Characteristics of phenol degradation genetic loci in the genome of bacteria Rhodococcus pyridinivorans strain 5Ap

  • Maryia I. Mandryk Belarusian State University, 4 Niezaliezhnasci Avenue, Minsk 220030, Belarus
  • Artur E. Akhremchuk Institute of Microbiology, National Academy of Sciences of Belarus, 2 Akademika Kuprevicha Street, Minsk 220084, Belarus
  • Leonid N. Valentovich Institute of Microbiology, National Academy of Sciences of Belarus, 2 Akademika Kuprevicha Street, Minsk 220084, Belarus
  • Ella V. Trushlis Belarusian State University, 4 Niezaliezhnasci Avenue, Minsk 220030, Belarus
  • Alina Yu. Larchenka Belarusian State University, 4 Niezaliezhnasci Avenue, Minsk 220030, Belarus
  • Svetlana L. Vasylenko Belarusian State University, 4 Niezaliezhnasci Avenue, Minsk 220030, Belarus

Abstract

The growth dynamics of the bacteria Rhodococcus pyridinivorans strain 5Ap in a medium with phenol (200 mg/L) was characterised. The bacteria reach the stationary phase after 24 h of cultivation. By this time phenol is completely utilised. As a result of whole-genome sequencing, it was established that the genome of bacteria R. pyridinivorans strain 5Ap is represented by a circular chromosome with a size of 5 220 735 base pairs (number in the GenBank database CP063450.1) and three circular megaplasmids – pSID with a size of 250 428 base pairs (CP063453.1), pRh5Ap-243 with a size of 243 288 base pairs (CP063452.1) and pNAPH with a size of 207 815 base pairs (CP063451.1). A comparison of the organisation of genes of the β-ketoadipate phenol degradation pathway in the genomes of 78 bacteria of the genus Rhodococcus of groups B (subgroups B1 and B2), C and D showed that, despite the high level of synteny in general, each group has characteristic features in the structure of the studied loci. Unlike other groups, in genomes of group C bacteria the pheA2A1 and catABC operons are separated by three genes, including fadA and fadI genes, which determine the alternative possibility of phenol oxidation with the formation of succinyl-CoA (in other groups, likely, only acetyl-CoA is formed). Rhodococci of group C and subgroup B1 have an additional locus in their genome, including the pheA2, pheA1 and catA genes. The second locus in bacteria of the subgroup B1, groups C and D includes the pcaIJ and pcaHGBLRF operons, while in bacteria of the subgroup B2 it includes the pcaIJ and pcaBLRF operons, and the pcaHG operon, encoding the components of protocatechuate-3,4-dioxygenase, is located in a different chromosomal locus. The regulatory regions of the pheA2A1 and catABC operons in the bacteria R. pyridinivorans strain 5Ap are similar to the known ones and contain binding sites for both the specific regulatory proteins PheR and CatR, respectively, and for the global catabolism regulator CRP. As a result of analysis of the pcaI – pcaB intergenic region of R. pyridinivorans strain 5Ap, six potential binding sites for the protein PcaR were identified. The nature of the location of these sites may indicate a dual role of the regulatory protein PcaR: as a repressor in a state unbound to the effector and as an activator in a state bound to the effector.

Author Biographies

Maryia I. Mandryk, Belarusian State University, 4 Niezaliezhnasci Avenue, Minsk 220030, Belarus

PhD (biology), docent; associate professor at the department of microbiology, faculty of biology

 

Artur E. Akhremchuk, Institute of Microbiology, National Academy of Sciences of Belarus, 2 Akademika Kuprevicha Street, Minsk 220084, Belarus

researcher at the laboratory «Center of analytical and genetic engineering research»

 

Leonid N. Valentovich, Institute of Microbiology, National Academy of Sciences of Belarus, 2 Akademika Kuprevicha Street, Minsk 220084, Belarus

PhD (biology), docent; head of the laboratory «Center of analytical and genetic engineering research»

 

Ella V. Trushlis, Belarusian State University, 4 Niezaliezhnasci Avenue, Minsk 220030, Belarus

junior researcher trainee at the laboratory of biotechnology, department of microbiology, faculty of biology

 

Alina Yu. Larchenka, Belarusian State University, 4 Niezaliezhnasci Avenue, Minsk 220030, Belarus

postgraduate student at the department of microbiology, faculty of biology

 

Svetlana L. Vasylenko, Belarusian State University, 4 Niezaliezhnasci Avenue, Minsk 220030, Belarus

PhD (biology); head of the department of microbiology, faculty of biology

 

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Published
2024-02-20
Keywords: Rhodococcus, phenol-degrading bacteria, phenol, genetic loci, genes of biodegradation, regulation
Supporting Agencies This work was carried out within the framework of the state programme of scientific research «Biotechnologies-2» for 2021–2025 (assignment 3.6.2) with financial support of the Belarusian Republican Foundation for Fundamental Research and the Ministry of Education of the Republic of Belarus (grant No. B22MV-029).
How to Cite
Mandryk, M. I., Akhremchuk, A. E., Valentovich, L. N., Trushlis, E. V., Larchenka, A. Y., & Vasylenko, S. L. (2024). Characteristics of phenol degradation genetic loci in the genome of bacteria Rhodococcus pyridinivorans strain 5Ap. Experimental Biology and Biotechnology, 1, 27-40. Retrieved from https://journals.bsu.by/index.php/biology/article/view/5990
Issue
No 1 (2024): Experimental Biology and Biotechnology
Section
Genetics and Molecular Biology

Copyright (c) 2024 Experimental Biology and Biotechnology

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