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Bryanskaya AV, Shipova AA, Rozanov AS, Kolpakova OA, Lazareva EV, Uvarova YE, Efimov VM, Zhmodik SM, Taran OP, Goryachkovskaya TN, Peltek SE. Diversity and Metabolism of Microbial Communities in a Hypersaline Lake along a Geochemical Gradient. Biology 2022; 11:biology11040605. [PMID: 35453804 PMCID: PMC9031644 DOI: 10.3390/biology11040605] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 11/16/2022]
Abstract
In the south of western Siberia (Russia), there are many unique and unexplored soda, saline, and freshwater lakes. In this study, the results are presented on microbial diversity, its metabolic potential, and their relation with a set of geochemical parameters for a hypersaline lake ecosystem in the Novosibirsk region (Oblast). The metagenomic approach used in this work allowed us to determine the composition and structure of a floating microbial community, the upper layer of silt, and the strata of bottom sediments in a natural saline lake via two bioinformatic approaches, whose results are in good agreement with each other. In the floating microbial community and in the upper layers of the bottom sediment, bacteria of the Proteobacteria (Gammaproteobacteria), Cyanobacteria, and Bacteroidetes phyla were found to predominate. The lower layers were dominated by Proteobacteria (mainly Deltaproteobacteria), Gemmatimonadetes, Firmicutes, and Archaea. Metabolic pathways were reconstructed to investigate the metabolic potential of the microbial communities and other hypothetical roles of the microbial communities in the biogeochemical cycle. Relations between different taxa of microorganisms were identified, as was their potential role in biogeochemical transformations of C, N, and S in a comparative structural analysis that included various ecological niches.
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Affiliation(s)
- Alla V. Bryanskaya
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Correspondence: or ; Tel.: +7-383-363-4963 (ext. 4120)
| | - Aleksandra A. Shipova
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Alexei S. Rozanov
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Oxana A. Kolpakova
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Elena V. Lazareva
- V.S. Sobolev Institute of Geology and Mineralogy SB RAS, 630090 Novosibirsk, Russia; (E.V.L.); (S.M.Z.)
| | - Yulia E. Uvarova
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Vadim M. Efimov
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Sergey M. Zhmodik
- V.S. Sobolev Institute of Geology and Mineralogy SB RAS, 630090 Novosibirsk, Russia; (E.V.L.); (S.M.Z.)
| | - Oxana P. Taran
- FRC Krasnoyarsk Science Center SB RAS, Institute of Chemistry and Chemical Technology SB RAS, 660036 Krasnoyarsk, Russia;
| | - Tatyana N. Goryachkovskaya
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Sergey E. Peltek
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
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Rozanov AS, Shekhovtsov SV, Bogacheva NV, Pershina EG, Ryapolova AV, Bytyak DS, S E Peltek. Production of subtilisin proteases in bacteria and yeast. Vavilovskii Zhurnal Genet Selektsii 2021; 25:125-134. [PMID: 34901710 PMCID: PMC8629363 DOI: 10.18699/vj21.015] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 11/19/2022] Open
Abstract
In this review, we discuss the progress in the study and modification of subtilisin proteases. Despite longstanding applications of microbial proteases and a large number of research papers, the search for new protease genes, the construction of producer strains, and the development of methods for their practical application are still relevant and important, judging by the number of citations of the research articles on proteases and their microbial producers. This enzyme class represents the largest share of the industrial production of proteins worldwide. This situation can explain the high level of interest in these enzymes and points to the high importance of designing domestic technologies for their manufacture. The review covers subtilisin classification, the history of their discovery, and subsequent research on the optimization of their properties. An overview of the classes of subtilisin proteases and related enzymes is provided too. There is a discussion about the problems with the search for (and selection of) subtilases from natural strains of various microorganisms, approaches to (and specifics of) their modification, as well as the relevant genetic engineering techniques. Details are provided on the methods for expression optimization of industrial subtilases of various strains: the details of the most important parameters of cultivation, i.e., composition of the media, culture duration, and the influence of temperature and pH. Also presented are the results of the latest studies on cultivation techniques: submerged and solid-state fermentation. From the literature data reviewed, we can conclude that native enzymes (i.e., those obtained from natural sources) currently hardly have any practical applications because of the decisive advantages of the enzymes modified by genetic engineering and having better properties: e.g., thermal stability, general resistance to detergents and specific resistance to various oxidants, high activity in various temperature ranges, independence from metal ions, and stability in the absence of calcium. The vast majority of subtilisin proteases are expressed in producer strains belonging to different species of the genus Bacillus. Meanwhile, there is an effort to adapt the expression of these enzymes to other microbes, in particular species of the yeast Pichia pastoris.
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Affiliation(s)
- A S Rozanov
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Laboratory of Molecular Biotechnologies, Novosibirsk, Russia
| | - S V Shekhovtsov
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Laboratory of Molecular Biotechnologies, Novosibirsk, Russia
| | - N V Bogacheva
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Laboratory of Molecular Biotechnologies, Novosibirsk, Russia
| | - E G Pershina
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Laboratory of Molecular Biotechnologies, Novosibirsk, Russia
| | - A V Ryapolova
- Innovation Centre "Biruch-NT", Malobykovo village, Belgorod region, Russia
| | - D S Bytyak
- Innovation Centre "Biruch-NT", Malobykovo village, Belgorod region, Russia
| | - S E Peltek
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Laboratory of Molecular Biotechnologies, Novosibirsk, Russia
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Uvarova YE, Bryanskaya AV, Rozanov AS, Shlyakhtun VN, Demidov EA, Starostin KV, Goryachkovskaya TN, Shekhovtsov SV, Slynko NM, Peltek SE. An integrated method for taxonomic identification of microorganisms. Vavilovskii Zhurnal Genet Selektsii 2021; 24:376-382. [PMID: 33659820 PMCID: PMC7716526 DOI: 10.18699/vj20.630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
For accurate species-level identification of microorganisms, researchers today increasingly use a
combination of standard microbiological cultivation and visual observation methods with molecular biological and genetic techniques that help distinguish between species and strains of microorganisms at the level
of DNA or RNA molecules. The aim of this work was to identify microorganisms from the ICG SB RAS Collection
using an integrated approach that involves a combination of various phenotypic and genotypic characteristics. Key molecular-genetic and phenotypic characteristics were determined for 93 microbial strains from the
ICG SB RAS Collection. The strains were characterized by means of morphological, physiological, moleculargenetic, and mass-spectrometric parameters. Specific features of the growth of the strains on different media
were determined, and cell morphology was evaluated. The strains were tested for the ability to utilize various
substrates. The strains studied were found to significantly differ in their biochemical characteristics. Physiological characteristics of the strains from the collection were identified too, e.g., the relationship with oxygen,
type of nutrition, suitable temperature and pH ranges, and NaCl tolerance. In this work, the microorganisms
analyzed were combined into separate groups based on the similarities of their phenotypic characteristics.
This categorization, after further refinement and expansion of the spectrum of taxa and their metabolic maps,
may serve as the basis for the creation of an “artificial” classification that can be used as a key for simplified and
quicker identification and recognition of microorganisms within both the ICG SB RAS Collection and other
collections
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Affiliation(s)
- Yu E Uvarova
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A V Bryanskaya
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A S Rozanov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - V N Shlyakhtun
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E A Demidov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - K V Starostin
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - T N Goryachkovskaya
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - S V Shekhovtsov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N M Slynko
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - S E Peltek
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Korzhuk AV, Myagkaya IN, Rozanov AS, Ershov NI, Saryg-Ool BOY, Malov VI, Gustaytis MA, Shipova AA, Lazareva EV, Peltek SE. Metagenomics data of microbial communities of natural organic matter from the dispersion train of sulfide tailings. Data Brief 2021; 35:106720. [PMID: 33537377 PMCID: PMC7838707 DOI: 10.1016/j.dib.2021.106720] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/16/2020] [Accepted: 01/05/2021] [Indexed: 12/02/2022] Open
Abstract
Below is data on the microbial diversity of natural organic matter from the Dispersion Train of Sulfide Tailings (northern Salaire Ridge, southwestern Siberia, Russia, Ursk Village). Data was obtained using 16s rRNA amplicon directed metagenomic sequencing on Illumina MiSeq. The raw sequence data used for analysis is available in NCBI under the Sequence Read Archive (SRA) with BioProject No. PRJNA670045 and SRA accession number SRX9314152, SRX9314376. The data sequences of the 16s rRNA gene are presented at the links MW142408-MW142413, MW142414-MW142447.
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Affiliation(s)
- Anton V Korzhuk
- Laboratory of molecular biotechnology, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 10 Lavrentjeva Ave., Novosibirsk 630090, Russia.,Kurchatov Genomics Center, Institute of Cytology and Genetics, SB RAS, 10 Lavrentjeva Ave., Novosibirsk 630090, Russia
| | - Irina N Myagkaya
- V.S. Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences (IGM SB RAS), Novosibirsk 630090, Russia
| | - Alexei S Rozanov
- Laboratory of molecular biotechnology, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 10 Lavrentjeva Ave., Novosibirsk 630090, Russia.,Kurchatov Genomics Center, Institute of Cytology and Genetics, SB RAS, 10 Lavrentjeva Ave., Novosibirsk 630090, Russia.,V.S. Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences (IGM SB RAS), Novosibirsk 630090, Russia
| | - Nikita I Ershov
- Laboratory of molecular biotechnology, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 10 Lavrentjeva Ave., Novosibirsk 630090, Russia
| | - Bagai-Ool Yu Saryg-Ool
- V.S. Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences (IGM SB RAS), Novosibirsk 630090, Russia
| | - Victor I Malov
- V.S. Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences (IGM SB RAS), Novosibirsk 630090, Russia
| | - Maria A Gustaytis
- V.S. Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences (IGM SB RAS), Novosibirsk 630090, Russia
| | - Aleksandra A Shipova
- Laboratory of molecular biotechnology, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 10 Lavrentjeva Ave., Novosibirsk 630090, Russia.,Kurchatov Genomics Center, Institute of Cytology and Genetics, SB RAS, 10 Lavrentjeva Ave., Novosibirsk 630090, Russia
| | - Elena V Lazareva
- V.S. Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences (IGM SB RAS), Novosibirsk 630090, Russia
| | - Sergey E Peltek
- Laboratory of molecular biotechnology, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 10 Lavrentjeva Ave., Novosibirsk 630090, Russia
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Bryanskaya AV, Shipova AA, Rozanov AS, Volkova OA, Lazareva EV, Uvarova YE, Goryachkovskaya TN, Peltek SE. Metagenomics dataset used to characterize microbiome in water and sediments of the lake Solenoe (Novosibirsk region, Russia). Data Brief 2020; 34:106709. [PMID: 33490329 PMCID: PMC7807203 DOI: 10.1016/j.dib.2020.106709] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/14/2020] [Accepted: 12/28/2020] [Indexed: 11/24/2022] Open
Abstract
This is data on the microbial diversity in the floating cyanobacterial community and sediment samples from the lake Solenoe (Novosibirsk region, Russia) obtained by metagenomic methods. Such a detailed data of the microbial diversity of the Novosibirsk oblast lake ecosystem was carried out for the first time. The purpose of our work was to reveal microbial taxonomic diversity and abundance, metabolic pathways and new enzyme findings the studied lake ecosystem using the next-generation sequencing (NGS) technology and metagenomic analysis. The data was obtained using metagenomics DNA whole genome sequencing (WGS) on Illumina NextSeq and NovaSeq. The raw sequence data used for analysis is available in NCBI under the Sequence Read Archive (SRA) with the BioProjects and SRA accession numbers: PRJNA493912 (SRR7943696), PRJNA493952 (SRR7943839) and PRJNA661775 (SRR12601635, SRR12601634, SRR12601633) corresponding to floating cyanobacterial community and sediment layers samples, respectively.
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Affiliation(s)
- Alla V Bryanskaya
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia.,Kurchatov Genomics Center of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia
| | - Aleksandra A Shipova
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia.,Kurchatov Genomics Center of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia
| | - Alexei S Rozanov
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia.,Kurchatov Genomics Center of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia
| | - Oxana A Volkova
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia.,Kurchatov Genomics Center of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia
| | - Elena V Lazareva
- The V.S. Sobolev Institute of Geology and Mineralogy SB RAS, 3 Koptyuga Aven., Novosibirsk 630090, Russia
| | - Yulia E Uvarova
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia.,Kurchatov Genomics Center of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia
| | - Tatyana N Goryachkovskaya
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia.,Kurchatov Genomics Center of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia
| | - Sergey E Peltek
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia.,Kurchatov Genomics Center of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia
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Rozanov AS, Pershina EG, Bogacheva NV, Shlyakhtun V, Sychev AA, Peltek SE. Diversity and occurrence of methylotrophic yeasts used in genetic engineering. Vavilovskii Zhurnal Genet Selektsii 2020; 24:149-157. [PMID: 33659794 PMCID: PMC7716571 DOI: 10.18699/vj20.602] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Methylotrophic yeasts have been used as the platform for expression of heterologous proteins since the
1980’s. They are highly productive and allow producing eukaryotic proteins with an acceptable glycosylation level.
The first Pichia pastoris-based system for expression of recombinant protein was developed on the basis of the treeexudate-
derived strain obtained in the US southwest. Being distributed free of charge for scientific purposes, this system
has become popular around the world. As methylotrophic yeasts were classified in accordance with biomolecular
markers, strains used for production of recombinant protein were reclassified as Komagataella phaffii. Although patent
legislation suggests free access to these yeasts, they have been distributed on a contract basis. Whereas their status
for commercial use is undetermined, the search for alternative stains for expression of recombinant protein continues.
Strains of other species of methylotrophic yeasts have been adapted, among which the genus Ogataea representatives
prevail. Despite the phylogenetic gap between the genus Ogataea and the genus Komagataella representatives,
it turned out possible to use classic vectors and promoters for expression of recombinant protein in all cases. There
exist expression systems based on other strains of the genus Komagataella as well as the genus Candida. The potential
of these microorganisms for genetic engineering is far from exhausted. Both improvement of existing expression systems
and development of new ones on the basis of strains obtained from nature are advantageous. Historically, strains
obtained on the southwest of the USA were used as expression systems up to 2009. Currently, expression systems
based on strains obtained in Thailand are gaining popularity. Since this group of microorganisms is widely represented
around the world both in nature and in urban environments, it may reasonably be expected that new expression systems
for recombinant proteins based on strains obtained in other regions of the globe will appear.
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Affiliation(s)
- A S Rozanov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E G Pershina
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N V Bogacheva
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - V Shlyakhtun
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Sychev
- Innovation Centre Biruch-NT, Belgorod region, Russia
| | - S E Peltek
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Rozanov AS, Zagrebel'nyĭ SN, Beklemishchev AB. [Cloning of Escherichia coli K12 xylose isomerase (glucose isomerase) and studying the enzymatic properties of its expression product]. Prikl Biokhim Mikrobiol 2009; 45:38-44. [PMID: 19235507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The coding region of Escherichia coli K12 xylose (glucose) isomerase gene was inserted into the pRAC expression vector and cloned in E. coli BL21 (DE3) cells. After induction of expression of the cloned gene, the proportion of recombinant xylose isomerase accounted for 40% of the total protein content. As a result of one-stage purification by affinity chromatography, a protein preparation of 90% purity was obtained. The recombinant enzyme catalyzed the isomerization of glucose to fructose and exhibited maximum activity (0.8 U/mg) at 45 degrees C and pH 6.8. The enzyme required Mg2+ ions as a cofactor. When Mg2+ and Co2+ ions were simultaneously present in the reaction medium, the enzyme activity increased by 15-20%. Complete replacement of Mg2+ with Co2+ decreased the enzyme activity. In the presence of Ca2+ at concentrations comparable to the concentration of Mg2+, the enzyme was not inhibited, although published data reported inhibition of similar enzymes by Ca2+. The recombinant enzyme exhibited a very low thermostability: it underwent a slow inactivation when incubated at 45 degrees C and was completely inactivated after incubation at 65 degrees C for 1 h.
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Rautian GS, Mironenko EV, Anokhin AP, Rozanov AS, Ata-Muradova FA. [Genetic and demographic structure of the Talysh population]. Genetika 1993; 29:837-844. [PMID: 8335241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Investigation was carried out in Talysh population in mountain region of South Azerbaijan. There is extended reproduction in the population. From XVIII till the beginning of XX century there were 3-3.6 offsprings in a family. In the last generation with completed reproduction, the family size raised to 7.13. Modern factors of population size dynamics are considered. It turned out that the main new factor (in conditions of increased family size) is the intensive migration from the population, mainly in men, that results in transformation of sex index in the reproductive age (ratio men/women is 0.77), and a large part of women stay unmarried. Crow index is Itot = 0.426, its components are Im = 0.115, If = 0.260.
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Ziuganov VV, Nezlin LP, Zotin AA, Rozanov AS. [The parasite-host relationships between the glochidia of the European pearl oyster Margaritifera margaritifera (Margaritiferidae: Bivalvia) and mass fish species in the European north of the USSR]. Parazitologiia 1990; 24:315-21. [PMID: 2147985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Narrow specificity of larvae (glochidia) of Margaritifera margaritifera to salmon in the rivers of the Kola Peninsula was proved experimentally. It was found that in the gills of minnow, the other mass fish in the northern rivers of the USSR, larvae of M. margaritifera cannot develop and perish. Reasons causing the narrow specificity of M. margaritifera to Salmonidae are discussed.
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