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

Authors

  • 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

Keywords:

oligonucleotides, polymerase chain reaction, salinicola, ec/-genes

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.

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

Ананьина Л.Н. и др. Salinicola socius gen. nov., sp. nov. - новая умеренно галофильнаябактерия из ассоциации микроорганизмов, утилизирующей нафталин // Микробиология. 2007. Т. 76, № 3. С. 369-376.

Ананьина Л.Н., Плотникова Е.Г. Новая система олигонуклеотидов для амплификации ес^генов бактерий семейства Нalomonadaceae // Вестник Уральской медицинской академической науки. 2011. Т. 4, № 1. С. 17.

Патрушев Л.И. Искусственные генетические системы. T. 1: Генная белковая инженерия. М.: Наука, 2004. 526 с.

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. 2007. Vol. 57. P. 1238-1242.

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. 2011. Vol. 10. P. 115. URL: http://www.microbialcellfactories.com/content/10/1/8 8.

Calderón M.I. et al. Complex regulation of the synthesis of the compatible solute ectoine in the halophilic bacterium Chromohalobacter salexigens DSM 3043T // Microbiology. 2004. Vol. 150. P. 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. 2010. Vol. 60. P. 963-971.

Designing PCR primers and probes URL: 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. 2013. Vol. 104. P. 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. 2007. Vol. 57. P. 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. 2002. Vol. 68, № 2. P. 772-783.

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 coralAcropora digitifera // Antonie van Leeuwenhoek. 2015. Vol. 108. P. 5973.

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. 2004. Vol. 27, № 3. P. 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. 2017. Vol. 19. P. 1-13. 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. 1999. Vol. 181. P. 91-99.

Pastor J.M. et al. Role of central metabolism in the osmoadaptation of the halophilic bacterium Chro-mohalobacter salexigens // J. Biol. Chem. 2013. Vol. 288, № 24. P. 17769-17781.

Raju K. et al. Salinicola rhizosphaerae sp. nov., isolated from the rhizosphere of the mangrove Avicennia marina // Int. J. Syst. Evol. Microbiol. 2016. Vol. 66. P. 1074-1079.

Raymond R.L. Microbial oxidation of n-paraffinic hydrocarbons // Develop. Ind. Microbiol. 1961. Vol. 2. P. 23-32.

Schwibbert K. et al. A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581T // Environ. Microbiol. 2011. Vol. 13. P. 1973-1994.

Versalovic J. et al. Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction // Meth. Cell. Mol. Biol. 1994. Vol. 5. P. 25-40.

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.

Downloads

Published

2018-10-31

Issue

No. 3 (2017): Вестник Пермского университета. Серия «Биология»=Bulletin of Perm University. Biology

Section

Микробиология

License

License agreement

 

How to Cite

DESIGN OF OLIGONUCLEOTIDE SYSTEM AND OPTIMIZATION OF CONDITIONS FOR AMPLIFICATION OF ecf-GENES OF BACTERIA OF GENUS SALINICOLA OF HALOMONADACEAE FAMILY. (2018). Bulletin of Perm University. Biology, 3, 297-303. https://press.psu.ru/index.php/bio/article/view/1867

Similar Articles

21-30 of 168

You may also start an advanced similarity search for this article.

Most read articles by the same author(s)