DESIGN OF OLIGONUCLEOTIDE SYSTEM AND OPTIMIZATION OF CONDITIONS FOR AMPLIFICATION OF ecf-GENES OF BACTERIA OF GENUS SALINICOLA OF HALOMONADACEAE FAMILY

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Published: Oct 31, 2018
Keywords:
oligonucleotides polymerase chain reaction salinicola ec/-genes

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Людмила/Lyudmila Николаевна/Nikolaevna Ананьина/Anan'ina
Institute of Ecology and Genetics of Microorganism UB RAS
Елена/Elena Анатольевна/Anatol'evna Шестакова/Shestakova
Institute of Ecology and Genetics of Microorganism UB RAS
Анна/Anna Александровна/Alexandrovna Пьянкова/Pyankova
Institute of Ecology and Genetics of Microorganism UB RAS
Елена/Elena Генриховна/Genrikhovna Плотникова/Plotnikova
Institute of Ecology and Genetics of Microorganism UB RAS; Perm State University

Abstract

Search for nucleotide sequences of ec/-operon from bacteria of Halomonadaceae family was carried out in open database of National Center for Biotechnology Information (USA) (https://www.ncbi.nlm.nih.gov). Analysis of aligned 33 nucleotide sequences from the members of genera Salinicola, Halomonas, Chromohalobacter, Kushneria, Cobetia and Halotalea allowed revealing conserved regions. The system of oligonucleotide primers was designed to these in order to amplify the ec/-operon fragment including genes: ec/A, which encodes L-2,4-diarninobutyrate acetyltransferase and eciB, which determines L-2,4-diaminobutyrate aminotransferase. Conditions for polymerase chain reaction were experimentally selected, as well as PCR-rnixture composition to amplify the ec/-operon site on DNA of bacteria of genus Salinicola.

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How to Cite
Ананьина/Anan’ina Л. Н., Шестакова/Shestakova Е. А., Пьянкова/Pyankova А. А., & Плотникова/Plotnikova Е. Г. (2018). DESIGN OF OLIGONUCLEOTIDE SYSTEM AND OPTIMIZATION OF CONDITIONS FOR AMPLIFICATION OF ecf-GENES OF BACTERIA OF GENUS SALINICOLA OF HALOMONADACEAE FAMILY. Bulletin of Perm University. Biology, (3), 297–303. Retrieved from https://press.psu.ru/index.php/bio/article/view/1867
Issue
No. 3 (2017): Вестник Пермского университета. Серия «Биология»=Bulletin of Perm University. Biology
Section
Микробиология

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Author Biographies

Людмила/Lyudmila Николаевна/Nikolaevna Ананьина/Anan'ina, Institute of Ecology and Genetics of Microorganism UB RAS

Candidate of biology, researcher of laboratory of molecular microbiology and biotechnology

Елена/Elena Анатольевна/Anatol'evna Шестакова/Shestakova, Institute of Ecology and Genetics of Microorganism UB RAS

Engineer of laboratory of molecular microbiology and biotechnology

Анна/Anna Александровна/Alexandrovna Пьянкова/Pyankova, Institute of Ecology and Genetics of Microorganism UB RAS

Engineer of the laboratory of molecular microbiology and biotechnology

Елена/Elena Генриховна/Genrikhovna Плотникова/Plotnikova, Institute of Ecology and Genetics of Microorganism UB RAS; Perm State University

Doctor of biology, leading researcher of laboratory of molecular microbiology and biotechnology;Professor of the Department of botany and plant genetics

References

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References

Aguilera M et al. Chromohalobacter salarius sp. nov., a moderately halophilic bacterium isolated from a solar saltern in Cabo de Gata, Almería, southern Spain. Int. J. Syst. Evol. Microbiol. V. 57 (2007): pp. 1238-1242.

Anan'ina L.N., Plotnikova E.G. [New oligonucleotide primer system for bacterial ect-genes amplification of Halomonadaceae famaly]. Vestnik Uralskoj medicinskoj academiceskoj nauki. V. 4, № 1 (2011): p. 17. (In Russ.).

Anan'ina L.N. et al. [Salinicola socius gen. nov., sp. nov., a moderately halophilic bacterium from a naphthalene-utilizing microbial association]. Mik-robiologija. V. 76, № 3 (2007): pp. 369-376. (In Russ.).

Cai L. et al. Comparative genomics study of polyhy-droxyalkanoates (PHA) and ectoine relevant genes from Halomonas sp. TD01 revealed extensive horizontal gene transfer events and co-evolutionary relationships. Microb. Cell Fact. V. 10, № 88 (2011): pp. 1-15. Available at: http://www.microbialcellfactories.com/content/10/1/ 88.

Calderón M.I. et al. Complex regulation of the synthesis of the compatible solute ectoine in the halophilic bacterium Chromohalobacter salexigens DSM 3043T. Microbiology. V. 150 (2004): pp. 3051-3063.

de la Haba R.R. et al. Taxonomic study of the genus Salinicola: transfer of Halomonas salaria and Chromohalobacter salarius to the genus Salinicola as Salinicola salarius comb. nov. and Salinicola halophilus nom. nov., respectively. Int. J. Syst. Evol. Microbiol. V. 60 (2010): pp. 963971.

Designing PCR primers and probes. Available at: https://eu. idtdna. com/pages/decoded/decoded-articles/pipettips/decoded/2013/10/21/designing-pcr-primers-and-probes.

Huo Y.-Y. et al. Salinicola peritrichatus sp. nov., isolated from deep-sea sediment. Antonie van Leeuwenhoek. V. 104 (2013): pp. 55-62.

Kim K.K. et al. Halomonas gomseomensis sp. nov., Halomonas janggokensis sp. nov., Halomonas salaria sp. nov. and Halomonas denitrificans sp. nov., moderately halophilic bacteria isolated from saline water. Int. J. Syst. Evol. Microbiol. V. 57 (2007): pp. 675-681.

Kuhlmann A.U., Bremer E. Osmotically regulated synthesis of the compatible solute ectoine in Bacillus pasteurii and related Bacillus spp. Appl. Environ. Microbiol. V. 68, № 2 (2002): pp. 772783.

Lepcha R.T. et al. Comparative 16S rRNA signatures and multilocus sequence analysis for the genus Salinicola and description of Salinicola acroporae sp. nov., isolated from coral Acropora digitifera. Antonie van Leeuwenhoek. V. 108 (2015): pp. 59-73.

Okamoto T. et al. Comparative phylogenetic analyses of Halomonas variabilis and related organisms based on 16S rRNA, gyrB and ectBC gene sequences. Syst. Appl. Microbiol. V. 27, № 3 (2004): pp. 323-333.

Olsson B.E. et al. Draft genome sequences of strains Salinicola socius SMB35T, Salinicola sp. MH3R3-1 and Chromohalobacter sp. SMB17 from the Verkhnekamsk potash mining region of Russia. Stand. Genomic. Sci. V. 19 (2017): pp. 113. DOI 10.1186/s40793-017-0251-5.

Ono H. et al. Characterization of biosynthetic enzymes for ectoine as a compatible solute in a moderately halophilic eubacterium, Halomonas elongate. J. Bacteriol. V. 181 (1999): pp. 91-99.

Pastor J.M. et al. Role of central metabolism in the Raymond R.L. Microbial oxidation of n-paraffinic osmoadaptation of the halophilic bacterium Chromohalobacter salexigens. J. Biol. Chem. V. 288, № 24 (2013): pp. 17769-17781.

Patrushev L.I. Iskusstvennye geneticeskie sistemy [Artificial genetic systems. Vol. 1. Genetic and protein engineering]. Moscow, Nauka Publ., 2004. 526 p. (In Russ).

Raju K., Sekar J., Vaiyapuri Ramalingam P. Salinicola rhizosphaerae sp. nov., isolated from the rhizosphere of the mangrove Avicennia marina. Int. J. Syst. Evol. Microbiol. V. 66 (2016): pp. 1074-1079.

Raymond R.L. Microbial oxidation of n-paraffinic hydrocarbons. Develop. Ind. Microbiol. V. 2 (1961): pp. 23-32.

Schwibbert K. et al. A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581T. Environ. Microbiol. V. 13 (2011): pp. 1973-1994.

Versalovic J. et al. Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Meth. Cell Mol. Biol. V. 5 (1994): pp.25-40.

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