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

Aregbesola, Oladipupo A.; Kumar, Ajit; Mokoena, Mduduzi P.; Olaniran, Ademola O.

doi:10.1007/s10142-021-00768-x

Cited by 11 publications

(2 citation statements)

References 87 publications

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“…CQQ001 (B. CQ001) which could degrade dexamethasone effectively was sequenced using Illumina Hiseq4000 in combination with third-generation sequencing technology to analyze the functional genes and metabolic pathways involved in dexamethasone degradation (Si et al 2019 ). The whole genome of Bacillus tropicus strain AOA-CPS1 (BtAOA) was sequenced using the Pacific Biosciences RS II sequencer to reveal that the strain harbored genes intimately related to the biodegradation of numerous chlorophenolic compounds (Aregbesola et al 2021 ). As far as is known, only small number of studies have focused on the mechanism of pyrethroid degradation by analysis of whole genome sequences.…”

Section: Introductionmentioning

confidence: 99%

Whole genome sequencing and analysis of fenvalerate degrading bacteria Citrobacter freundii CD-9

et al. 2022

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Citrobacter freundii CD-9 is a Gram-negative bacteria sourced from factory sludge that can use fenvalerate as its sole carbon source and has a broad degradation spectrum for pyrethroid pesticides. The whole genome of CD-9 sequenced using Illumina HiSeq PE150 was reported in this study. The CD-9 genome size was 5.33 Mb and the G + C content was 51.55%. A total of 5291 coding genes, 9 5s-rRNA, and 79 tRNA were predicted bioinformatically. 3586 genes annotated to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database that can be involved in 173 metabolic pathways, including various microbial metabolic pathways that degrade exogenous chemicals, especially those that degrade aromatic compounds, and also produce a variety of bioactive substances. Fifty genes related to pyrethroid degradation were identified in the C. freundii CD-9 genome, including 9 dioxygenase, 25 hydrolase, and 16 esterase genes. Notably, RT-qPCR results showed that from the predicted 13 genes related to fenvalerate degradation, the expression of six genes, including esterase, HAD family hydrolase, lipolytic enzyme, and gentisic acid dioxygenase, was induced in the presence of fenvalerate. In this study, the key genes and degradation mechanism of C. freundii CD-9 were analyzed and the results provide scientific evidence to support its application in environmental bioremediation. It can establish application models for different environmental pollution management by constructing genetically engineered bacteria for efficient fenvalerate or developing enzyme formulations that can be industrially produced.

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Section: Introductionmentioning

confidence: 99%

Whole genome sequencing and analysis of fenvalerate degrading bacteria Citrobacter freundii CD-9

et al. 2022

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show abstract

“…CQQ001 (B. CQ001) which could degrade dexamethasone effectively was sequenced using Illumina Hiseq4000 in combination with third-generation sequencing technology to analyze the functional genes and metabolic pathways involved in dexamethasone degradation (Si et al 2019). The whole genome of Bacillus tropicus strain AOA-CPS1 (BtAOA) was sequenced using the Paci c Biosciences RS II sequencer to reveal that the strain harbored genes intimately related to the biodegradation of numerous chlorophenolic compounds (Aregbesola et al 2021). As far as is known, only small number of studies have focused on the mechanism of pyrethroid degradation by analysis of whole genome sequences.…”

Section: Introductionmentioning

confidence: 99%

Whole Genome Sequencing and Analysis of Fenvalerate Degrading Bacteria Citrobacter freundii CD-9

Zhou

Lei

Tang

et al. 2022

Preprint

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Citrobacter freundii CD-9 is a gram-negative bacteria sourced from factory sludge that can use fenvalerate as its sole carbon source and has a broad degradation spectrum for pyrethroid pesticides. The whole genome of CD-9 sequenced using Illumina HiSeq PE150 was reported in this study. The CD-9 genome size was 5.33 Mb and the G + C content was 51.55%. A total of 5,291 coding genes, 9 5s- rRNA, and 79 tRNA were predicted bioinformatically. 3586 genes annotated to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database that can be involved in 173 metabolic pathways, including various microbial metabolic pathways that degrade exogenous chemicals, especially those that degrade aromatic compounds, and also produce a variety of bioactive substances. Fifty genes related to pyrethroid degradation were identified in the C. freundii CD-9 genome, including 9 dioxygenase, 25 hydrolase, and 16 esterase genes. Notably, RT-qPCR results showed that from the predicted 13 genes related to fenvalerate degradation, the expression of six genes, including esterase, HAD family hydrolase, lipolytic enzyme, and gentisic acid dioxygenase, was induced in the presence of fenvalerate. In this study, the key genes and degradation mechanism of C. freundii CD-9 were analyzed and the results provide scientific evidence to support its application in environmental bioremediation.

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Exploring and targeting potential druggable antimicrobial resistance targets ArgS, SecY, and MurA in Staphylococcus sciuri with TCM inhibitors through a subtractive genomics strategy

Khan¹,

Sohail²,

Yaseen³

et al. 2023

Funct Integr Genomics

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

Cited by 11 publications

References 87 publications

Whole genome sequencing and analysis of fenvalerate degrading bacteria Citrobacter freundii CD-9

Whole genome sequencing and analysis of fenvalerate degrading bacteria Citrobacter freundii CD-9

Whole Genome Sequencing and Analysis of Fenvalerate Degrading Bacteria Citrobacter freundii CD-9

Exploring and targeting potential druggable antimicrobial resistance targets ArgS, SecY, and MurA in Staphylococcus sciuri with TCM inhibitors through a subtractive genomics strategy

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