A biaryl-linked tripeptide from Planomonospora leads to widespread class of minimal RiPP gene clusters

AbstractMicrobial natural products impress by their bioactivity, structural diversity and ingenious biosynthesis. While screening the rare actinobacterial genus Planomonospora, cyclopeptides 1A and 1B were discovered, featuring an unusual Tyr-His biaryl-bridging across a tripeptide scaffold, with the sequences N-acetyl-Tyr-Tyr-His (1A) and N-acetyl-Tyr-Phe-His (1B). Genome analysis of the 1A producing strain pointed to-wards a ribosomal synthesis of 1A, from a pentapeptide precursor encoded by the tiny 18-nucleotide gene bycA, to our knowledge the smallest gene ever reported. Further, biaryl instalment is performed by the closely linked gene bycB, encoding a cytochrome P450 monooxygenase. Biosynthesis of 1A was confirmed by heterologous production in Streptomyces, yielding the mature product. Bioinformatic analysis of related cytochrome P450 monooxygenases indicated that they constitute a widespread family of pathways, associated to 5-aa coding sequences in approximately 200 (actino)bacterial genomes, all with potential for a biaryl linkage between amino acids 1 and 3. We propose the name biarylicins for this newly discovered family of RiPPs.

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Biocatalytic Conversion of Avermectin to 4"-Oxo-Avermectin: Characterization of Biocatalytically Active Bacterial Strains and of Cytochrome P450 Monooxygenase Enzymes and Their Genes

Applied and Environmental Microbiology ◽

10.1128/aem.71.11.6968-6976.2005 ◽

2005 ◽

Vol 71 (11) ◽

pp. 6968-6976 ◽

Cited By ~ 22

Author(s):

Volker Jungmann ◽

István Molnár ◽

Philip E. Hammer ◽

D. Steven Hill ◽

Ross Zirkle ◽

...

Keyword(s):

Escherichia Coli ◽

Cytochrome P450 ◽

Recombinant Proteins ◽

Oxidation Reaction ◽

Cytochrome P450 Monooxygenases ◽

Enzyme Kinetic ◽

Bacterial Strains ◽

P450 Monooxygenase ◽

P450 Monooxygenases

ABSTRACT 4"-Oxo-avermectin is a key intermediate in the manufacture of the agriculturally important insecticide emamectin benzoate from the natural product avermectin. Seventeen biocatalytically active Streptomyces strains with the ability to oxidize avermectin to 4"-oxo-avermectin in a regioselective manner have been discovered in a screen of 3,334 microorganisms. The enzymes responsible for this oxidation reaction in these biocatalytically active strains were found to be cytochrome P450 monooxygenases (CYPs) and were termed Ema1 to Ema17. The genes for Ema1 to Ema17 have been cloned, sequenced, and compared to reveal a new subfamily of CYPs. Ema1 to Ema16 have been overexpressed in Escherichia coli and purified as His-tagged recombinant proteins, and their basic enzyme kinetic parameters have been determined.

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Cytochrome P450 Monooxygenases and Interactions of Psychotropic Drugs: A Five-Year Update

The International Journal of Psychiatry in Medicine ◽

10.2190/29np-2xpn-x0me-mqwu ◽

1995 ◽

Vol 25 (3) ◽

pp. 277-290 ◽

Cited By ~ 16

Author(s):

Winston W. Shen

Keyword(s):

Cytochrome P450 ◽

Psychotropic Drugs ◽

Selective Serotonin Reuptake Inhibitors ◽

Gene Clusters ◽

Serum Levels ◽

Cytochrome P450s ◽

Cytochrome P450 Monooxygenases ◽

P450 Monooxygenases ◽

Human Cytochrome ◽

Enzymatic Induction

Objective: This article is a five-year update on a previous review article ( International Journal of Psychiatry in Medicine, 21:47–56, 1991) on cytochrome P450 monooxygenases and interactions of psychotropic drugs. Method: In the literature review, the recent committee work on nomenclature of the P450 superfamily are highlighted. Then, the author reviewed gene clusters of three human cytochrome P450s— CYP1A2, CYP2D6, and CYP3A4 with the focus on the changes of serum levels of the coadministered psychotropic drugs in the context of enzymatic induction and inhibition of these three hepatic enzymes. Results: As indicated in one table, the author stratified probes, inducers, inhibitors, chemical reactions, and substrates under these three gene clusters. As shown in another simple table, the author compared the hepatic enzymatic inhibitions of four selective serotonin reuptake inhibitors and pointed out the inhibition potentials of fluvoxamine at CYP1A2, fluoxetine and paroxetine at CYP2D6, and fluoxetine and fluvoxamine at CYP3A4 if these two SSRIs have higher serum concentrations. Conclusion: The author suggests that with these systematic approaches, this rapidly adding knowledge can help psychiatrists better understand psychotropic drug interactions and maximize the benefits of patients' psychopharmacotherapy.

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Comprehensive Analyses of Cytochrome P450 Monooxygenases and Secondary Metabolite Biosynthetic Gene Clusters in Cyanobacteria

International Journal of Molecular Sciences ◽

10.3390/ijms21020656 ◽

2020 ◽

Vol 21 (2) ◽

pp. 656 ◽

Cited By ~ 4

Author(s):

Makhosazana Jabulile Khumalo ◽

Nomfundo Nzuza ◽

Tiara Padayachee ◽

Wanping Chen ◽

Jae-Hyuk Yu ◽

...

Keyword(s):

Cytochrome P450 ◽

Secondary Metabolites ◽

Secondary Metabolite ◽

Gene Clusters ◽

Cytochrome P450 Monooxygenases ◽

Biosynthetic Gene ◽

Mycobacterial Species ◽

Biosynthetic Gene Clusters ◽

P450 Monooxygenases ◽

Cyanobacterial Species

The prokaryotic phylum Cyanobacteria are some of the oldest known photosynthetic organisms responsible for the oxygenation of the earth. Cyanobacterial species have been recognised as a prosperous source of bioactive secondary metabolites with antibacterial, antiviral, antifungal and/or anticancer activities. Cytochrome P450 monooxygenases (CYPs/P450s) contribute to the production and diversity of various secondary metabolites. To better understand the metabolic potential of cyanobacterial species, we have carried out comprehensive analyses of P450s, predicted secondary metabolite biosynthetic gene clusters (BGCs), and P450s located in secondary metabolite BGCs. Analysis of the genomes of 114 cyanobacterial species identified 341 P450s in 88 species, belonging to 36 families and 79 subfamilies. In total, 770 secondary metabolite BGCs were found in 103 cyanobacterial species. Only 8% of P450s were found to be part of BGCs. Comparative analyses with other bacteria Bacillus, Streptomyces and mycobacterial species have revealed a lower number of P450s and BGCs and a percentage of P450s forming part of BGCs in cyanobacterial species. A mathematical formula presented in this study revealed that cyanobacterial species have the highest gene-cluster diversity percentage compared to Bacillus and mycobacterial species, indicating that these diverse gene clusters are destined to produce different types of secondary metabolites. The study provides fundamental knowledge of P450s and those associated with secondary metabolism in cyanobacterial species, which may illuminate their value for the pharmaceutical and cosmetics industries.

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Ancient Bacterial Class Alphaproteobacteria Cytochrome P450 Monooxygenases Can Be Found in Other Bacterial Species

International Journal of Molecular Sciences ◽

10.3390/ijms22115542 ◽

2021 ◽

Vol 22 (11) ◽

pp. 5542

Author(s):

Nomfundo Nzuza ◽

Tiara Padayachee ◽

Puleng Rosinah Syed ◽

Justyna Dorota Kryś ◽

Wanping Chen ◽

...

Keyword(s):

Cytochrome P450 ◽

Bacterial Species ◽

Gene Clusters ◽

Side Chain ◽

Cytochrome P450 Monooxygenases ◽

Biosynthetic Gene Clusters ◽

Genome Data ◽

P450 Monooxygenases ◽

Large Numbers ◽

Cyanobacterial Species

Cytochrome P450 monooxygenases (CYPs/P450s), heme-thiolate proteins, are well-known players in the generation of chemicals valuable to humans and as a drug target against pathogens. Understanding the evolution of P450s in a bacterial population is gaining momentum. In this study, we report comprehensive analysis of P450s in the ancient group of the bacterial class Alphaproteobacteria. Genome data mining and annotation of P450s in 599 alphaproteobacterial species belonging to 164 genera revealed the presence of P450s in only 241 species belonging to 82 genera that are grouped into 143 P450 families and 214 P450 subfamilies, including 77 new P450 families. Alphaproteobacterial species have the highest average number of P450s compared to Firmicutes species and cyanobacterial species. The lowest percentage of alphaproteobacterial species P450s (2.4%) was found to be part of secondary metabolite biosynthetic gene clusters (BGCs), compared other bacterial species, indicating that during evolution large numbers of P450s became part of BGCs in other bacterial species. Our study identified that some of the P450 families found in alphaproteobacterial species were passed to other bacterial species. This is the first study to report on the identification of CYP125 P450, cholesterol and cholest-4-en-3-one hydroxylase in alphaproteobacterial species (Phenylobacterium zucineum) and to predict cholesterol side-chain oxidation capability (based on homolog proteins) by P. zucineum.

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Distribution and Diversity of Cytochrome P450 Monooxygenases in the Fungal Class Tremellomycetes

International Journal of Molecular Sciences ◽

10.3390/ijms20122889 ◽

2019 ◽

Vol 20 (12) ◽

pp. 2889 ◽

Cited By ~ 4

Author(s):

Olufunmilayo Olukemi Akapo ◽

Tiara Padayachee ◽

Wanping Chen ◽

Abidemi Paul Kappo ◽

Jae-Hyuk Yu ◽

...

Keyword(s):

Cytochrome P450 ◽

Cytochrome P450 Monooxygenases ◽

The Novel ◽

Human Pathogens ◽

Fungal Cell ◽

P450 Monooxygenase ◽

Over Expression ◽

P450 Monooxygenases ◽

Genome Wide ◽

Novel Drug

Tremellomycetes, a fungal class in the subphylum Agaricomycotina, contain well-known opportunistic and emerging human pathogens. The azole drug fluconazole, used in the treatment of diseases caused by some species of Tremellomycetes, inhibits cytochrome P450 monooxygenase CYP51, an enzyme that converts lanosterol into an essential component of the fungal cell membrane ergosterol. Studies indicate that mutations and over-expression of CYP51 in species of Tremellomycetes are one of the reasons for fluconazole resistance. Moreover, the novel drug, VT-1129, that is in the pipeline is reported to exert its effect by binding and inhibiting CYP51. Despite the importance of CYPs, the CYP repertoire in species of Tremellomycetes has not been reported to date. This study intends to address this research gap. Comprehensive genome-wide CYP analysis revealed the presence of 203 CYPs (excluding 16 pseudo-CYPs) in 23 species of Tremellomycetes that can be grouped into 38 CYP families and 72 CYP subfamilies. Twenty-three CYP families are new and three CYP families (CYP5139, CYP51 and CYP61) were conserved across 23 species of Tremellomycetes. Pathogenic cryptococcal species have 50% fewer CYP genes than non-pathogenic species. The results of this study will serve as reference for future annotation and characterization of CYPs in species of Tremellomycetes.

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Structural diversity of human xenobiotic-metabolizing cytochrome P450 monooxygenases

Biochemical and Biophysical Research Communications ◽

10.1016/j.bbrc.2005.08.190 ◽

2005 ◽

Vol 338 (1) ◽

pp. 331-336 ◽

Cited By ~ 89

Author(s):

Eric F. Johnson ◽

C. David Stout

Keyword(s):

Cytochrome P450 ◽

Structural Diversity ◽

Cytochrome P450 Monooxygenases ◽

P450 Monooxygenases

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Cytochrome P450 Enzymes as Key Drivers of Alkaloid Chemical Diversification in Plants

Frontiers in Plant Science ◽

10.3389/fpls.2021.682181 ◽

2021 ◽

Vol 12 ◽

Author(s):

Trinh-Don Nguyen ◽

Thu-Thuy T. Dang

Keyword(s):

Cytochrome P450 ◽

Structural Diversity ◽

Plant Evolution ◽

Cytochrome P450 Monooxygenases ◽

Cytochrome P450 Enzymes ◽

P450 Monooxygenases ◽

Anti Cancer ◽

Psychedelic Drugs ◽

Cancer Agent ◽

Alkaloid Metabolism

Plants produce more than 20,000 nitrogen-containing heterocyclic metabolites called alkaloids. These chemicals serve numerous eco-physiological functions in the plants as well as medicines and psychedelic drugs for human for thousands of years, with the anti-cancer agent vinblastine and the painkiller morphine as the best-known examples. Cytochrome P450 monooxygenases (P450s) play a key role in generating the structural variety that underlies this functional diversity of alkaloids. Most alkaloid molecules are heavily oxygenated thanks to P450 enzymes’ activities. Moreover, the formation and re-arrangement of alkaloid scaffolds such as ring formation, expansion, and breakage that contribute to their structural diversity and bioactivity are mainly catalyzed by P450s. The fast-expanding genomics and transcriptomics databases of plants have accelerated the investigation of alkaloid metabolism and many players behind the complexity and uniqueness of alkaloid biosynthetic pathways. Here we discuss recent discoveries of P450s involved in the chemical diversification of alkaloids and how these inform our approaches in understanding plant evolution and producing plant-derived drugs.

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In Silico Structural Modeling and Analysis of Interactions of Tremellomycetes Cytochrome P450 Monooxygenases CYP51s with Substrates and Azoles

International Journal of Molecular Sciences ◽

10.3390/ijms22157811 ◽

2021 ◽

Vol 22 (15) ◽

pp. 7811

Author(s):

Olufunmilayo Olukemi Akapo ◽

Joanna M. Macnar ◽

Justyna D. Kryś ◽

Puleng Rosinah Syed ◽

Khajamohiddin Syed ◽

...

Keyword(s):

Cytochrome P450 ◽

Structural Analysis ◽

In Silico ◽

Web Application ◽

Cytochrome P450 Monooxygenases ◽

Agglomerative Clustering ◽

Ligand Complex ◽

P450 Monooxygenase ◽

Study Results

Cytochrome P450 monooxygenase CYP51 (sterol 14α-demethylase) is a well-known target of the azole drug fluconazole for treating cryptococcosis, a life-threatening fungal infection in immune-compromised patients in poor countries. Studies indicate that mutations in CYP51 confer fluconazole resistance on cryptococcal species. Despite the importance of CYP51 in these species, few studies on the structural analysis of CYP51 and its interactions with different azole drugs have been reported. We therefore performed in silico structural analysis of 11 CYP51s from cryptococcal species and other Tremellomycetes. Interactions of 11 CYP51s with nine ligands (three substrates and six azoles) performed by Rosetta docking using 10,000 combinations for each of the CYP51-ligand complex (11 CYP51s × 9 ligands = 99 complexes) and hierarchical agglomerative clustering were used for selecting the complexes. A web application for visualization of CYP51s’ interactions with ligands was developed (http://bioshell.pl/azoledocking/). The study results indicated that Tremellomycetes CYP51s have a high preference for itraconazole, corroborating the in vitro effectiveness of itraconazole compared to fluconazole. Amino acids interacting with different ligands were found to be conserved across CYP51s, indicating that the procedure employed in this study is accurate and can be automated for studying P450-ligand interactions to cater for the growing number of P450s.

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