Whole-genome sequencing, genome mining, metabolic reconstruction and evolution of pentachlorophenol and other xenobiotic degradation pathways in Bacillus tropicus strain AOA-CPS1

Abstract

A pentachlorophenol degrading bacterium was isolated from effluent of a wastewater treatment plant in Durban, South Africa, and identified as Bacillus tropicus strain AOA-CPS1 (BtAOA). The isolate degraded 29% of pentachlorophenol (PCP) within 9 days at an initial PCP concentration of 100 mg L−1 and 62% of PCP when the initial concentration was set at 350 mg L−1. The whole-genome of BtAOA was sequenced using Pacific Biosciences RS II sequencer with the Single Molecule, Real-Time (SMRT) Link (version 7.0.1.66975) and analysed using the HGAP4-de-novo assembly application. The contigs were annotated at NCBI, RASTtk and PROKKA prokaryotic genome annotation pipelines. The BtAOA genome is comprised of a 5,246,860-bp chromosome and a 58,449-bp plasmid with a GC content of 35.4%. The metabolic reconstruction for BtAOA showed that the organism has been naturally exposed to various chlorophenolic compounds including PCP and other xenobiotics. The chromosome encodes genes for core processes, stress response and PCP catabolic genes. Analogues of PCP catabolic gene (cpsBDCAE, and p450) sequences were identified from the NCBI annotation data, PCR-amplified from the whole genome of BtAOA, cloned into pET15b expression vector, overexpressed in E. coli BL21 (DE3) expression host, purified and characterized. Sequence mining and comparative analysis of the metabolic reconstruction of the BtAOA genome with closely related strains suggests that the operon encoding the first two enzymes in the PCP degradation pathway were acquired from a pre-existing pterin-carbinolamine dehydratase subsystem. The other two enzymes were recruited via horizontal gene transfer (HGT) from the pool of hypothetical proteins with no previous specific function, while the last enzyme was recruited from pre-existing enzymes from the TCA or serine-glyoxalase cycle via HGT events. This study provides a comprehensive understanding of the role of BtAOA in PCP degradation and its potential exploitation for bioremediation of other xenobiotic compounds.

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Acknowledgments

The authors thank the University of KwaZulu-Natal for the Ph.D. fellowship.

Funding

This study was financially supported by the National Research Foundation, South Africa (Grant No: 94036 and 92803).

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O.A., A.O. and A.K. conceived and designed the project; O.A. and A.K. designed the experiments; O.A. performed the experiments; M.P. contributed reagents and materials; O.A., A.K., M.P. and A.O. wrote the manuscript; all the authors have read and approved the manuscript.

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Correspondence to Ademola O. Olaniran.

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Aregbesola, O.A., Kumar, A., Mokoena, M.P. et al. Whole-genome sequencing, genome mining, metabolic reconstruction and evolution of pentachlorophenol and other xenobiotic degradation pathways in Bacillus tropicus strain AOA-CPS1. Funct Integr Genomics 21, 171–193 (2021). https://doi.org/10.1007/s10142-021-00768-x

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Keywords

  • Bacillus tropicus
  • Whole-genome sequencing
  • phenylalanine-4-monooxygenase
  • Pterin-carbinolamine dehydratase
  • Ring-cleaving dioxygenase