiency (GATEs). It turned out that the up-regulated GATE mRNAs were much shorter on average than the down-regulated ones, and their GC content was higher; moreover, they contained motifs with C residues located in GC-rich environments. Our findings reveal the specific features of mRNAs that make them potential targets for NSUN2 and expand our understanding of the role of NSUN2 in controlling translation and, possibly, in mRNA sorting into exosomes implemented through the methylation of cytosine residues.
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Lomakin YA, Zvyagin IV, Ovchinnikova LA, Kabilov MR, Staroverov DB, Mikelov A, Tupikin AE, Zakharova MY, Bykova NA, Mukhina VS, Favorov AV, Ivanova M, Simaniv T, Rubtsov YP, Chudakov DM, Zakharova MN, Illarioshkin SN, Belogurov AA, Gabibov AG. Deconvolution of B cell receptor repertoire in multiple sclerosis patients revealed a delay in tBreg maturation. Front Immunol 2022; 13:803229. [PMID: 36052064 PMCID: PMC9425031 DOI: 10.3389/fimmu.2022.803229] [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: 10/27/2021] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundB lymphocytes play a pivotal regulatory role in the development of the immune response. It was previously shown that deficiency in B regulatory cells (Bregs) or a decrease in their anti-inflammatory activity can lead to immunological dysfunctions. However, the exact mechanisms of Bregs development and functioning are only partially resolved. For instance, only a little is known about the structure of their B cell receptor (BCR) repertoires in autoimmune disorders, including multiple sclerosis (MS), a severe neuroinflammatory disease with a yet unknown etiology. Here, we elucidate specific properties of B regulatory cells in MS.MethodsWe performed a prospective study of the transitional Breg (tBreg) subpopulations with the CD19+CD24highCD38high phenotype from MS patients and healthy donors by (i) measuring their content during two diverging courses of relapsing-remitting MS: benign multiple sclerosis (BMS) and highly active multiple sclerosis (HAMS); (ii) analyzing BCR repertoires of circulating B cells by high-throughput sequencing; and (iii) measuring the percentage of CD27+ cells in tBregs.ResultsThe tBregs from HAMS patients carry the heavy chain with a lower amount of hypermutations than tBregs from healthy donors. The percentage of transitional CD24highCD38high B cells is elevated, whereas the frequency of differentiated CD27+ cells in this transitional B cell subset was decreased in the MS patients as compared with healthy donors.ConclusionsImpaired maturation of regulatory B cells is associated with MS progression.
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Affiliation(s)
- Yakov A. Lomakin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
| | - Ivan V. Zvyagin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
| | - Leyla A. Ovchinnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch Russian Academy of Sciences (RAS), Novosibirsk, Russia
| | - Dmitriy B. Staroverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
| | - Artem Mikelov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alexey E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch Russian Academy of Sciences (RAS), Novosibirsk, Russia
| | - Maria Y. Zakharova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Nadezda A. Bykova
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences (RAS), Moscow, Russia
| | - Vera S. Mukhina
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences (RAS), Moscow, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences (RAS), Moscow, Russia
| | - Alexander V. Favorov
- Vavilov Institute of General Genetics, Russian Academy of Sciences (RAS), Moscow, Russia
- Quantitative Sciences Division, Department of Oncology, Johns Hopkins University, Baltimore, MD, United States
| | - Maria Ivanova
- Neuroinfection Department of the Research Center of Neurology, Moscow, Russia
| | - Taras Simaniv
- Neuroinfection Department of the Research Center of Neurology, Moscow, Russia
| | - Yury P. Rubtsov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
| | - Dmitriy M. Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Maria N. Zakharova
- Neuroinfection Department of the Research Center of Neurology, Moscow, Russia
| | | | - Alexey A. Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
- Department of Biological Chemistry, Evdokimov Moscow State University of Medicine and Dentistry, Moscow, Russia
- *Correspondence: Alexey A. Belogurov Jr., ; Alexander G. Gabibov,
| | - Alexander G. Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
- Department of Life Sciences, Higher School of Economics, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- *Correspondence: Alexey A. Belogurov Jr., ; Alexander G. Gabibov,
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18
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Kiselev IS, Kulakova OG, Danilova LV, Baturina OA, Kabilov MR, Popova EV, Boyko AN, Favorova OO. [Genome-Wide Analysis of DNA Methylation in Cd4+ T Lymphocytes of Patients with Primary Progressive Multiple Sclerosis Indicates Involvement of This Epigenetic Process in the Disease Immunopathogenesis]. Mol Biol (Mosk) 2022; 56:468-475. [PMID: 35621102 DOI: 10.31857/s0026898422030089] [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: 10/18/2021] [Accepted: 11/02/2021] [Indexed: 06/15/2023]
Abstract
The pathogenesis of multiple sclerosis (MS), a chronic disease of the CNS, includes autoimmune and neurodegenerative components. In most cases, patients develop relapsing-remitting MS (RRMS), while 10-15% of patients develop primary progressive MS (PPMS), which differs from RRMS in the mechanisms of the pathological process, some demographic, and some clinical characteristics. These differences may be explained by the epigenetic regulation of gene expression in PPMS including DNA methylation as one of the key epigenetic processes. The features of DNA methylation in various cell populations in PPMS patients remain understudied. The goal of this study is to identify differentially methylated CpG sites (DMSs) of the genome of CD4+ T lymphocytes, which characterize PPMS. The study included eight treatment-naive PPMS patients and eight healthy controls. Genome-wide analysis of DNA methylation of CD4+ T lymphocytes was performed using high-density DNA microarrays. We have identified 108 DMSs, which distinguish PPMS patients from healthy controls. In PPMS patients 81% of the DMSs are hypermethylated. More than a half of the identified DMSs are located in known genes in CpG islands and adjacent regions, which indicates a high functional significance of these DMSs in PPMS development. Analysis of the overrepresentation of DMS-containing genes in the main biological processes demonstrates their involvement in the regulation of cell adhesion to the extracellular matrix and the development of the immune response, i.e., antigen processing and presentation, and development of the immune system. Genome-wide analysis of DNA methylation in CD4+ T lymphocytes of PPMS patients indicates the involvement of this epigenetic process in the immunopathogenesis of the disease. These results may help better understand the pathogenesis of this severe form of MS.
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Affiliation(s)
- I S Kiselev
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
- National Medical Research Center for Cardiology, Moscow, 121552 Russia
| | - O G Kulakova
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
- National Medical Research Center for Cardiology, Moscow, 121552 Russia
| | - L V Danilova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991 Russia
- Johns Hopkins School of Medicine, Baltimore, MD 21205 USA
| | - O A Baturina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - M R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - E V Popova
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
| | - A N Boyko
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
- Federal Center for Brain and Neurotechnology, Federal Medical and Biological Agency of the Russian Federation, Moscow, 117997 Russia
| | - O O Favorova
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
- National Medical Research Center for Cardiology, Moscow, 121552 Russia
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Babaylova ES, Gopanenko AV, Tupikin AE, Kabilov MR, Malygin AA, Karpova GG. Deficiency of the Ribosomal Protein uL5 Leads to Significant Rearrangements of the Transcriptional and Translational Landscapes in Mammalian Cells. Int J Mol Sci 2021; 22:ijms222413485. [PMID: 34948282 PMCID: PMC8706191 DOI: 10.3390/ijms222413485] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/23/2022] Open
Abstract
Protein uL5 (formerly called L11) is an integral component of the large (60S) subunit of the human ribosome, and its deficiency in cells leads to the impaired biogenesis of 60S subunits. Using RNA interference, we reduced the level of uL5 in HEK293T cells by three times, which caused an almost proportional decrease in the content of the fraction corresponding to 80S ribosomes, without a noticeable diminution in the level of polysomes. By RNA sequencing of uL5-deficient and control cell samples, which were those of total mRNA and mRNA from the polysome fraction, we identified hundreds of differentially expressed genes (DEGs) at the transcriptome and translatome levels and revealed dozens of genes with altered translational efficiency (GATEs). Transcriptionally up-regulated DEGs were mainly associated with rRNA processing, pre-mRNA splicing, translation and DNA repair, while down-regulated DEGs were genes of membrane proteins; the type of regulation depended on the GC content in the 3′ untranslated regions of DEG mRNAs. The belonging of GATEs to up-regulated and down-regulated ones was determined by the coding sequence length of their mRNAs. Our findings suggest that the effects observed in uL5-deficient cells result from an insufficiency of translationally active ribosomes caused by a deficiency of 60S subunits.
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20
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Komarevtsev SK, Evseev PV, Shneider MM, Popova EA, Tupikin AE, Stepanenko VN, Kabilov MR, Shabunin SV, Osmolovskiy AA, Miroshnikov KA. Gene Analysis, Cloning, and Heterologous Expression of Protease from a Micromycete Aspergillus ochraceus Capable of Activating Protein C of Blood Plasma. Microorganisms 2021; 9:1936. [PMID: 34576831 PMCID: PMC8471544 DOI: 10.3390/microorganisms9091936] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/05/2021] [Accepted: 09/08/2021] [Indexed: 12/16/2022] Open
Abstract
Micromycetes are known to secrete numerous enzymes of biotechnological and medical potential. Fibrinolytic protease-activator of protein C (PAPC) of blood plasma from micromycete Aspergillus ochraceus VKM-F4104D was obtained in recombinant form utilising the bacterial expression system. This enzyme, which belongs to the proteinase-K-like proteases, is similar to the proteases encoded in the genomes of Aspergillus fumigatus ATCC MYA-4609, A. oryzae ATCC 42149 and A. flavus 28. Mature PAPC-4104 is 282 amino acids long, preceded by the 101-amino acid propeptide necessary for proper folding and maturation. The recombinant protease was identical to the native enzyme from micromycete in terms of its biological properties, including an ability to hydrolyse substrates of activated protein C (pGlu-Pro-Arg-pNA) and factor Xa (Z-D-Arg-Gly-Arg-pNA) in conjugant reactions with human blood plasma. Therefore, recombinant PAPC-4104 can potentially be used in medicine, veterinary science, diagnostics, and other applications.
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Affiliation(s)
- Sergei K. Komarevtsev
- Biology Department, Lomonosov Moscow State University, 119234 Moscow, Russia; (E.A.P.); (A.A.O.)
- All-Russian Scientific Research Veterinary Institute of Pathology, Pharmacology and Therapy, 394087 Voronezh, Russia; (S.V.S.); (K.A.M.)
| | - Peter V. Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (M.M.S.); (V.N.S.)
| | - Mikhail M. Shneider
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (M.M.S.); (V.N.S.)
| | - Elizaveta A. Popova
- Biology Department, Lomonosov Moscow State University, 119234 Moscow, Russia; (E.A.P.); (A.A.O.)
| | - Alexey E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.E.T.); (M.R.K.)
| | - Vasiliy N. Stepanenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (M.M.S.); (V.N.S.)
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.E.T.); (M.R.K.)
| | - Sergei V. Shabunin
- All-Russian Scientific Research Veterinary Institute of Pathology, Pharmacology and Therapy, 394087 Voronezh, Russia; (S.V.S.); (K.A.M.)
| | - Alexander A. Osmolovskiy
- Biology Department, Lomonosov Moscow State University, 119234 Moscow, Russia; (E.A.P.); (A.A.O.)
- All-Russian Scientific Research Veterinary Institute of Pathology, Pharmacology and Therapy, 394087 Voronezh, Russia; (S.V.S.); (K.A.M.)
| | - Konstantin A. Miroshnikov
- All-Russian Scientific Research Veterinary Institute of Pathology, Pharmacology and Therapy, 394087 Voronezh, Russia; (S.V.S.); (K.A.M.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (M.M.S.); (V.N.S.)
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21
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Tyurin M, Kabilov MR, Smirnova N, Tomilova OG, Yaroslavtseva O, Alikina T, Glupov VV, Kryukov VY. Can Potato Plants Be Colonized with the Fungi Metarhizium and Beauveria under Their Natural Load in Agrosystems? Microorganisms 2021; 9:1373. [PMID: 34202827 PMCID: PMC8306205 DOI: 10.3390/microorganisms9071373] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 05/26/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 12/26/2022] Open
Abstract
Beauveria and Metarhizium fungi are facultative plant endophytes that provide plant growth-stimulating, immunomodulatory, and other beneficial effects. However, little is known about the level of plant colonization by these fungi under natural conditions. We assessed the endophytic colonization of potatoes (Solanum tuberosum) with entomopathogenic fungi at their natural load in soils (102-104 colony-forming units per g). Microbiological analyses of soils and plant organs, as well as a metagenomic analysis of potato roots and leaves, were conducted in three locations in Western Siberia, consisting of conventional agrosystems and kitchen gardens. The fungi were isolated at a relatively high frequency from unsterilized roots (up to 53% of Metarhizium-positive plants). However, the fungi were sparsely isolated from the internal tissues of roots, stems, and leaves (3%). Among the genus Metarhizium, two species, M. robertsii and M. brunneum, were detected in plants as well as in soils, and the first species was predominant. A metagenomic analysis of internal potato tissues showed a low relative abundance of Beauveria and Metarhizium (<0.3%), and the communities were represented primarily by phytopathogens. We suggest that colonization of the internal tissues of potatoes occurs sporadically under a natural load of entomopathogenic fungi in soils. The lack of stable colonization of potato plants with Beauveria and Metarhizium may be due to competition with phytopathogens.
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Affiliation(s)
- Maksim Tyurin
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, 630091 Novosibirsk, Russia; (O.G.T.); (O.Y.); (V.V.G.)
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.R.K.); (T.A.)
| | - Natalia Smirnova
- Institute of Soil Science and Agrochemistry, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia;
| | - Oksana G. Tomilova
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, 630091 Novosibirsk, Russia; (O.G.T.); (O.Y.); (V.V.G.)
| | - Olga Yaroslavtseva
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, 630091 Novosibirsk, Russia; (O.G.T.); (O.Y.); (V.V.G.)
| | - Tatyana Alikina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.R.K.); (T.A.)
| | - Viktor V. Glupov
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, 630091 Novosibirsk, Russia; (O.G.T.); (O.Y.); (V.V.G.)
| | - Vadim Yu Kryukov
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, 630091 Novosibirsk, Russia; (O.G.T.); (O.Y.); (V.V.G.)
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22
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Gopanenko AV, Kolobova AV, Tupikin AE, Kabilov MR, Malygin AA, Karpova GG. Knockdown of the Ribosomal Protein eL38 in HEK293 Cells Changes the Translational Efficiency of Specific Genes. Int J Mol Sci 2021; 22:ijms22094531. [PMID: 33926116 PMCID: PMC8123606 DOI: 10.3390/ijms22094531] [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] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/22/2021] [Accepted: 04/24/2021] [Indexed: 11/23/2022] Open
Abstract
The protein eL38 is one of the smallest proteins of the mammalian ribosome, which is a component of its large (60S) subunit. The haploinsufficiency of eL38 in mice leads to the Tail-short mutant phenotype characterized by defects in the development of the axial skeleton caused by the poor translation of mRNA subsets of Hox genes. Using the ribosome profiling assay applied to HEK293 cells knocked down of eL38, we examined the effects of the lack of eL38 in 60S subunits on gene expression at the level of translation. A four-fold decrease in the cell content of eL38 was shown to result in significant changes in the translational efficiencies of 150 genes. Among the genes, whose expression at the level of translation was enhanced, there were mainly those associated with basic metabolic processes; namely, translation, protein folding, chromosome organization, splicing, and others. The set of genes with reduced translation efficiencies contained those that are mostly involved in the processes related to the regulation of transcription, including the activation of Hox genes. Thus, we demonstrated that eL38 insufficiency significantly affects the expression of certain genes at the translational level. Our findings facilitate understanding the possible causes of some anomalies in eL38-deficient animals.
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23
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Butina TV, Bukin YS, Petrushin IS, Tupikin AE, Kabilov MR, Belikov SI. Extended Evaluation of Viral Diversity in Lake Baikal through Metagenomics. Microorganisms 2021; 9:760. [PMID: 33916464 PMCID: PMC8066274 DOI: 10.3390/microorganisms9040760] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 01/31/2021] [Revised: 03/22/2021] [Accepted: 03/31/2021] [Indexed: 11/16/2022] Open
Abstract
Lake Baikal is a unique oligotrophic freshwater lake with unusually cold conditions and amazing biological diversity. Studies of the lake's viral communities have begun recently, and their full diversity is not elucidated yet. Here, we performed DNA viral metagenomic analysis on integral samples from four different deep-water and shallow stations of the southern and central basins of the lake. There was a strict distinction of viral communities in areas with different environmental conditions. Comparative analysis with other freshwater lakes revealed the highest similarity of Baikal viromes with those of the Asian lakes Soyang and Biwa. Analysis of new data, together with previously published data allowed us to get a deeper insight into the diversity and functional potential of Baikal viruses; however, the true diversity of Baikal viruses in the lake ecosystem remains still unknown. The new metaviromic data will be useful for future studies of viral composition, distribution, and the dynamics associated with global climatic and anthropogenic impacts on this ecosystem.
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Affiliation(s)
- Tatyana V. Butina
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, 664033 Irkutsk, Russia; (I.S.P.); (S.I.B.)
| | - Yurij S. Bukin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, 664033 Irkutsk, Russia; (I.S.P.); (S.I.B.)
| | - Ivan S. Petrushin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, 664033 Irkutsk, Russia; (I.S.P.); (S.I.B.)
| | - Alexey E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.E.T.); (M.R.K.)
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.E.T.); (M.R.K.)
| | - Sergey I. Belikov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, 664033 Irkutsk, Russia; (I.S.P.); (S.I.B.)
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24
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Polenogova OV, Noskov YA, Yaroslavtseva ON, Kryukova NA, Alikina T, Klementeva TN, Andrejeva J, Khodyrev VP, Kabilov MR, Kryukov VY, Glupov VV. Influence of Bacillus thuringiensis and avermectins on gut physiology and microbiota in Colorado potato beetle: Impact of enterobacteria on susceptibility to insecticides. PLoS One 2021; 16:e0248704. [PMID: 33760838 PMCID: PMC7990289 DOI: 10.1371/journal.pone.0248704] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 10/31/2020] [Accepted: 03/03/2021] [Indexed: 11/19/2022] Open
Abstract
Gut physiology and the bacterial community play crucial roles in insect susceptibility to infections and insecticides. Interactions among Colorado potato beetle Leptinotarsa decemlineata (Say), its bacterial associates, pathogens and xenobiotics have been insufficiently studied. In this paper, we present our study of the survival, midgut histopathology, activity of digestive enzymes and bacterial communities of L. decemlineata larvae under the influence of Bacillus thuringiensis var. tenebrionis (morrissoni) (Bt), a natural complex of avermectins and a combination of both agents. Moreover, we estimated the impact of culturable enterobacteria on the susceptibility of the larvae to Bt and avermectins. An additive effect between Bt and avermectins was established regarding the mortality of the larvae. Both agents led to the destruction of midgut tissues, a decrease in the activity of alpha-amylases and alkaline proteinases, a decrease in the Spiroplasma leptinotarsae relative abundance and a strong elevation of Enterobacteriaceae abundance in the midgut. Moreover, an elevation of the enterobacterial CFU count was observed under the influence of Bt and avermectins, and the greatest enhancement was observed after combined treatment. Insects pretreated with antibiotics were less susceptible to Bt and avermectins, but reintroduction of the predominant enterobacteria Enterobacter ludwigii, Citrobacter freundii and Serratia marcescens increased susceptibility to both agents. We suggest that enterobacteria play an important role in the acceleration of Bt infection and avermectin toxicoses in L. decemlineata and that the additive effect between Bt and avermectin may be mediated by alterations in the bacterial community.
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Affiliation(s)
- Olga V. Polenogova
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Yury A. Noskov
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- National Research Tomsk State University, Tomsk, Russia
| | - Olga N. Yaroslavtseva
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Natalya A. Kryukova
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Tatyana Alikina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Tatyana N. Klementeva
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Jelizaveta Andrejeva
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Viktor P. Khodyrev
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Vadim Yu Kryukov
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- National Research Tomsk State University, Tomsk, Russia
| | - Viktor V. Glupov
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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25
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Gopanenko AV, Kolobova AV, Meschaninova MI, Venyaminova AG, Tupikin AE, Kabilov MR, Malygin AA, Karpova GG. Knockdown of the mRNA encoding the ribosomal protein eL38 in mammalian cells causes a substantial reorganization of genomic transcription. Biochimie 2021; 184:132-142. [PMID: 33675855 DOI: 10.1016/j.biochi.2021.02.017] [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: 12/13/2020] [Revised: 02/19/2021] [Accepted: 02/26/2021] [Indexed: 02/08/2023]
Abstract
The ribosomal protein eL38 is a component of the mammalian translation machine. The deletion of the Rpl38 locus in mice results in the Tail-short (Ts) mutant phenotype characterized by a shortened tail and other defects in the axial skeleton development. Here, using the next-generation sequencing of total RNA from HEK293 cells knocked down of eL38 mRNA by transfection with specific siRNAs, we examined the effect of reduced eL38 content on genomic transcription. An approximately 4-fold decrease in the level of eL38 was shown to cause changes in the expression of nearly 1500 genes. Among the down-regulated genes, there were those responsible for p53 activity, Ca2+ metabolism and several signaling processes, as well as genes involved in the organization and functioning of the cytoskeleton. The genes related to rRNA processing and translation, along with many others, including those whose dysregulation is associated with developmental disorders, turned out to be up-regulated. Thus, we demonstrated that the decreased RPL38 expression leads to a significant reorganization of genomic transcription. Our findings suggest a possible link between the balance of eL38 and genes implicated in osteogenesis, thereby contributing to the elucidation of the reasons for the appearance of the above Ts mutant phenotype in animals.
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Affiliation(s)
- Alexander V Gopanenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Alena V Kolobova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Maria I Meschaninova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Alya G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Alexey E Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Alexey A Malygin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Galina G Karpova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
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26
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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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27
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Noskov YA, Kabilov MR, Polenogova OV, Yurchenko YA, Belevich OE, Yaroslavtseva ON, Alikina TY, Byvaltsev AM, Rotskaya UN, Morozova VV, Glupov VV, Kryukov VY. A Neurotoxic Insecticide Promotes Fungal Infection in Aedes aegypti Larvae by Altering the Bacterial Community. Microb Ecol 2021; 81:493-505. [PMID: 32839879 DOI: 10.1007/s00248-020-01567-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/27/2020] [Indexed: 06/11/2023]
Abstract
Symbiotic bacteria have a significant impact on the formation of defensive mechanisms against fungal pathogens and insecticides. The microbiome of the mosquito Aedes aegypti has been well studied; however, there are no data on the influence of insecticides and pathogenic fungi on its structure. The fungus Metarhizium robertsii and a neurotoxic insecticide (avermectin complex) interact synergistically, and the colonization of larvae with hyphal bodies is observed after fungal and combined (conidia + avermectins) treatments. The changes in the bacterial communities (16S rRNA) of Ae. aegypti larvae under the influence of fungal infection, avermectin toxicosis, and their combination were studied. In addition, we studied the interactions between the fungus and the predominant cultivable bacteria in vitro and in vivo after the coinfection of the larvae. Avermectins increased the total bacterial load and diversity. The fungus decreased the diversity and insignificantly increased the bacterial load. Importantly, avermectins reduced the relative abundance of Microbacterium (Actinobacteria), which exhibited a strong antagonistic effect towards the fungus in in vitro and in vivo assays. The avermectin treatment led to an increased abundance of Chryseobacterium (Flavobacteria), which exerted a neutral effect on mycosis development. In addition, avermectin treatment led to an elevation of some subdominant bacteria (Pseudomonas) that interacted synergistically with the fungus. We suggest that avermectins change the bacterial community to favor the development of fungal infection.
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Affiliation(s)
- Y A Noskov
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia, 630091.
- National Research Tomsk State University, Tomsk, Russia, 634050.
| | - M R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia, 630090
| | - O V Polenogova
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia, 630091
| | - Y A Yurchenko
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia, 630091
| | - O E Belevich
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia, 630091
| | - O N Yaroslavtseva
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia, 630091
| | - T Y Alikina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia, 630090
| | - A M Byvaltsev
- Novosibirsk State University, Novosibirsk, Russia, 630090
| | - U N Rotskaya
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia, 630091
| | - V V Morozova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia, 630090
| | - V V Glupov
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia, 630091
| | - V Y Kryukov
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia, 630091
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28
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Kozhieva M, Naumova N, Alikina T, Boyko A, Vlassov V, Kabilov MR. The Core of Gut Life: Firmicutes Profile in Patients with Relapsing-Remitting Multiple Sclerosis. Life (Basel) 2021; 11:life11010055. [PMID: 33466726 PMCID: PMC7828771 DOI: 10.3390/life11010055] [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: 11/29/2020] [Revised: 12/27/2020] [Accepted: 01/11/2021] [Indexed: 12/26/2022] Open
Abstract
The multiple sclerosis (MS) incidence rate has been increasing in Russia, but the information about the gut bacteriobiome in the MS-afflicted patients is scarce. Using the Illumina MiSeq sequencing of 16S rRNA gene amplicons, we aimed to analyze the Firmicutes phylum and its taxa in a cohort of Moscow patients with relapsing-remitting MS, assessing the effects of age, BMI, disease modifying therapy (DMT), disability (EDSS), and gender. Among 1252 identified bacterial OTUs, 857 represented Firmicutes. The phylum was the most abundant also in sequence reads, overall averaging 74 ± 13%. The general linear model (GLM) analysis implicated Firmicutes/Clostridia/Clostridiales/Lachospiraceae/Blautia/Blautia wexlerae as increasing with BMI, and only Lachospiraceae/Blautia/Blautia wexlerae as increasing with age. A marked DMT-related decrease in Firmicutes was observed in females at the phylum, class (Clostridia), and order (Clostridiales) levels. The results of our study implicate DMT and gender as factors shaping the fecal Firmicutes assemblages. Together with the gender-dependent differential MS incidence growth rate in the country, the results suggest the likely involvement of gender-specific pathoecological mechanisms underlying the occurrence of the disease, switching between its phenotypes and response to disease-modifying therapies. Overall, the presented profile of Firmicutes can be used as a reference for more detailed research aimed at elucidating the contribution of this core phylum and its lower taxa into the etiology and progression of relapsing-remitting multiple sclerosis.
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Affiliation(s)
- Madina Kozhieva
- Department of Neurology, Neurosurgery and Medical Genetics of the Pirogov Medical University, 117513 Moscow, Russia;
| | - Natalia Naumova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (T.A.); (V.V.); (M.R.K.)
- Correspondence: or
| | - Tatiana Alikina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (T.A.); (V.V.); (M.R.K.)
| | - Alexey Boyko
- Department of Neuroimmunology of the Federal Center of CVPI, 117513 Moscow, Russia;
| | - Valentin Vlassov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (T.A.); (V.V.); (M.R.K.)
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (T.A.); (V.V.); (M.R.K.)
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29
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Babaylova ES, Kolobova AV, Gopanenko AV, Tupikin AE, Kabilov MR, Malygin AA, Karpova GG. The human ribosomal protein eL29 binds in vivo to the cognate mRNA by interacting with its coding sequence, as revealed from in-cell cross-linking data. Biochimie 2020; 177:68-77. [DOI: 10.1016/j.biochi.2020.07.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 01/21/2023]
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30
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Osterman IA, Chervontseva ZS, Evfratov SA, Sorokina AV, Rodin VA, Rubtsova MP, Komarova ES, Zatsepin TS, Kabilov MR, Bogdanov AA, Gelfand MS, Dontsova OA, Sergiev PV. Translation at first sight: the influence of leading codons. Nucleic Acids Res 2020; 48:6931-6942. [PMID: 32427319 PMCID: PMC7337518 DOI: 10.1093/nar/gkaa430] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/07/2020] [Accepted: 05/14/2020] [Indexed: 01/31/2023] Open
Abstract
First triplets of mRNA coding region affect the yield of translation. We have applied the flowseq method to analyze >30 000 variants of the codons 2-11 of the fluorescent protein reporter to identify factors affecting the protein synthesis. While the negative influence of mRNA secondary structure on translation has been confirmed, a positive role of rare codons at the beginning of a coding sequence for gene expression has not been observed. The identity of triplets proximal to the start codon contributes more to the protein yield then more distant ones. Additional in-frame start codons enhance translation, while Shine-Dalgarno-like motifs downstream the initiation codon are inhibitory. The metabolic cost of amino acids affects the yield of protein in the poor medium. The most efficient translation was observed for variants with features resembling those of native Escherichia coli genes.
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Affiliation(s)
- Ilya A Osterman
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,Lomonosov Moscow State University, Moscow 119992, Russia
| | - Zoe S Chervontseva
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,A.A.Kharkevich Institute for Information Transmission Problems, Moscow 127051, Russia
| | | | - Alena V Sorokina
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia
| | | | - Maria P Rubtsova
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,Lomonosov Moscow State University, Moscow 119992, Russia
| | - Ekaterina S Komarova
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,Lomonosov Moscow State University, Moscow 119992, Russia
| | - Timofei S Zatsepin
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,Lomonosov Moscow State University, Moscow 119992, Russia
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | | | - Mikhail S Gelfand
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,A.A.Kharkevich Institute for Information Transmission Problems, Moscow 127051, Russia
| | - Olga A Dontsova
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,Lomonosov Moscow State University, Moscow 119992, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Petr V Sergiev
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,Lomonosov Moscow State University, Moscow 119992, Russia
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31
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Butina TV, Bukin YS, Krasnopeev AS, Belykh OI, Tupikin AE, Kabilov MR, Sakirko МV, Belikov SI. Estimate of the diversity of viral and bacterial assemblage in the coastal water of Lake Baikal. FEMS Microbiol Lett 2020; 366:5484837. [PMID: 31049590 DOI: 10.1093/femsle/fnz094] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 09/01/2017] [Accepted: 04/30/2019] [Indexed: 12/27/2022] Open
Abstract
In this study, we analysed the diversity and composition of double-stranded DNA viral and bacterial communities within the sample of surface coastal water of Southern Baikal through metagenomics and deep sequencing of the 16S ribosomal RNA gene, respectively. The 16S rRNA gene analysis has revealed 14 phyla and dominance of the 'Actinobacteria' (43.6%), 'Proteobacteria' (25.2%) and 'Bacteroidetes' (11.5%). The bacterial composition was similar to that obtained previously in Lake Baikal littoral zone. Out of 1 030 169 processed virome reads, 37.4% of sequences (385 421) were identified as viral; 15.1% were identified as nonviral and related to the domains Eukarya, Bacteria and Archaea; and 47.5% had no matches in the databases. The identified virotypes belonged to different families and were predicted to infect a wide range of organisms, from bacteria to mammals. Six families (Myoviridae, Poxviridae, Mimiviridae, Siphoviridae, Phycodnaviridae and Podoviridae) were dominant accounting for more than 90% of the identified sequences (48.3%, 17.4%, 8.3%, 6.8%, 5.8% and 4.1%, respectively). In contrast to other freshwater systems, high percentage of the Poxviridae and Mimiviridae was recorded in the water sample of Lake Baikal.
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Affiliation(s)
- Tatyana V Butina
- Laboratory of Analytical and Bioorganic Chemistry, Limnological Institute, Siberian Branch of Russian Academy of Sciences, 3, Ulan-Batorskaya street, Irkutsk, 664033, Russia
| | - Yurij S Bukin
- Laboratory of Genosystematics, Limnological Institute, Siberian Branch of Russian Academy of Sciences, 3, Ulan-Batorskaya street, Irkutsk, 664033, Russia.,Department of Biotechnology and Bioinformatics, National Research Irkutsk State Technical University, 83, Lermontov street, Irkutsk, 664074, Russia
| | - Andrey S Krasnopeev
- Laboratory of Aquatic Microbiology, Limnological Institute, Siberian Branch of Russian Academy of Sciences, 3, Ulan-Batorskaya street, Irkutsk, 664033, Russia
| | - Olga I Belykh
- Laboratory of Aquatic Microbiology, Limnological Institute, Siberian Branch of Russian Academy of Sciences, 3, Ulan-Batorskaya street, Irkutsk, 664033, Russia
| | - Aleksey E Tupikin
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Avenue, Novosibirsk, 630090, Russia
| | - Marsel R Kabilov
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Avenue, Novosibirsk, 630090, Russia
| | - Мaria V Sakirko
- Laboratory of Hydrochemistry and Atmosphere Chemistry, Limnological Institute, Siberian Branch of Russian Academy of Sciences, 3, Ulan-Batorskaya street, Irkutsk, 664033, Russia
| | - Sergey I Belikov
- Laboratory of Analytical and Bioorganic Chemistry, Limnological Institute, Siberian Branch of Russian Academy of Sciences, 3, Ulan-Batorskaya street, Irkutsk, 664033, Russia
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32
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Krasitskaya VV, Goncharova NS, Biriukov VV, Bashmakova EE, Kabilov MR, Baykov IK, Sokolov AE, Frank LA. The Ca 2+ -Regulated Photoprotein Obelin as a Tool for SELEX Monitoring and DNA Aptamer Affinity Evaluation. Photochem Photobiol 2020; 96:1041-1046. [PMID: 32304233 DOI: 10.1111/php.13274] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/29/2020] [Indexed: 12/11/2022]
Abstract
Bioluminescent solid-phase analysis was proposed to monitor the selection process and to determine binding characteristics of the aptamer-target complexes during design and development of the specific aptamers. The assay involves Ca2+ -regulated photoprotein obelin as a simple, sensitive and fast reporter. Applicability and the prospects of the approach were exemplified by identification of DNA aptamers to cardiac troponin I, a highly specific early biomarker for acute myocardial infarction. Two structurally different aptamers specific to various epitopes of troponin I were obtained and then tested in a model bioluminescent assay.
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Affiliation(s)
| | | | | | - Eugenia E Bashmakova
- Institute of Biophysics SB RAS, Federal Research Center KSC SB RAS, Krasnoyarsk, Russia
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Ivan K Baykov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Aleksey E Sokolov
- Siberian Federal University, Krasnoyarsk, Russia.,Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Krasnoyarsk, Russia
| | - Ludmila A Frank
- Institute of Biophysics SB RAS, Federal Research Center KSC SB RAS, Krasnoyarsk, Russia.,Siberian Federal University, Krasnoyarsk, Russia
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33
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Kutikhin AG, Tupikin AE, Matveeva VG, Shishkova DK, Antonova LV, Kabilov MR, Velikanova EA. Human Peripheral Blood-Derived Endothelial Colony-Forming Cells Are Highly Similar to Mature Vascular Endothelial Cells yet Demonstrate a Transitional Transcriptomic Signature. Cells 2020; 9:cells9040876. [PMID: 32260159 PMCID: PMC7226818 DOI: 10.3390/cells9040876] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [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: 03/02/2020] [Revised: 03/30/2020] [Accepted: 04/02/2020] [Indexed: 02/06/2023] Open
Abstract
Endothelial colony-forming cells (ECFC) are currently considered as a promising cell population for the pre-endothelialization or pre-vascularization of tissue-engineered constructs, including small-diameter biodegradable vascular grafts. However, the extent of heterogeneity between ECFC and mature vascular endothelial cells (EC) is unclear. Here, we performed a transcriptome-wide study to compare gene expression profiles of ECFC, human coronary artery endothelial cells (HCAEC), and human umbilical vein endothelial cells (HUVEC). Characterization of the abovementioned cell populations was carried out by immunophenotyping, tube formation assay, and evaluation of proliferation capability while global gene expression profiling was conducted by means of RNA-seq. ECFC were similar to HUVEC in terms of immunophenotype (CD31+vWF+KDR+CD146+CD34-CD133-CD45-CD90-) and tube formation activity yet had expectedly higher proliferative potential. HCAEC and HUVEC were generally similar to ECFC with regards to their global gene expression profile; nevertheless, ECFC overexpressed specific markers of all endothelial lineages (NRP2, NOTCH4, LYVE1), in particular lymphatic EC (LYVE1), and had upregulated extracellular matrix and basement membrane genes (COL1A1, COL1A2, COL4A1, COL4A2). Proteomic profiling for endothelial lineage markers and angiogenic molecules generally confirmed RNA-seq results, indicating ECFC as an intermediate population between HCAEC and HUVEC. Therefore, gene expression profile and behavior of ECFC suggest their potential to be applied for a pre-endothelialization of bioartificial vascular grafts, whereas in terms of endothelial hierarchy they differ from HCAEC and HUVEC, having a transitional phenotype.
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Affiliation(s)
- Anton G. Kutikhin
- Research Institute for Complex Issues of Cardiovascular Diseases, 6 Sosnovy Boulevard, Kemerovo 650002, Russia; (V.G.M.); (D.K.S.); (L.V.A.); (E.A.V.)
- Correspondence: ; Tel.: +7-960-907-70-67
| | - Alexey E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia; (A.E.T.); (M.R.K.)
| | - Vera G. Matveeva
- Research Institute for Complex Issues of Cardiovascular Diseases, 6 Sosnovy Boulevard, Kemerovo 650002, Russia; (V.G.M.); (D.K.S.); (L.V.A.); (E.A.V.)
| | - Daria K. Shishkova
- Research Institute for Complex Issues of Cardiovascular Diseases, 6 Sosnovy Boulevard, Kemerovo 650002, Russia; (V.G.M.); (D.K.S.); (L.V.A.); (E.A.V.)
| | - Larisa V. Antonova
- Research Institute for Complex Issues of Cardiovascular Diseases, 6 Sosnovy Boulevard, Kemerovo 650002, Russia; (V.G.M.); (D.K.S.); (L.V.A.); (E.A.V.)
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia; (A.E.T.); (M.R.K.)
| | - Elena A. Velikanova
- Research Institute for Complex Issues of Cardiovascular Diseases, 6 Sosnovy Boulevard, Kemerovo 650002, Russia; (V.G.M.); (D.K.S.); (L.V.A.); (E.A.V.)
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34
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Babaylova ES, Gopanenko AV, Bulygin KN, Tupikin AE, Kabilov MR, Malygin AA, Karpova GG. mRNA regions where 80S ribosomes pause during translation elongation in vivo interact with protein uS19, a component of the decoding site. Nucleic Acids Res 2020; 48:912-923. [PMID: 31802126 PMCID: PMC6954443 DOI: 10.1093/nar/gkz1145] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 11/21/2019] [Accepted: 11/25/2019] [Indexed: 11/25/2022] Open
Abstract
In eukaryotic ribosomes, the conserved protein uS19, formerly known as S15, extends with its C-terminal tail to the decoding site. The cross-linking of uS19 to the A site codon has been detected using synthetic mRNAs bearing 4-thiouridine (s4U) residues. Here, we showed that the A-site tRNA prevents this cross-linking and that the P site codon does not contact uS19. Next, we focused on determining uS19-mRNA interactions in vivo by applying the photoactivatable-ribonucleoside enhancing cross-linking and immunoprecipitation method to a stable HEK293 cell line producing FLAG-tagged uS19 and grown in a medium containing s4U. We found that when translation was stopped by cycloheximide, uS19 was efficiently cross-linked to mRNA regions with a high frequency of Glu, Lys and, more rarely, Arg codons. The results indicate that the complexes, in which the A site codon is not involved in the formation of the mRNA-tRNA duplex, are present among the cycloheximide-arrested 80S complexes, which implies pausing of elongating ribosomes at the above mRNA regions. Thus, our findings demonstrate that the human ribosomal protein uS19 interacts with mRNAs during translation elongation and highlight the regions of mRNAs where ribosome pausing occurs, bringing new structural and functional insights into eukaryotic translation in vivo.
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Affiliation(s)
- Elena S Babaylova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia
| | - Alexander V Gopanenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia
| | - Konstantin N Bulygin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia
| | - Alexey E Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia
| | - Alexey A Malygin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Galina G Karpova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
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Gopanenko AV, Malygin AA, Kossinova OA, Tupikin AE, Kabilov MR, Karpova GG. Degenerate consensus sequences in the 3'-untranslated regions of cellular mRNAs as specific motifs potentially involved in the YB-1-mediated packaging of these mRNAs. Biochimie 2020; 170:152-162. [PMID: 31935443 DOI: 10.1016/j.biochi.2020.01.005] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/09/2020] [Indexed: 02/08/2023]
Abstract
The multifunctional protein YB-1 has previously been shown to be the only protein of the cytoplasmic extract of HEK293 cells, which is able to specifically interact with imperfect RNA hairpins containing motifs that are often found in exosomal (e) RNAs. In addition, it has been revealed that similar hairpins formed by degenerate consensus sequences corresponding to three eRNA-specific motifs are responsible for the cooperative binding of YB-1 to RNA in vitro. Here, using the photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation method applied to HEK293 cells producing FLAG-labeled YB-1, we identified mRNAs cross-linked to YB-1 in vivo and then carried out a search for the aforementioned sequences in the regions of the YB-1 cross-linking sites. It turned out that many of the mRNAs found cross-linked to YB-1 encode proteins associated with various regulatory processes, including responses to stress. More than half of all cross-linked mRNAs contained degenerate consensus sequences, which were preferably located in 3'-untranslated regions (UTRs), where most of the YB-1 cross-linking sites appeared, although not close to these sequences. Furthermore, YB-1 was mainly cross-linked to those mRNAs with degenerate consensus sequences, which could be classified as packaged because their translation levels were low compared to cellular levels. This suggests that the cooperative binding of YB-1 to mRNAs through the above sequences probably triggers the well-known multimerization of YB-l, leading to the packaging of these mRNAs. Thus, our findings indicate a previously unknown link between the degenerate consensus sequences present in the 3'-UTRs of many cytoplasmic mRNAs and YB-1-mediated translational silencing.
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Affiliation(s)
- Alexander V Gopanenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk, 630090, Russia
| | - Alexey A Malygin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk, 630090, Russia; Department of Molecular Biology, Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Olga A Kossinova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk, 630090, Russia
| | - Alexey E Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk, 630090, Russia
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk, 630090, Russia
| | - Galina G Karpova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk, 630090, Russia; Department of Molecular Biology, Novosibirsk State University, Novosibirsk, 630090, Russia.
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36
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Kozhieva M, Naumova N, Alikina T, Boyko A, Vlassov V, Kabilov MR. Primary progressive multiple sclerosis in a Russian cohort: relationship with gut bacterial diversity. BMC Microbiol 2019; 19:309. [PMID: 31888483 PMCID: PMC6937728 DOI: 10.1186/s12866-019-1685-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [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: 09/21/2019] [Accepted: 12/15/2019] [Indexed: 12/20/2022] Open
Abstract
Background Gut microbiota has been increasingly acknowledged to shape significantly human health, contributing to various autoimmune diseases, both intestinal and non-intestinal, including multiple sclerosis (MS). Gut microbiota studies in patients with relapsing remitting MS strongly suggested its possible role in immunoregulation; however, the profile and potential of gut microbiota involvement in patients with primary progressive MS (PPMS) patients has received much less attention due to the rarity of this disease form. We compared the composition and structure of faecal bacterial assemblage using Illumina MiSeq sequencing of V3-V4 hypervariable region of 16S rRNA genes amplicons in patients with primary progressive MS and in the healthy controls. Results Over all samples 12 bacterial phyla were identified, containing 21 classes, 25 orders, 54 families, 174 genera and 1256 operational taxonomic units (OTUs). The Firmicutes phylum was found to be ultimately dominating both in OTUs richness (68% of the total bacterial OTU number) and in abundance (71% of the total number of sequence reads), followed by Bacteroidetes (12 and 16%, resp.) and Actinobacteria (7 and 6%, resp.). Summarily in all samples the number of dominant OTUs, i.e. OTUs with ≥1% relative abundance, was 13, representing much less taxonomic richness (three phyla, three classes, four orders, six families and twelve genera) as compared to the total list of identified OTUs and accounting for 30% of the sequence reads number in the healthy cohort and for 23% in the PPMS cohort. Human faecal bacterial diversity profiles were found to differ between PPMS and healthy cohorts at different taxonomic levels in minor or rare taxa. Marked PPMS-associated increase was found in the relative abundance of two dominant OTUs (Gemmiger sp. and an unclassified Ruminococcaceae). The MS-related differences were also found at the level of minor and rare OTUs (101 OTUs). These changes in OTUs’ abundance translated into increased bacterial assemblage diversity in patients. Conclusion The findings are important for constructing a more detailed global picture of the primary progressive MS-associated gut microbiota, contributing to better understanding of the disease pathogenesis.
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Affiliation(s)
- Madina Kozhieva
- Department of Neurology, Neurosurgery and Medical Genetics of the Pirogov Medical University, Ostrovitianova 1, 117513, Moscow, Russia
| | - Natalia Naumova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev 8, Novosibirsk, 630090, Russia.
| | - Tatiana Alikina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev 8, Novosibirsk, 630090, Russia
| | - Alexey Boyko
- Department of Neurology, Neurosurgery and Medical Genetics of the Pirogov Medical University, Ostrovitianova 1, 117513, Moscow, Russia.,Department of Neuroimmunology of the Federal Center of CVPI, Ostrovitianova 1 str 10, 117513, Moscow, Russia
| | - Valentin Vlassov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev 8, Novosibirsk, 630090, Russia
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev 8, Novosibirsk, 630090, Russia
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Kryukov VY, Kabilov MR, Smirnova N, Tomilova OG, Tyurin MV, Akhanaev YB, Polenogova OV, Danilov VP, Zhangissina SK, Alikina T, Yaroslavtseva ON, Glupov VV. Bacterial decomposition of insects post-Metarhizium infection: Possible influence on plant growth. Fungal Biol 2019; 123:927-935. [PMID: 31733735 DOI: 10.1016/j.funbio.2019.09.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 09/24/2019] [Accepted: 09/30/2019] [Indexed: 12/26/2022]
Abstract
Strains of entomopathogenic fungi may have substantial differences in their final stages of mycosis. Insect cadavers are usually overgrown with mycelium after colonization of the insect body, but in many cases, bacterial decomposition of the colonized hosts occurs. We used two Metarhizium robertsii strains in the work: Mak-1 (cadavers become overgrown with mycelium and conidia) and P-72 (cadavers decay after fungal colonization). We conducted a comparative analysis of gut and cadaver microbiota in Colorado potato beetle larvae using 16S rRNA gene sequencing after infection with these strains. In addition, we estimated the content of different forms of nitrogen in cadavers and the influence of cadavers on the growth of Solanum lycopersicum on sand substrates under laboratory conditions. It was shown that infections did not lead to a significant shift in the midgut bacterial communities of infected insects compared to those of untreated insects. Importantly, bacterial communities were similar in both types of cadaver, with predominantly enterobacteria. Decomposing cadavers (P-72) were characterized by increased nitrate and ammonium, and they had a stronger growth-promoting effect on plants compared to cadavers overgrown with mycelium and conidia (Mak-1). We also estimated the colonization and growth of plants after treatment with conidia of both strains cultivated on artificial medium. Both cultures successfully colonized plants, but strain P-72 showed stronger growth promotion than Mak-1. We propose that the use of deviant strains that are unable to sporulate on cadavers leads to a faster (though only passive) flow of nitrogen from killed insects to plants.
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Affiliation(s)
- Vadim Y Kryukov
- Institute of Systematics and Ecology of Animals SB RAS, Frunze str., 11, 630091 Novosibirsk, Russia.
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev av. 8, Novosibirsk 630090, Russia
| | - Natalya Smirnova
- Institute of Soil Science and Agrochemistry SB RAS, Lavrentiev av. 8/2, Novosibirsk 630090, Russia
| | - Oksana G Tomilova
- Institute of Systematics and Ecology of Animals SB RAS, Frunze str., 11, 630091 Novosibirsk, Russia
| | - Maksim V Tyurin
- Institute of Systematics and Ecology of Animals SB RAS, Frunze str., 11, 630091 Novosibirsk, Russia
| | - Yuriy B Akhanaev
- Institute of Systematics and Ecology of Animals SB RAS, Frunze str., 11, 630091 Novosibirsk, Russia
| | - Olga V Polenogova
- Institute of Systematics and Ecology of Animals SB RAS, Frunze str., 11, 630091 Novosibirsk, Russia
| | - Viktor P Danilov
- Siberian Federal Scientific Centre of Agro-Bio Technologies (SFSCA) of the RAS, Novosibirsk Region, Krasnoobsk, PO Box 463, 630501, Russia
| | - Saule K Zhangissina
- Institute of Cytology and Genetics SB RAS, Lavrentyev av. 10, Novosibirsk 630090, Russia
| | - Tatiana Alikina
- Institute of Soil Science and Agrochemistry SB RAS, Lavrentiev av. 8/2, Novosibirsk 630090, Russia
| | - Olga N Yaroslavtseva
- Institute of Systematics and Ecology of Animals SB RAS, Frunze str., 11, 630091 Novosibirsk, Russia
| | - Viktor V Glupov
- Institute of Systematics and Ecology of Animals SB RAS, Frunze str., 11, 630091 Novosibirsk, Russia
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Abstract
Recently the relationship between gut microbiota changes and the development of immune-mediated diseases of the central nervous system (CNS) has been reported. This review presents literature data on the effect of gut microbiota on the function of the immune and nervous systems. The authors discuss possible mechanisms of the relationship between gut microbiota changes and CNS diseases on the model of multiple sclerosis (MS).
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Affiliation(s)
- M Kh Kozhieva
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - M V Melnikov
- Pirogov Russian National Research Medical University, Moscow, Russia; Institute of Immunology, Moscow, Russia
| | - V S Rogovsky
- Pirogov Russian National Research Medical University, Moscow, Russia
| | | | | | - A N Boyko
- Pirogov Russian National Research Medical University, Moscow, Russia
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Krasitskaya VV, Chaukina VV, Abroskina MV, Vorobyeva MA, Ilminskaya AA, Kabilov MR, Prokopenko SV, Nevinsky GA, Venyaminova AG, Frank LA. Bioluminescent aptamer-based sandwich-type assay of anti-myelin basic protein autoantibodies associated with multiple sclerosis. Anal Chim Acta 2019; 1064:112-118. [PMID: 30982509 DOI: 10.1016/j.aca.2019.03.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 12/12/2022]
Abstract
Bioluminescent solid-phase sandwich-type microassay was developed to detect multiple sclerosis (MS)-associated autoantibodies in human sera. The assay is based on two different 2'-F-Py RNA aptamers against the target autoantibodies as biospecific elements, and Ca2+-regulated photoprotein obelin as a reporter. The paper describes elaboration of the assay and its application to 91 serum samples from patients with clinically definite MS and 86 ones from individuals healthy in terms of MS. Based on the receiver-operator curve (ROC) analysis, the chosen threshold value as clinical decision limit offers sensitivity of 63.7% and specificity of 94.2%. The area under the ROC curve (AUC) value of 0.87 shows a good difference between the groups under investigation. The likelihood ratio of 10.97 proves the diagnostic value of the assay and its potential as one of the laboratory MS-tests.
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Affiliation(s)
- Vasilisa V Krasitskaya
- Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, 660036, Russia.
| | - Valentina V Chaukina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Maria V Abroskina
- State Medical University named after V.F. Voino-Yasenetsky, Krasnoyarsk, 660022, Russia
| | - Maria A Vorobyeva
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | | | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Semyon V Prokopenko
- State Medical University named after V.F. Voino-Yasenetsky, Krasnoyarsk, 660022, Russia
| | - Georgy A Nevinsky
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Alya G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Ludmila A Frank
- Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, 660036, Russia
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Polenogova OV, Kabilov MR, Tyurin MV, Rotskaya UN, Krivopalov AV, Morozova VV, Mozhaitseva K, Kryukova NA, Alikina T, Kryukov VY, Glupov VV. Parasitoid envenomation alters the Galleria mellonella midgut microbiota and immunity, thereby promoting fungal infection. Sci Rep 2019; 9:4012. [PMID: 30850650 PMCID: PMC6408550 DOI: 10.1038/s41598-019-40301-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 10/02/2018] [Accepted: 02/12/2019] [Indexed: 12/26/2022] Open
Abstract
Gut bacteria influence the development of different pathologies caused by bacteria, fungi and parasitoids in insects. Wax moth larvae became more susceptible to fungal infections after envenomation by the ectoparasitoid Habrobracon hebetor. In addition, spontaneous bacterioses occurred more often in envenomated larvae. We analyzed alterations in the midgut microbiota and immunity of the wax moth in response to H. hebetor envenomation and topical fungal infection (Beauveria bassiana) alone or in combination using 16S rRNA sequencing, an analysis of cultivable bacteria and a qPCR analysis of immunity- and stress-related genes. Envenomation led to a predominance shift from enterococci to enterobacteria, an increase in CFUs and the upregulation of AMPs in wax moth midguts. Furthermore, mycosis nonsignificantly increased the abundance of enterobacteria and the expression of AMPs in the midgut. Combined treatment led to a significant increase in the abundance of Serratia and a greater upregulation of gloverin. The oral administration of predominant bacteria (Enterococcus faecalis, Enterobacter sp. and Serratia marcescens) to wax moth larvae synergistically increased fungal susceptibility. Thus, the activation of midgut immunity might prevent the bacterial decomposition of envenomated larvae, thus permitting the development of fungal infections. Moreover, changes in the midgut bacterial community may promote fungal killing.
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Affiliation(s)
- Olga V Polenogova
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630091, Russia
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Maksim V Tyurin
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630091, Russia
| | - Ulyana N Rotskaya
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630091, Russia
| | - Anton V Krivopalov
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630091, Russia
| | - Vera V Morozova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Kseniya Mozhaitseva
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630091, Russia
| | - Nataliya A Kryukova
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630091, Russia
| | - Tatyana Alikina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Vadim Yu Kryukov
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630091, Russia.
| | - Viktor V Glupov
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630091, Russia
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Kichigin IG, Lisachov AP, Giovannotti M, Makunin AI, Kabilov MR, O'Brien PCM, Ferguson-Smith MA, Graphodatsky AS, Trifonov VA. First report on B chromosome content in a reptilian species: the case of Anolis carolinensis. Mol Genet Genomics 2018; 294:13-21. [PMID: 30146671 DOI: 10.1007/s00438-018-1483-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 07/31/2018] [Accepted: 08/22/2018] [Indexed: 11/26/2022]
Abstract
Supernumerary elements of the genome are often called B chromosomes. They usually consist of various autosomal sequences and, because of low selective pressure, are mostly pseudogenized and contain many repeats. There are numerous reports on B chromosomes in mammals, fish, invertebrates, plants, and fungi, but only a few of them have been studied using sequencing techniques. However, reptilian supernumerary chromosomes have been detected only cytogenetically and never sequenced or analyzed at the molecular level. One model squamate species with available genome sequence is Anolis carolinensis. The scope of the present article is to describe the genetic content of A. carolinensis supernumerary chromosomes. In this article, we confirm the presence of B chromosomes in this species by reverse painting and synaptonemal complex analysis. We applied low-pass high-throughput sequencing to analyze flow-sorted B chromosomes. Anole B chromosomes exhibit similar traits to other supernumerary chromosomes from different taxons: they contain two genes related to cell division control (INCENP and SPIRE2), are enriched in specific repeats, and show a high degree of pseudogenization. Therefore, the present study confirms that reptilian B chromosomes resemble supernumerary chromosomes of other taxons.
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Affiliation(s)
- Ilya G Kichigin
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, 630090, Russia.
| | - Artem P Lisachov
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia
| | - Massimo Giovannotti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Alex I Makunin
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, 630090, Russia
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Patricia C M O'Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
| | - Malcolm A Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
| | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Vladimir A Trifonov
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
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42
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Kashinskaya EN, Simonov EP, Kabilov MR, Izvekova GI, Andree KB, Solovyev MM. Diet and other environmental factors shape the bacterial communities of fish gut in an eutrophic lake. J Appl Microbiol 2018; 125:1626-1641. [PMID: 30091826 DOI: 10.1111/jam.14064] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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: 06/29/2018] [Revised: 07/31/2018] [Accepted: 08/04/2018] [Indexed: 12/13/2022]
Abstract
AIMS The aim of this work was to study the gut microbial diversity from eight species of wild fish with different feeding habits, digestive physiology (gastric vs agastric) and provide comparative structural analysis of the microbial communities within their environment (food items, water, sediments and macrophytes). METHODS AND RESULTS The microbiota of fish gut and their prey items were studied using next generation high-throughput sequencing of the 16S ribosomal RNA genes. A scatter plot based on PCoA scores demonstrated the microbiota formed three groups: (i) stomach and intestinal mucosa (IM), (ii) stomach and intestinal content (IC), and (iii) prey and environment. Comparisons using ANOSIM showed significant differences among IC of omnivorous, zoobenthivorous, zooplanktivorous-piscivorous fishes (P ≤ 0·1). No significant difference was detected for mucosa from the same groups (P > 0·1). CONCLUSIONS Neither the interspecies differences in fish diet nor their phylogenetic position had any effect on the microbiome of the IM, but diet did influence the composition of the microbiota of the IC. SIGNIFICANCE AND IMPACT OF THE STUDY The data demonstrate that fish harboured specific groups of bacteria that do not completely reflect the microbiota of the environment or prey.
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Affiliation(s)
- E N Kashinskaya
- Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - E P Simonov
- Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- Siberian Federal University, Krasnoyarsk, Russia
| | - M R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Novosibirsk, Russia
| | - G I Izvekova
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Nekouzskii raion, Yaroslavskaya oblast, Russia
| | - K B Andree
- IRTA-SCR, San Carlos de la Rapita, Tarragona, Spain
| | - M M Solovyev
- Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- Tomsk State University, Tomsk, Russia
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Gopanenko AV, Malygin AA, Tupikin AE, Laktionov PP, Kabilov MR, Karpova GG. Human ribosomal protein eS1 is engaged in cellular events related to processing and functioning of U11 snRNA. Nucleic Acids Res 2017; 45:9121-9137. [PMID: 28666385 PMCID: PMC5587755 DOI: 10.1093/nar/gkx559] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 06/15/2017] [Accepted: 06/20/2017] [Indexed: 01/22/2023] Open
Abstract
Ribosomal proteins are involved in many cellular processes through interactions with various RNAs. Here, applying the photoactivatable-ribonucleoside-enhanced cross-linking and immunoprecipitation approach to HEK293 cells overproducing ribosomal protein (rp) eS1, we determined the products of RNU5A-1 and RNU11 genes encoding U5 and U11 snRNAs as the RNA partners of ribosome-unbound rp eS1. U11 pre-snRNA-associated rp eS1 was revealed in the cytoplasm and nucleus where rp eS1-bound U11/U12 di-snRNP was also found. Utilizing recombinant rp eS1 and 4-thiouridine-containing U11 snRNA transcript, we identified an N-terminal peptide contacting the U-rich sequence in the Sm site-containing RNA region. We also showed that the rp eS1 binding site on U11 snRNA is located in the cleft between stem-loops I and III and that its structure mimics the respective site on the 18S rRNA. It was found that cell depletion of rp eS1 leads to a decrease in the splicing efficiency of minor introns and to an increase in the level of U11 pre-snRNA with the unprocessed 3' terminus. Our findings demonstrate the engagement of human rp eS1 in events related to the U11 snRNA processing and to minor-class splicing. Contacts of rp eS1 with U5 snRNA in the minor pre-catalytic spliceosome are discussed.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Escherichia coli/genetics
- Escherichia coli/metabolism
- HEK293 Cells
- Humans
- Introns
- Models, Molecular
- Nucleic Acid Conformation
- Protein Biosynthesis
- Protein Conformation, alpha-Helical
- Protein Interaction Domains and Motifs
- RNA Splicing
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/metabolism
- RNA, Small Nuclear/chemistry
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosomes/genetics
- Ribosomes/metabolism
- Spliceosomes/genetics
- Spliceosomes/metabolism
- Thiouridine/metabolism
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Affiliation(s)
- Alexander V. Gopanenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Molecular Biology, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexey A. Malygin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Molecular Biology, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexey E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Pavel P. Laktionov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Galina G. Karpova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Molecular Biology, Novosibirsk State University, Novosibirsk 630090, Russia
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44
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Grosheva AS, Zharkov DO, Stahl J, Gopanenko AV, Tupikin AE, Kabilov MR, Graifer DM, Karpova GG. Recognition but no repair of abasic site in single-stranded DNA by human ribosomal uS3 protein residing within intact 40S subunit. Nucleic Acids Res 2017; 45:3833-3843. [PMID: 28334742 PMCID: PMC5397187 DOI: 10.1093/nar/gkx052] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 01/13/2017] [Accepted: 01/19/2017] [Indexed: 01/04/2023] Open
Abstract
Isolated human ribosomal protein uS3 has extra-ribosomal functions including those related to base excision DNA repair, e.g. AP lyase activity that nicks double-stranded (ds) DNA 3΄ to the abasic (AP) site. However, the ability of uS3 residing within ribosome to recognize and cleave damaged DNA has never been addressed. Here, we compare interactions of single-stranded (ss) DNA and dsDNA bearing AP site with human ribosome-bound uS3 and with the isolated protein, whose interactions with ssDNA were not yet studied. The AP lyase activity of free uS3 was much higher with ssDNA than with dsDNA, whereas ribosome-bound uS3 was completely deprived of this activity. Nevertheless, an exposed peptide of ribosome-bound uS3 located far away from the putative catalytic center previously suggested for isolated uS3 cross-linked to full-length uncleaved ssDNA, but not to dsDNA. In contrast, free uS3 cross-linked mainly to the 5΄-part of the damaged DNA strand after its cleavage at the AP site. ChIP-seq analysis showed preferential uS3 binding to nucleolus-associated chromatin domains. We conclude that free and ribosome-bound uS3 proteins interact with AP sites differently, exhibiting their non-translational functions in DNA repair in and around the nucleolus and in regulation of DNA damage response in looped DNA structures, respectively.
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Affiliation(s)
- Anastasia S. Grosheva
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
| | - Dmitry O. Zharkov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Joachim Stahl
- Max-Delbrück-Center for Molecular Medicine, D-13092 Berlin, Germany
| | - Alexander V. Gopanenko
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexey E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
| | - Dmitri M. Graifer
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Galina G. Karpova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
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45
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Martemyanov VV, Podgwaite JD, Belousova IA, Pavlushin SV, Slavicek JM, Baturina OA, Kabilov MR, Ilyinykh AV. A comparison of the adaptations of strains of Lymantria dispar multiple nucleopolyhedrovirus to hosts from spatially isolated populations. J Invertebr Pathol 2017; 146:41-46. [PMID: 28392286 DOI: 10.1016/j.jip.2017.04.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 12/01/2016] [Revised: 03/17/2017] [Accepted: 04/05/2017] [Indexed: 11/18/2022]
Abstract
The adaptation of pathogens to either their hosts or to environmental conditions is the focus of many current ecological studies. In this work we compared the ability of six spatially-distant Lymantria dispar (gypsy moth) multiple nucleopolyhedrovirus (LdMNPV) strains (three from eastern North America and three from central Asia) to induce acute infection in gypsy moth larvae. We also sequenced the complete genome of one Asian (LdMNPV-27/0) and one North American (LdMNPV-45/0) strain which were used for bioassay. We found that all of the North American virus strains, with the exception of one, demonstrated higher potency than the Asian virus strains, either in North American (Lymantria dispar) larvae or, in Asian (Lymantria dispar asiatica) larvae. Complete genome sequencing revealed two gene deletions in the LdMNPV-27/0 strain: the virus enhancin factor gene (vef-1) and the baculovirus repeated orf gene (bro-p). These deletions were not seen in the LdMNPV-45/0 strain nor in other American strains available in archiving systems. We also found deletions of the bro-e and bro-o genes in LdMNPV-45/0 strain but not in the LdMNPV-27/0 strain. The phylogenetic inference with an alignment of the 37 core gene nucleotide sequences revealed the close relationship of the LdMNPV-45/0 strain with other American strains accessed in GenBank (Ab-a624 and 5-6) while the LdMNPV-27/0 strain was clustered together with the LdMNPV-3054 strain (isolated in Spain) instead of predicted clustering with LdMNPV- 3029 (isolated in Asia). Our study demonstrated that first, different LdMNPV isolates from the same metapopulations of L. dispar exhibit little or no difference in the degree of virulence towards host larvae and second, that locality of host population is not an important driver of LdMNPV virulence. Virulence of LdMNPV is determined only by viral genetics. The genetic differences between North American and Central Asian virus strains are discussed.
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Affiliation(s)
- V V Martemyanov
- Laboratory of Ecological Parasitology, Institute of Systematics and Ecology of Animals SB RAS, Frunze str. 11, 630091 Novosibirsk, Russia; Biological Institute, National Research Tomsk State University, Lenin av. 36, 634050 Tomsk, Russia.
| | - J D Podgwaite
- USDA Forest Service, Northern Research Station, 51 Mill Pond Rd., Hamden, CT 06514, United States.
| | - I A Belousova
- Laboratory of Ecological Parasitology, Institute of Systematics and Ecology of Animals SB RAS, Frunze str. 11, 630091 Novosibirsk, Russia; Institute of Biology, Irkutsk State University, Karl Marx str. 1, Irkutsk 664003, Russia.
| | - S V Pavlushin
- Laboratory of Ecological Parasitology, Institute of Systematics and Ecology of Animals SB RAS, Frunze str. 11, 630091 Novosibirsk, Russia.
| | - J M Slavicek
- USDA Forest Service, Northern Research Station, 359 Main Rd., Delaware, OH 43015, United States.
| | - O A Baturina
- Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentyev av. 8, 630090 Novosibirsk, Russia.
| | - M R Kabilov
- Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentyev av. 8, 630090 Novosibirsk, Russia.
| | - A V Ilyinykh
- Laboratory of Insect Pathology, Institute of Systematics and Ecology of Animal SB RAS, Frunze str. 11, 630091 Novosibirsk, Russia.
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46
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Kossinova OA, Gopanenko AV, Tamkovich SN, Krasheninina OA, Tupikin AE, Kiseleva E, Yanshina DD, Malygin AA, Ven'yaminova AG, Kabilov MR, Karpova GG. Cytosolic YB-1 and NSUN2 are the only proteins recognizing specific motifs present in mRNAs enriched in exosomes. Biochim Biophys Acta Proteins Proteom 2017; 1865:664-673. [PMID: 28341602 DOI: 10.1016/j.bbapap.2017.03.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 03/16/2017] [Accepted: 03/20/2017] [Indexed: 12/27/2022]
Abstract
Exosomes, membranous vesicles secreted by various cells, are involved in intercellular communication and carry vast repertoires of RNAs and proteins. Processes mediating RNA sorting into exosomes are currently poorly understood. Using bioinformatics approaches, three structural motifs ACCAGCCU, CAGUGAGC and UAAUCCCA have been discovered as enriched in exosomal mRNAs and long noncoding RNAs. Here, utilizing short RNA hairpins, each containing one of the motifs, in a pull-down assay of cytosolic extract of human embryonic kidney 293 (HEK293) cells, we prove that multifunctional RNA-binding protein YB-1 specifically interacts with all three motifs, whereas methyltransferase NSUN2 recognizes only the motif CAGUGAGC. RNA hairpins other than those mentioned above pull out neither YB-1 nor NSUN2. Both these proteins are found in exosomes secreted by HEK293 cells. YB-1 for all that is detected as a form having a slightly higher electrophoretic mobility than that of YB-1 associated with the above RNA hairpins, assuming changes in posttranslational modifications of the protein during its transfer from cytoplasm into exosomes. Next generation sequencing of total exosomal RNA (eRNA) reveals a large representative set of RNA species, including mRNAs containing the above-mentioned motifs. The degree of enrichment in exosomes with this kind of mRNAs strongly depends on the locations of eRNA-specific motifs within the mRNA sequences. Altogether, our findings point to YB-1 and NSUN2 as possible mediators of the process of transfer of specific mRNAs into exosomes, allowing us to speculate on an involvement of these proteins in the mRNA sorting via the recognition of the above motifs.
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Affiliation(s)
- Olga A Kossinova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia
| | - Alexander V Gopanenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia; Department of Molecular Biology, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Svetlana N Tamkovich
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia; Department of Molecular Biology, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Olga A Krasheninina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia
| | - Alexey E Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia
| | - Elena Kiseleva
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 10, Novosibirsk 630090, Russia
| | - Darya D Yanshina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia
| | - Alexey A Malygin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia; Department of Molecular Biology, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alia G Ven'yaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia
| | - Galina G Karpova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, Russia; Department of Molecular Biology, Novosibirsk State University, Novosibirsk 630090, Russia.
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47
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Martemyanov VV, Belousova IA, Pavlushin SV, Dubovskiy IM, Ershov NI, Alikina TY, Kabilov MR, Glupov VV. Phenological asynchrony between host plant and gypsy moth reduces insect gut microbiota and susceptibility to Bacillus thuringiensis. Ecol Evol 2016; 6:7298-7310. [PMID: 28725398 PMCID: PMC5513265 DOI: 10.1002/ece3.2460] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [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: 04/25/2016] [Revised: 07/26/2016] [Accepted: 08/12/2016] [Indexed: 01/15/2023] Open
Abstract
The phenological synchrony between the emergence of overwintering herbivorous insects and the budding of host plants is considered a crucial factor in the population dynamics of herbivores. However, the mechanisms driving the interactions between the host plant, herbivores, and their pathogens are often obscure. In the current study, an artificially induced phenological asynchrony was used to investigate how the asynchrony between silver birch Betula pendula and gypsy moth Lymantria dispar affects the immunity of the insect to bacteria, its susceptibility to the entomopathogenic bacteria Bacillus thuringiensis, and the diversity in its midgut microbiota. The lysozyme-like activity in both the midgut and hemolymph plasma and the nonspecific esterase activity and antimicrobial peptide gene expression in the midgut were studied in both noninfected and B. thuringiensis-infected larvae. Our results provide the first evidence that phenologically asynchronous larvae are less susceptible to B. thuringiensis infection than phenologically synchronous larvae, and our results show that these effects are related to the high basic levels and B. thuringiensis-induced levels of lysozyme-like activities. Moreover, a 16S rRNA analysis revealed that dramatic decreases in the diversity of the larval gut bacterial consortia occurred under the effect of asynchrony. Larvae infected with B. thuringiensis presented decreased microbiota diversity if the larvae were reared synchronously with the host plant but not if they were reared asynchronously. Our study demonstrates the significant effect of phenological asynchrony on innate immunity-mediated interactions between herbivores and entomopathogenic bacteria and highlights the role of nonpathogenic gut bacteria in these interactions.
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Affiliation(s)
- Vyacheslav V. Martemyanov
- Laboratory of Ecological ParasitologyInstitute of Systematics and Ecology of Animals Siberian BranchRussian Academy of SciencesNovosibirskRussia
- Biological InstituteNational Research Tomsk State UniversityTomskRussia
| | - Irina A. Belousova
- Laboratory of Ecological ParasitologyInstitute of Systematics and Ecology of Animals Siberian BranchRussian Academy of SciencesNovosibirskRussia
- Institute of BiologyIrkutsk State UniversityIrkutskRussia
| | - Sergey V. Pavlushin
- Laboratory of Ecological ParasitologyInstitute of Systematics and Ecology of Animals Siberian BranchRussian Academy of SciencesNovosibirskRussia
| | - Ivan M. Dubovskiy
- Laboratory of Insect PathologyInstitute of Systematics and Ecology of Animals Siberian BranchRussian Academy of SciencesNovosibirskRussia
| | - Nikita I. Ershov
- Institute of Cytology and GeneticsSiberian BranchRussian Academy of SciencesNovosibirskRussia
| | - Tatyana Y. Alikina
- Genomics Core FacilityInstitute of Chemical Biology and Fundamental MedicineSiberian BranchRussian Academy of SciencesNovosibirskRussia
| | - Marsel R. Kabilov
- Genomics Core FacilityInstitute of Chemical Biology and Fundamental MedicineSiberian BranchRussian Academy of SciencesNovosibirskRussia
| | - Victor V. Glupov
- Laboratory of Insect PathologyInstitute of Systematics and Ecology of Animals Siberian BranchRussian Academy of SciencesNovosibirskRussia
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48
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Kurilshikov A, Livanova NN, Fomenko NV, Tupikin AE, Rar VA, Kabilov MR, Livanov SG, Tikunova NV. Comparative Metagenomic Profiling of Symbiotic Bacterial Communities Associated with Ixodes persulcatus, Ixodes pavlovskyi and Dermacentor reticulatus Ticks. PLoS One 2015; 10:e0131413. [PMID: 26154300 PMCID: PMC4496043 DOI: 10.1371/journal.pone.0131413] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/01/2015] [Indexed: 12/29/2022] Open
Abstract
Ixodes persulcatus, Ixodes pavlovskyi, and Dermacentor reticulatus ticks inhabiting Western Siberia are responsible for the transmission of a number of etiological agents that cause human and animal tick-borne diseases. Because these ticks are abundant in the suburbs of large cities, agricultural areas, and popular tourist sites and frequently attack people and livestock, data regarding the microbiomes of these organisms are required. Using metagenomic 16S profiling, we evaluate bacterial communities associated with I. persulcatus, I. pavlovskyi, and D. reticulatus ticks collected from the Novosibirsk region of Russia. A total of 1214 ticks were used for this study. DNA extracted from the ticks was pooled according to tick species and sex. Sequencing of the V3-V5 domains of 16S rRNA genes was performed using the Illumina Miseq platform. The following bacterial genera were prevalent in the examined communities: Acinetobacter (all three tick species), Rickettsia (I. persulcatus and D. reticulatus) and Francisella (D. reticulatus). B. burgdorferi sensu lato and B. miyamotoi sequences were detected in I. persulcatus and I. pavlovskyi but not in D. reticulatus ticks. The pooled samples of all tick species studied contained bacteria from the Anaplasmataceae family, although their occurrence was low. DNA from A. phagocytophilum and Candidatus Neoehrlichia mikurensis was first observed in I. pavlovskyi ticks. Significant inter-species differences in the number of bacterial taxa as well as intra-species diversity related to tick sex were observed. The bacterial communities associated with the I. pavlovskyi ticks displayed a higher biodiversity compared with those of the I. persulcatus and D. reticulatus ticks. Bacterial community structure was also diverse across the studied tick species, as shown by permutational analysis of variance using the Bray-Curtis dissimilarity metric (p = 0.002). Between-sex variation was confirmed by PERMANOVA testing in I. persulcatus (p = 0.042) and I. pavlovskyi (p = 0.042) ticks. Our study indicated that 16S metagenomic profiling could be used for rapid assessment of the occurrence of medically important bacteria in tick populations inhabiting different natural biotopes and therefore the epidemic danger of studied foci.
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Affiliation(s)
- Alexander Kurilshikov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
- * E-mail:
| | - Natalya N. Livanova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
- Institute of Systematics and Ecology of Animals SB RAS, Novosibirsk, Russia
| | - Nataliya V. Fomenko
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Alexey E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Vera A. Rar
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | | | - Nina V. Tikunova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
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49
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Fomenko NV, Khvorostova YV, Ignatieva OA, Akimov IA, Trukhina AV, Gasilova NA, Kabilov MR, Ivanov MK. [The species variety of microflora in samples from urogenital tract of female patients of large network laboratory and its dependence of content of lactobaccilli]. Klin Lab Diagn 2015; 60:59-64. [PMID: 26031169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The evaluation of content of DNA of lactobaccilli and particular types of aerobic anaerobic opportunistic bacteria in sampling of scrapes from urogenital tract offemale patients of the network laboratory INVITRO was implemented. The technique of polymerase chain reaction in real-time was implemented. It is demonstrated that decreasing of content of lactobaccilli in total bacterial mass isfollowed by increasing of occurrence, concentration and relative content of all types of opportunistic pathogens except ureaplasmna. These changes are expressed in different degree for different types of opportunistic pathogens. The increasing of varieties of types of microflora of urogenital tract under decreasing of content of lactobaccilli is noted.
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50
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Lomakin YA, Zakharova MY, Stepanov AV, Dronina MA, Smirnov IV, Bobik TV, Pyrkov AY, Tikunova NV, Sharanova SN, Boitsov VM, Vyazmin SY, Kabilov MR, Tupikin AE, Krasnov AN, Bykova NA, Medvedeva YA, Fridman MV, Favorov AV, Ponomarenko NA, Dubina MV, Boyko AN, Vlassov VV, Belogurov AA, Gabibov AG. Heavy-light chain interrelations of MS-associated immunoglobulins probed by deep sequencing and rational variation. Mol Immunol 2014; 62:305-14. [PMID: 24534716 DOI: 10.1016/j.molimm.2014.01.013] [Citation(s) in RCA: 13] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 01/17/2014] [Accepted: 01/22/2014] [Indexed: 01/21/2023]
Abstract
The mechanisms triggering most of autoimmune diseases are still obscure. Autoreactive B cells play a crucial role in the development of such pathologies and, in particular, production of autoantibodies of different specificities. The combination of deep-sequencing technology with functional studies of antibodies selected from highly representative immunoglobulin combinatorial libraries may provide unique information on specific features in the repertoires of autoreactive B cells. Here, we have analyzed cross-combinations of the variable regions of human immunoglobulins against the myelin basic protein (MBP) previously selected from a multiple sclerosis (MS)-related scFv phage-display library. On the other hand, we have performed deep sequencing of the sublibraries of scFvs against MBP, Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1), and myelin oligodendrocyte glycoprotein (MOG). Bioinformatics analysis of sequencing data and surface plasmon resonance (SPR) studies have shown that it is the variable fragments of antibody heavy chains that mainly determine both the affinity of antibodies to the parent autoantigen and their cross-reactivity. It is suggested that LMP1-cross-reactive anti-myelin autoantibodies contain heavy chains encoded by certain germline gene segments, which may be a hallmark of the EBV-specific B cell subpopulation involved in MS triggering.
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Affiliation(s)
- Yakov A Lomakin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maria Yu Zakharova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexey V Stepanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maria A Dronina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ivan V Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia; Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Tatyana V Bobik
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Yu Pyrkov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nina V Tikunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Svetlana N Sharanova
- Russian State Medical University, Department of Neurology & Neurosurgery, Moscow Multiple Sclerosis Center at the City Hospital #11, Moscow, Russia
| | - Vitali M Boitsov
- St. Petersburg Academic University, Nanotechnology Research and Education Centre, Russian Academy of Sciences, St. Petersburg, Russia
| | - Sergey Yu Vyazmin
- St. Petersburg Academic University, Nanotechnology Research and Education Centre, Russian Academy of Sciences, St. Petersburg, Russia
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia; Genomics Core Facility, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexey E Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia; Genomics Core Facility, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia; Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey N Krasnov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nadezda A Bykova
- Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Yulia A Medvedeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia; Institut de Medicina Predictiva I Personalitzada del Càncer, Badalona (Barcelona), Spain
| | - Marina V Fridman
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Alexander V Favorov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia; Department of Oncology, Division of Biostatistics and Bioinformatics, Johns Hopkins University School of Medicine, Baltimore, MD, USA; State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIGenetika, Moscow, Russia
| | - Natalia A Ponomarenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Michael V Dubina
- St. Petersburg Academic University, Nanotechnology Research and Education Centre, Russian Academy of Sciences, St. Petersburg, Russia
| | - Alexey N Boyko
- Russian State Medical University, Department of Neurology & Neurosurgery, Moscow Multiple Sclerosis Center at the City Hospital #11, Moscow, Russia
| | - Valentin V Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia
| | - Alexey A Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia; Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander G Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia; Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia; Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
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