Activity of alkanmonooxygenase alkB gene in strains of hydrocarbon-oxidizing bacteria isolated from petroleum products

Alkanmonooxygenase enzymes AlkB and Cyp153 are responsible for the aerobic degradation of n-alkanes of petroleum and petroleum products. To prove the usage of n-alkanes from oil and petroleum products by hydrocarbon- oxidizing bacteria isolated from aviation kerosene TS-1 and automobile gasoline AI-...

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Published in:Vavilov Journal of Genetics and Breeding
Main Authors: T. N. Shapiro, N. A. Manucharova, E. S. Lobakova, Т. Н. Шапиро, Н. А. Манучарова, Е. С. Лобакова
Other Authors: The research was carried out with the financial support of the Russian National Science Foundation grant No. 21-14-00076 “Diversity and biotechnological potential of the soil microbiome under anthropogenic and abiogenic loads” and partly supported by the Interdisciplinary Scientific and Educational School of Moscow University “Molecular Technologies of the Living Systems and Synthetic Biology”.
Format: Article in Journal/Newspaper
Language:English
Published: Institute of Cytology and Genetics of Siberian Branch of the RAS 2022
Subjects:
Online Access:https://vavilov.elpub.ru/jour/article/view/3479
https://doi.org/10.18699/VJGB-22-70
id ftjvavilov:oai:oai.vavilov.elpub.ru:article/3479
record_format openpolar
institution Open Polar
collection Vavilov Journal of Genetics and Breeding
op_collection_id ftjvavilov
language English
topic ПЦР в реальном времени
petroleum products
hydrocarbon-oxidizing bacteria
biodegradation
alkanmonooxygenase
alk B gene
real-time PCR
нефтепродукты
углеводородокисляющие бактерии
биодеградация
алканмонооксигеназы
ген alk B
spellingShingle ПЦР в реальном времени
petroleum products
hydrocarbon-oxidizing bacteria
biodegradation
alkanmonooxygenase
alk B gene
real-time PCR
нефтепродукты
углеводородокисляющие бактерии
биодеградация
алканмонооксигеназы
ген alk B
T. N. Shapiro
N. A. Manucharova
E. S. Lobakova
Т. Н. Шапиро
Н. А. Манучарова
Е. С. Лобакова
Activity of alkanmonooxygenase alkB gene in strains of hydrocarbon-oxidizing bacteria isolated from petroleum products
topic_facet ПЦР в реальном времени
petroleum products
hydrocarbon-oxidizing bacteria
biodegradation
alkanmonooxygenase
alk B gene
real-time PCR
нефтепродукты
углеводородокисляющие бактерии
биодеградация
алканмонооксигеназы
ген alk B
description Alkanmonooxygenase enzymes AlkB and Cyp153 are responsible for the aerobic degradation of n-alkanes of petroleum and petroleum products. To prove the usage of n-alkanes from oil and petroleum products by hydrocarbon- oxidizing bacteria isolated from aviation kerosene TS-1 and automobile gasoline AI-95, the detection of the key genes alkB, Alk1, Alk2, Alk3 and Cyp153 encoding alkanmonooxygenases AlkB and Cyp153 (responsible for the oxidation of hydrocarbons with a certain chain length) was carried out. It was found that bacterial strains isolated from TS-1 jet fuel, except Deinococcus sp. Bi7, had at least one of the studied n-alkane degradation genes. The strains Sphingobacterium multivorum Bi2; Alcaligenes faecalis Bi3; Rhodococcus sp. Bi4; Sphingobacterium sp. Bi5; Rhodococcus erythropolis Bi6 contained the alkB gene. In the strains of hydrocarbon-oxidizing bacteria isolated from gasoline AI- 95, this alkanmonooxygenase gene was not detected. Using the real-time PCR method, the activity of the alkB gene in all bacterial strains isolated from petroleum products was analyzed and the number of its copies was determined. By real-time PCR using a primer with a different sequence of nucleotides to detect the alkB gene, its activity was established in all bacterial strains isolated from gasoline AI-95; besides, the strain Paenibacillus agaridevorans Bi11 was assigned to the group with a high level of its activity (1290 copies/ml). According to the assessment of the growth of isolated hydrocarbon-oxidizing bacteria on a solid Evans mineral medium with the addition of the model mixture of hydrocarbons, the strains were divided into three groups. The distributions of strains of hydrocarbon-oxidizing bacteria in the groups based on the activity of the alkB gene and groups formed based on the growth ability and use of the model mixture of hydrocarbons and petroleum products were found to be consistent. The results obtained indicate that we need to use a complex of molecular and physiological methods for a comprehensive ...
author2 The research was carried out with the financial support of the Russian National Science Foundation grant No. 21-14-00076 “Diversity and biotechnological potential of the soil microbiome under anthropogenic and abiogenic loads” and partly supported by the Interdisciplinary Scientific and Educational School of Moscow University “Molecular Technologies of the Living Systems and Synthetic Biology”.
format Article in Journal/Newspaper
author T. N. Shapiro
N. A. Manucharova
E. S. Lobakova
Т. Н. Шапиро
Н. А. Манучарова
Е. С. Лобакова
author_facet T. N. Shapiro
N. A. Manucharova
E. S. Lobakova
Т. Н. Шапиро
Н. А. Манучарова
Е. С. Лобакова
author_sort T. N. Shapiro
title Activity of alkanmonooxygenase alkB gene in strains of hydrocarbon-oxidizing bacteria isolated from petroleum products
title_short Activity of alkanmonooxygenase alkB gene in strains of hydrocarbon-oxidizing bacteria isolated from petroleum products
title_full Activity of alkanmonooxygenase alkB gene in strains of hydrocarbon-oxidizing bacteria isolated from petroleum products
title_fullStr Activity of alkanmonooxygenase alkB gene in strains of hydrocarbon-oxidizing bacteria isolated from petroleum products
title_full_unstemmed Activity of alkanmonooxygenase alkB gene in strains of hydrocarbon-oxidizing bacteria isolated from petroleum products
title_sort activity of alkanmonooxygenase alkb gene in strains of hydrocarbon-oxidizing bacteria isolated from petroleum products
publisher Institute of Cytology and Genetics of Siberian Branch of the RAS
publishDate 2022
url https://vavilov.elpub.ru/jour/article/view/3479
https://doi.org/10.18699/VJGB-22-70
genre Arctic
genre_facet Arctic
op_source Vavilov Journal of Genetics and Breeding; Том 26, № 6 (2022); 575-582
Вавиловский журнал генетики и селекции; Том 26, № 6 (2022); 575-582
2500-3259
2500-0462
10.18699/VJGB-22-6
op_relation https://vavilov.elpub.ru/jour/article/view/3479/1647
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Cappelletti M., Fedi S., Frascari D., Ohtake H., Turner R.J., Zannoni D. Analyses of both the alkB gene transcriptional start site and alkB promoter-inducing properties of Rhodococcus sp. strain BCP1 grown on n-alkanes. Appl. Environ. Microbiol. 2011;77(5):1619-1627. DOI 10.1128/AEM.01987-10.
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Heiss-Blanquet S., Benoit Y., Marechaux C., Monot F. Assessing the role of alkane hydroxylase genotypes in environmental samples by competitive PCR. J. Appl. Microbiol. 2005;99(6):1392-1403. DOI 10.1111/j.1365-2672.2005.02715.x.
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spelling ftjvavilov:oai:oai.vavilov.elpub.ru:article/3479 2023-05-15T14:28:30+02:00 Activity of alkanmonooxygenase alkB gene in strains of hydrocarbon-oxidizing bacteria isolated from petroleum products Активность гена алканмонооксигеназы alkB у штаммов углеводородокисляющих бактерий, выделенных из нефтепродуктов T. N. Shapiro N. A. Manucharova E. S. Lobakova Т. Н. Шапиро Н. А. Манучарова Е. С. Лобакова The research was carried out with the financial support of the Russian National Science Foundation grant No. 21-14-00076 “Diversity and biotechnological potential of the soil microbiome under anthropogenic and abiogenic loads” and partly supported by the Interdisciplinary Scientific and Educational School of Moscow University “Molecular Technologies of the Living Systems and Synthetic Biology”. 2022-10-09 application/pdf https://vavilov.elpub.ru/jour/article/view/3479 https://doi.org/10.18699/VJGB-22-70 eng eng Institute of Cytology and Genetics of Siberian Branch of the RAS https://vavilov.elpub.ru/jour/article/view/3479/1647 Andreoni V., Bernasconi S., Colombo M., van Beilen J.B., Cavalca L. Detection of genes for alkane and naphthalene catabolism in Rhodococcus sp. strain 1BN. Environ. Microbiol. 2000;2:572-577. DOI 10.1046/j.1462-2920.2000.00134.x. Cappelletti M., Fedi S., Frascari D., Ohtake H., Turner R.J., Zannoni D. Analyses of both the alkB gene transcriptional start site and alkB promoter-inducing properties of Rhodococcus sp. strain BCP1 grown on n-alkanes. Appl. Environ. Microbiol. 2011;77(5):1619-1627. DOI 10.1128/AEM.01987-10. Coon M.J. Cytochrome P450: nature’s most versatile biological catalyst. Annu. Rev. Pharmacol. Toxicol. 2005;45:1-25. Dedov A.G., Ivanova E.A., Sandzhieva D.A., Kashcheeva P.B., Buznik V.M., Lobakova E.S., Kirpichnikov M.P., Ishkov A.G. New materials and ecology: biocomposites for aquatic remediation. Theor. Found. Chem. Eng. 2017;51(4):617-630. DOI 0.1134/S0040579517040042. Evans C.G.T., Herbert D., Tempest D.W. The continuous cultivation of micro-organisms: 2. Construction of a chemostat. In: Methods in Microbiology. Vol. 2. London; New York: Academic Press, 1970: 277-327. DOI 10.1016/S0580-9517(08)70227-7. Funhoff E.G., Bauer U., García-Rubio I., Witholt B., van Beilen J.B. CYP153A6, a soluble P450 oxygenase catalyzing terminal-alkane hydroxylation. J. Bacteriol. 2006;188(14):5220-5227. DOI 10.1128/JB.00286-06. Heiss-Blanquet S., Benoit Y., Marechaux C., Monot F. Assessing the role of alkane hydroxylase genotypes in environmental samples by competitive PCR. J. Appl. Microbiol. 2005;99(6):1392-1403. DOI 10.1111/j.1365-2672.2005.02715.x. Ivanova A.E., Kravchenko I.K., Sukhacheva M.V., Kanat’eva A.Y., Kurganov A.A. Hydrocarbon-oxidizing potential and genes for n- alkane biodegradation in a new acidophilic mycobacterial association from sulfur blocks. Microbiology. 2014;83(6):764-772. Johnson E.L., Hyman M.R. Propane and n-butane oxidation by Pseudomonas putida GPo1. Appl. Environ. Microbiol. 2006;72(1):950-952. DOI 10.1128/AEM.72.1.950-952.2006. Karimova S.A. Corrosion is the main enemy of aviation. Nauka i Zhizn’ = Science and Life. 2007;6:63-65. (in Russian) Kato T., Miyanaga A., Kanaya S., Morikawa M. Alkane inducible proteins in Geobacillus thermoleovorans B23. BMC Microbiol. 2009; 9(1):1-9. DOI 10.1186/1471-2180-9-60. Kloos K., Munch J.C., Schloter M. A new method for the detection of alkane-monooxygenase homologous genes (alkB) in soils based on PCR-hybridization. J. Microbiol. Methods. 2006;66(3):486-496. DOI 10.1016/j.mimet.2006.01.014. Kohno T., Sugimoto Y., Sei K., Mori K. Design of PCR primers and gene probes for general detection of alkane-degrading bacteria. Microbes Environ. 2002;17:114-121. DOI 10.1264/jsme2.17.114. Korshunova A.V., Tourova T.P., Shestakova N.M., Mikhailova E.M., Nazina T.N., Poltaraus A.B. Detection and transcription of n-alkane biodegradation genes (alkB) in the genome of a hydrocarbonoxidizing bacterium Geobacillus subterraneus K. Microbiology. 2011;80(5):682-691. Likhoshvay A., Lomakina A., Grachev M. The complete alk sequences of Rhodococcus erythropolis from Lake Baikal. Springerplus. 2014; 3(1):1-5. DOI 10.1186/2193-1801-3-621. Liu C., Shao Z. Alcanivorax dieselolei sp. nov., a novel alkane-degrading bacterium isolated from sea water and deep-sea sediment. Int. J. Syst. Evol. Microbiol. 2005;55(3):1181-1186. DOI 10.1099/ijs.0.63443-0. Lomakina A.V., Pogodaeva T.V., Morozov I.V., Zemskaya T.I. Microbial communities of the discharge zone of oil- and gas-bearing fluids in low-mineral Lake Baikal. Microbiology. 2014;83(3):278-287. DOI 10.1134/S0026261714030126. Lysak L.V., Dobrovol’skaya T.G., Skvortsova I.N. Methods for Assessing the Bacterial Diversity of Soils and the Identification of Soil Bacteria. Moscow: MAX Press Publ., 2003. (in Russian) Manucharova N.A., Pozdnyakov L.A., Vlasova A.P., Yanovich A.S., Ksenofontova N.A., Kovalenko M.A., Stepanov A.L. Metabolically active prokaryotic complex in grassland and forests’ sod-podzol under polycyclic aromatic hydrocarbon influence. Forests. 2021; 12(8):1103. DOI 10.3390/f12081103. Martin-Sanchez P.M., Becker R., Gorbushina A.A., Toepel J. An improved test for the evaluation of hydrocarbon degradation capacities of diesel-contaminating microorganisms. Int. Biodeterior. Biodegr. 2018;129:89-94. DOI 10.1016/j.ibiod.2018.01.009. Mohanty G., Mukherji S. Biodegradation rate of diesel range n-alkanes by bacterial cultures Exiguobacterium aurantiacum and Burkholderia cepacia. Int. Biodeterior. Biodegr. 2008;61(3):240-250. DOI 10.1016/j.ibiod.2007.06.011. Paisse S., Duran R., Coulon F., Goñi-Urriza M. Are alkane hydroxylase genes (alkB) relevant to assess petroleum bioremediation processes in chronically polluted coastal sediments? Appl. Microbiol. Biotechnol. 2011;92(4):835-844. DOI 10.1016/j.ibiod.2007.06.011. Powell S.M., Ferguson S.H., Bowman J.P., Snape I. Using real-time PCR to assess changes in the hydrocarbon-degrading microbial community in Antarctic soil during bioremediation. Microb. Ecol. 2006;52(3):523-532. DOI 10.1007/s00248-006-9131-z. Redmond M.C., Valentine D.L., Sessions A.L. Identification of novel methane-, ethane-, and propane-oxidizing bacteria at marine hydrocarbon seeps by stable isotope probing. Appl. Environ. Microbiol. 2010;76(19):6412-6422. 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Microbiology. 2008;77(5):625-627. https://vavilov.elpub.ru/jour/article/view/3479 doi:10.18699/VJGB-22-70 Authors who publish their articles in this journal give their consent to the following:Authors reserve their rights and vest the journal with the authority to make the first publication of their manuscripts, which would automatically be licensed upon the expiry of 6 months after publication subject to the terms of Creative Commons Attribution License; the latter will allow anyone to disseminate the article in question, with mandatory preservation of references to the authors of the original article and to its first publication in this journal.Authors may display their articles on the Internet (for example, in the Institute’s data warehouse or on a personal website) prior to or during the process of their consideration by this journal, as it may lead to a more productive discussion and expand the number of references to the article in question (see The Effect of Open Access). 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CC-BY Vavilov Journal of Genetics and Breeding; Том 26, № 6 (2022); 575-582 Вавиловский журнал генетики и селекции; Том 26, № 6 (2022); 575-582 2500-3259 2500-0462 10.18699/VJGB-22-6 ПЦР в реальном времени petroleum products hydrocarbon-oxidizing bacteria biodegradation alkanmonooxygenase alk B gene real-time PCR нефтепродукты углеводородокисляющие бактерии биодеградация алканмонооксигеназы ген alk B info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion 2022 ftjvavilov https://doi.org/10.18699/VJGB-22-70 https://doi.org/10.18699/VJGB-22-6 2022-10-11T17:02:55Z Alkanmonooxygenase enzymes AlkB and Cyp153 are responsible for the aerobic degradation of n-alkanes of petroleum and petroleum products. To prove the usage of n-alkanes from oil and petroleum products by hydrocarbon- oxidizing bacteria isolated from aviation kerosene TS-1 and automobile gasoline AI-95, the detection of the key genes alkB, Alk1, Alk2, Alk3 and Cyp153 encoding alkanmonooxygenases AlkB and Cyp153 (responsible for the oxidation of hydrocarbons with a certain chain length) was carried out. It was found that bacterial strains isolated from TS-1 jet fuel, except Deinococcus sp. Bi7, had at least one of the studied n-alkane degradation genes. The strains Sphingobacterium multivorum Bi2; Alcaligenes faecalis Bi3; Rhodococcus sp. Bi4; Sphingobacterium sp. Bi5; Rhodococcus erythropolis Bi6 contained the alkB gene. In the strains of hydrocarbon-oxidizing bacteria isolated from gasoline AI- 95, this alkanmonooxygenase gene was not detected. Using the real-time PCR method, the activity of the alkB gene in all bacterial strains isolated from petroleum products was analyzed and the number of its copies was determined. By real-time PCR using a primer with a different sequence of nucleotides to detect the alkB gene, its activity was established in all bacterial strains isolated from gasoline AI-95; besides, the strain Paenibacillus agaridevorans Bi11 was assigned to the group with a high level of its activity (1290 copies/ml). According to the assessment of the growth of isolated hydrocarbon-oxidizing bacteria on a solid Evans mineral medium with the addition of the model mixture of hydrocarbons, the strains were divided into three groups. The distributions of strains of hydrocarbon-oxidizing bacteria in the groups based on the activity of the alkB gene and groups formed based on the growth ability and use of the model mixture of hydrocarbons and petroleum products were found to be consistent. The results obtained indicate that we need to use a complex of molecular and physiological methods for a comprehensive ... 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