Analysis and preliminary characterisation of the cytochrome P450 monooxygenases from Frankia sp. EuI1c (Frankia inefficax sp.)

Lau, Ian C.-K.; Nelson, David R.; Bell, Stephen

doi:10.1016/j.abb.2019.05.007

Cited by 9 publications

(6 citation statements)

References 67 publications

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“…P450s, ferredoxins, and smBGCs data for Firmicutes species were retrieved from published articles [30,31] and used for comparative analysis. Ferredoxins proteins used for data mining were retrieved from published articles [70][71][72][73][74][75][76][77][78][79][80][81][82][83][84].…”

Section: Comparative Analysis Of P450s Ferredoxins and Smbgcs Datamentioning

confidence: 99%

Contrasting Health Effects of Bacteroidetes and Firmicutes Lies in Their Genomes: Analysis of P450s, Ferredoxins, and Secondary Metabolite Clusters

Nkosi

Padayachee

Gront

et al. 2022

IJMS

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Species belonging to the bacterial phyla Bacteroidetes and Firmicutes represent over 90% of the gastrointestinal microbiota. Changes in the ratio of these two bacterial groups were found to have contrasting health effects, including obesity and inflammatory diseases. Despite the availability of many bacterial genomes, comparative genomic studies on the gene pools of these two bacterial groups concerning cytochrome P450 monooxygenases (P450s), ferredoxins, and secondary metabolite biosynthetic gene clusters (smBGCs) are not reported. This study is aimed to address this research gap. The study revealed the presence of diverse sets of P450s, ferredoxins, and smBGCs in their genomes. Bacteroidetes species have the highest number of P450 families, ferredoxin cluster-types, and smBGCs compared to Firmicutes species. Only four P450 families, three ferredoxin cluster types, and five smBGCs are commonly shared between these two bacterial groups. Considering the above facts, we propose that the contrasting effects of these two bacterial groups on the host are partly due to the distinct nature of secondary metabolites produced by these organisms. Thus, the cause of the contrasting health effects of these two bacterial groups lies in their gene pools.

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Section: Comparative Analysis Of P450s Ferredoxins and Smbgcs Datamentioning

confidence: 99%

Contrasting Health Effects of Bacteroidetes and Firmicutes Lies in Their Genomes: Analysis of P450s, Ferredoxins, and Secondary Metabolite Clusters

Nkosi

Padayachee

Gront

et al. 2022

IJMS

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“…It is rare for a proline residue to directly follow the acid–alcohol pair. ,− For example, none of the 57 human CYPs or the 68 or 47 bacterial CYPs from Frankia inefficax sp. or Mycobacterium marinum, respectively, have a proline at this position. , These differences result in the glutamate residue (E249) in GcoA having a different conformation and being held further from the heme (8.1 Å, PDB code: 5NCB) than the glutamate in the CYP199A4 T252E mutant (4.2 Å, PDB code: 7REH; Figure ). Our hypothesis is that we should be able to improve the peroxygenase activity of CYP199A4 over that of the single T252E mutant by modifying the nearby residues of the I-helix.…”

Section: Introductionmentioning

confidence: 99%

“…There is also an unusual proline and glycine pair of residues immediately after the glutamate residue in the amino acid sequence of GcoA (Figures and S1). It is rare for a proline residue to directly follow the acid–alcohol pair. ,− For example, none of the 57 human CYPs or the 68 or 47 bacterial CYPs from Frankia inefficax sp. or Mycobacterium marinum, respectively, have a proline at this position. , These differences result in the glutamate residue (E249) in GcoA having a different conformation and being held further from the heme (8.1 Å, PDB code: 5NCB) than the glutamate in the CYP199A4 T252E mutant (4.2 Å, PDB code: 7REH; Figure ).…”

Section: Introductionmentioning

confidence: 99%

Engineering Peroxygenase Activity into Cytochrome P450 Monooxygenases through Modification of the Oxygen Binding Region

Podgorski,

Akter,

Churchman

et al. 2024

ACS Catal.

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Cytochrome P450 enzymes (CYPs) are biocatalysts for the generation of fine chemicals including natural products, drug metabolites, and flavor and fragrance compounds. However, both the high cost of the required nicotinamide cofactors and their need for additional electron transfer proteins limit their use. Here, we investigate whether CYPs can be converted into more efficient peroxygenases through protein engineering of the enzyme's oxygen activation machinery. We improve the peroxygenase activity by modifying selected residues within the I-helix to more closely resemble those of a natural peroxygenase. We produced mutants containing two, four, and six mutations, within this region of the Ihelix. In our model CYP system, the double mutant in which glutamine and glutamate residues replaced aspartate and threonine, respectively, was found to have significantly higher peroxygenase activity for the O-demethylation of 4-methoxybenzoic acid than a single glutamate mutant prototype. Importantly, it functioned better at lower H 2 O 2 concentrations and could convert all the added substrate to product. All the mutants maintained the stereoselectivity of the CYP enzyme for the epoxidation of 4-vinylbenzoic acid. The X-ray crystal structures of these enzymes showed significant structural changes at the oxygen-binding groove in the I-helix. In crystallo reactions with 4-methylbenzoic acid exhibit electron density corresponding to the 4-(hydroxymethyl)benzoic acid metabolite. We extended this mutagenesis strategy to a bacterial steroid-hydroxylating CYP and an uncharacterized CYP from a thermophilic bacterium. In these instances, we generate peroxygenases, which catalyze the regio-and stereoselective hydroxylation of progesterone and the hydroxylation of fatty acids at low hydrogen peroxide concentrations.

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“…There have been limited studies on the bacterial CYPs (Parvez et al 2016;Mthetwa et al 2018;Senate et al 2019;Lau et al 2019;Khumalo et al 2020) compared to eukaryotes (Parvez et al 2016). Nevertheless, observations on the role of CYPs in bacterial pathogenesis (Kweon et al 2020), use of CYP141 for diagnosis of Mycobacterium tuberculosis (Darban-Sarokhalil et al 2011) and indispensability of CYP121 for the existence of tuberculosis pathogen (McLean et al 2008) demonstrated its importance in infectious bacteria.…”

Section: Introductionmentioning

confidence: 99%

Understanding the nature and dynamics of Mycobacterium ulcerans cytochrome P450 monooxygenases (CYPs) – a bioinformatics approach

Sur¹

2021

Acta Biol Szeged

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Cytochrome P450 monooxygenases (CYPs or P450s) are catalytically versatile hemoproteins, associated with drug metabolism, substrate utilization and pathogenesis. Mycobacterium ulcerans is a human pathogen causing Buruli ulcer. The study intended to investigate frequency and diversity of CYPs from M. ulcerans strains, understand the pan-CYPome clustering patterns and interconnection of CYPs using bioinformatics tools. M. ulcerans strains demonstrated the presence of 261 CYPs categorized into 35 families and 38 subfamilies. CYP138, CYP140, CYP189 and CYP125 were the ﬂourishing families. Around, 20 CYP families and 20 subfamilies were conserved. Flourishing and conserved CYP families/subfamilies were associated with lipid metabolism, substrate utilization etc. CYP140 had a role in pathogenesis. CYP279 was the least dominant family. CYP135, CYP183, CYP190, CYP271 and CYP276 were diagnostic markers for M. ulcerans subsp. shinshuense strain ATCC 33728 and M. ulcerans strain P7741. The pan-CYPome specified that M. ulcerans is evolving by gaining CYPs. CYP centric clustering revealed diversity and resemblances among M. ulcerans strains. More diverse nature of the M. ulcerans strain Harvey could be attributed to its larger size and geographical location. Co-occurrence network demonstrated mutual associations amongst substantial number of CYP families/subfamilies. This work provided comprehensive understanding of previously unexplored CYPs from M. ulcerans.

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Analysis and preliminary characterisation of the cytochrome P450 monooxygenases from Frankia sp. EuI1c (Frankia inefficax sp.)

Abstract: Analysis and preliminary characterisation of the cytochrome P450 monooxygenases from Frankia sp. EuI1c (Frankia inefficax sp.

Cited by 9 publications

References 67 publications

Contrasting Health Effects of Bacteroidetes and Firmicutes Lies in Their Genomes: Analysis of P450s, Ferredoxins, and Secondary Metabolite Clusters

Contrasting Health Effects of Bacteroidetes and Firmicutes Lies in Their Genomes: Analysis of P450s, Ferredoxins, and Secondary Metabolite Clusters

Engineering Peroxygenase Activity into Cytochrome P450 Monooxygenases through Modification of the Oxygen Binding Region

Understanding the nature and dynamics of Mycobacterium ulcerans cytochrome P450 monooxygenases (CYPs) – a bioinformatics approach

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