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Cloning, sequencing, and expression in Escherichia coli of a cytochrome P450 gene from Cunninghamella elegans

Rong-Fu Wang, Wei-Wen Cao, Ashraf A. Khan, Carl E. Cerniglia
DOI: http://dx.doi.org/10.1111/j.1574-6968.2000.tb09168.x 55-61 First published online: 1 July 2000


A polyclonal antibody against microsomes of a fungus, Cunninghamella elegans, was used to screen a C. elegans cDNA library. A cDNA clone, containing an open reading frame (ORF) encoding a protein of 389 amino acids (aa), was obtained. GenBank comparison (BLAST) showed that the protein was closely related to P450 because a heme-binding region, which is highly conserved in all P450 sequences, was found in the ORF protein. Using an oligo probe designed from this C. elegans heme-binding region to rescreen the cDNA library, we obtained three new clones. Sequence comparison showed that the three clones, with different length cDNA inserts, were from the same mRNA of the C. elegans P450 gene. One clone had the full C. elegans P450 gene, encoding 473 aa with a molecular mass of 54 958.60, whereas the 389 was a part of the 473 aa without the N-terminal. The entire C. elegans P450 gene was successfully subcloned and overexpressed in a plasmid–Escherichia coli system (pQE30). Immunostaining with three antibodies (CYP1A1, CYP2E1, and CYP3A1) against mammalian P450 enzymes and benzidine staining for hemoproteins showed positive results for the recombinant protein expressed in E. coli. A phylogenetic tree was constructed by comparison of other fungal P450s to the C. elegans sequence. The C. elegans P450 clustered close to the cyp51 family and was named cyp509A1 by the International Committee on the Nomenclature for Cytochrome P450 Enzymes.

  • P450
  • Cloning
  • Expression
  • Cunninghamella elegans

1 Introduction

The filamentous fungus, Cunninghamella elegans, is a zygomycete, which has been used as a microbial model of mammalian metabolism and for the biodegradation of priority pollutants [14]. C. elegans ATCC 36112 metabolizes or biotransforms numerous structurally diverse compounds, such as polycyclic aromatic hydrocarbons (PAHs), crude oil components, drugs, and N-,S-,O-heterocyclic aromatic compounds, by phase I and phase II enzymes [5]. The phase I reactions catalyzed by cytochrome P450 in C. elegans include aliphatic and aromatic hydroxylation, N- and O-dealkylation and N- and S-oxidation [511]. The involvement of cytochrome P450 enzymes in the metabolism of PAHs and pharmaceutical compounds by C. elegans is based on carbon monoxide difference spectra (absorption at 450 nm), enzyme activities, cytochrome P450 inhibitors, 18O2 incorporation experiments, and spectra of metabolites that are similar to those formed by mammalian cytochrome P450 enzyme systems [2,8,9].

Little is known about the molecular genetics of C. elegans, except for studies of the enolase and the 6-phosphogluconate dehydrogenase conducted in this laboratory [12,13]. The use of molecular biology techniques to characterize fungal cytochrome P450 enzyme systems has greatly enhanced our understanding of fungal biotransformation of xenobiotics, especially since it is difficult to purify fungal microsomal P450 proteins using conventional biochemical techniques [14]. Since many of the phase I and phase II enzymes are localized in the microsomal fraction of the cell [5], a polyclonal antibody against C. elegans microsomes was used to screen a C. elegans cDNA library in this study. The isolation and characterization of three cDNA clones encoding a C. elegans cytochrome P450 is reported in this article.

2 Materials and methods

2.1 Mycelia, microsomes, cDNA library and rabbit antiserum preparations

C. elegans ATCC 36112 was grown in Sabouraud dextrose broth (Difco Laboratories, Detroit, MI) at room temperature without shaking. After 5 days of incubation, the mycelium was harvested by filtration and washed with deionized water. Freshly prepared C. elegans mycelium was frozen in liquid nitrogen and sent on dry ice to Clontech Laboratories, Inc. (Palo Alto, CA) for custom mRNA preparation and custom cDNA library construction. Microsomes isolated from C. elegans mycelia [5] were sent to Alpha Diagnostic (San Antonio, TX) for custom antiserum preparation from rabbit (the antibody titer was 104).

2.2 Screening the cDNA library, amplification and DNA sequence analysis

Rabbit antiserum raised to C. elegans microsomes was used to screen the unamplified C. elegans cDNA library. The cDNA library (5×103/90-mm plate) was mixed with Escherichia coli Y1090, which had been cultured in LB broth [15]–0.2% maltose–10 mM MgSO4. After 20 min adsorption, 3 ml LB-soft top agarose (0.6%) at 55°C was added and immediately poured onto an LB agar plate. The plate was incubated at 42°C for 3.5 h. A nitrocellulose filter previously saturated in 10 mM IPTG (isopropyl β-D-thiogalactopyranoside) was placed onto the top agarose. The plate was incubated at 37°C for 3.5 h. The nitrocellulose filter was removed, rinsed with a buffer containing 50 mM Tris, pH 8.0, 150 mM NaCl, and 0.05% Tween-20, blocked with 10% nonfat dry milk, and then incubated with 1:500 diluted rabbit anti-C. elegans microsome polyclonal antibody. Alkaline phosphatase-conjugated mouse anti-rabbit IgG (Sigma Chemical Co., St. Louis, MO) was diluted to 1:7000 for use as the secondary antibody. 5-Bromo-4-chloro-3-indolyl-phosphate/nitroblue tetrazolium (Bio-Rad Laboratories, Hercules, CA) was used for color development.

Positive phage plaques were selected and rescreened at a low plaque density (100 plaques/90-mm plate). The purified plaques were picked with toothpicks and placed into tubes containing a PCR reaction mixture. PCR amplification of the insert cDNA was carried out without isolation of the phage DNA. The PCR protocol was the same as described previously [16] except that the annealing temperature was 58°C. PCR primers were designed from the λgt11 vector upstream and downstream of the insert. The forward primer, λgt11-A1, was 5′-GGATTGGTGGCGACGACT; the reverse primer, λgt11-A2, had the sequence 5′-GACATGGCCTGCCCGGTT. The amplified PCR products were purified from agarose gels by a gel extraction kit (Qiagen, Inc., Valencia, CA). Purified PCR products were sequenced directly using primers λgt11-A1 and λgt11-A2. ABI Prism BigDye Terminator Cycle Sequencing Ready Reaction Kit (PE Applied Biosystems, Foster City, CA) was used for sequencing, following the manufacturer's instructions. An automatic ABI Prism 310 sequencer (PE Applied Biosystems) was used for electrophoresis.

For full insert sequence determination, the PCR products from this cDNA clone were subcloned into the pGEM-T Easy vector, following the manufacturer's instructions (Promega Co., Madison, WI). A QIAprep Spin Miniprep kit (Qiagen) was used for isolation of the plasmid. The isolated plasmid from the subclone was used for sequencing. After obtaining insert sequence information from both ends, new sequencing primers were designed from the sequences until all of the insert sequence had been sequenced from both strands. Oligonucleotide primers were purchased from Universal DNA, Inc. (Tigard, OR).

After the highly conserved heme-binding region was found from the sequence, a heme probe for C. elegans was designed with the sequence 5′-TTCTCAAATGGTAACAGACAATGTATTGGT. The heme probe was labeled with a DIG oligo 3′-end labeling kit, following the manufacturer's instructions (Boehringer Mannheim Co., Indianapolis, IN) and used to rescreen the C. elegans cDNA library. A Plaque-lift hybridization procedure was used for the screening, following the DIG system user's guide for filter hybridization. The DIG Easy Hyb from Boehringer was used as the hybridization solution, with prehybridizing for 2 h at 42°C and hybridizing overnight at 42°C.

DNA sequence analysis, translation, and alignment with related genes and proteins were carried out using the computer programs Lasergene (DNASTAR, Inc., Madison, WI) and Align Plus (Scientific Educational Software, State Line, PA). The Lasergene was used for the construction of the tree using the Clustal method. The GenBank program BLAST [17] was used to find similar sequences from GenBank.

2.3 Construction of a plasmid expressing His-tagged C. elegans P450

After the C. elegans P450 gene sequence was determined, the gene (without vector sequence) was amplified by PCR from the cDNA clone. Three primers were designed for the amplification of the C. elegans P450 gene. The forward primers, 450-F1-Bam and 450-F2-Bam, had the sequences cgggatccACAAATGGTTCAACTTGGAAA and cgggatccAATAATTTCATTTTTAAACGACTAAACGT, respectively. Capital letters in the sequence represent the starting sequence of the full C. elegans P450 gene or the 389-amino acid (aa) open reading frame (ORF) without the start codon, ATG. Lower-case letters in the sequence represent the site for BamHI digestion. The reverse primer, 450-R-Hind, had the sequence ccaagcttTTAATATCTTCTCTTGAATCGGATT. Capital letters in the sequence are complementary to the reverse sequence of the 3′ end, including the stop codon of the C. elegans P450 gene. Lower-case letters represent the site for HindIII digestion. The PCR products were purified from agarose gels by a gel extraction kit (Qiagen) and digested with BamHI and HindIII. The PCR products were then ligated with BamHI- and HindIII-digested plasmid pQE30, a His-tagged expression vector for E. coli (Qiagen). E. coli strain SG13009 (Qiagen) was used as a host for the transformation and expression of the P450 gene.

2.4 SDS–PAGE analysis of the recombinant protein induced from the pQE30-CE-P450 clone

Bacterial cells harboring the CE-P450 clone were cultured to OD600=0.7–0.9 in 100 ml LB containing ampicillin (100 μg ml−1) and kanamycin (25 μg ml−1). IPTG (1.5 mM) was added to induce expression of the recombinant protein and the culture was shaken continuously at 37°C for 5 h. After induction, the cells were harvested by centrifugation at 10 000×g for 10 min at 4°C. The pellet was suspended in buffer B (8 M urea, 0.1 M Na-phosphate, 0.01 M Tris, pH 8.0) and freeze-thawed three times to break the cells. These were centrifuged again at 10 000×g. Both the supernatant and the pellet, after treatment with SDS buffer, were analyzed by SDS–PAGE in a Mini-Protean II Dual Slab Cell (Bio-Rad).

2.5 Immunostaining of the recombinant P450 protein expressed from the pQE30-CE E. coli clone

IPTG-induced cells from the pQE30-CE E. coli clone were lysed by sonication. The pellet was resuspended in SDS sample buffer, boiled for 5 min and centrifuged at 14 000×g for 5 min. The supernatant was used for SDS–PAGE and then transferred to a nitrocellulose membrane in a mini trans-blot electrophoretic transfer cell (Bio-Rad). The membrane was stained with 0.1% fast green (Bio-Rad) in 10% acetic acid and 50% methanol, then cut into strips to separate the sample lanes. Monoclonal antibody (mAb) against rat P450 1A1 (PM10, used for the identification of the polycyclic aromatic hydrocarbon induced P450 1A1), mAb against rat P450 3A1 (PM40, prepared against purified rat P450 3A1), and rat liver microsomes for positive control (AM10, prepared from male Fischer F344 rats and used as a control for P450 enzyme activity assays) were purchased from Oxford Biomedical Research, Inc. (Oxford, MI). A goat anti-rat CYP2E1 polyclonal antibody was purchased from Daichi Pure Chemical Co. (Tokyo).

2.6 Benzidine staining of hemoproteins

Benzidine dihydrochloride was used to detect hemoproteins in SDS gels following the method of Moore et al. [18].

2.7 GenBank accession number

The C. elegans P450 gene was deposited in the GenBank database with accession number AF249299.

3 Results and discussion

We have shown earlier that the cytochrome P450 of C. elegans is involved in the metabolism and biotransformation of a number of xenobiotics [611]. In this paper, we present the cloning, sequencing, and expression of a cytochrome P450 gene of C. elegans. Initially, a cDNA library of C. elegans was constructed into the EcoRI site of the λgt11 vector. The cDNA library was then screened with the help of polyclonal antibodies raised against C. elegans microsomes, where cytochrome P450 is localized [5]. Antibody screening yielded one positive clone. Nucleotide sequence analysis of the clone suggested the presence of an ORF encoding a 389-aa protein with MW 44 971.10. The amino acid homology search with the known GenBank database sequences found 506 matches, all belonging to the cytochrome P450 family of genes.

All the cytochrome P450 genes contain a highly conserved heme-binding region, FxxGxxxCxG [19]. This conserved region is regarded as a fingerprint for the identification of cytochrome P450 genes. Based upon this conserved region, Kullman and Matsumura [20] confirmed the presence of a cytochrome P450 gene in the fungus Phanerochaete chrysosporium.

In order to demonstrate the relatedness of the 389-aa clone to cytochrome P450, an oligo probe corresponding to the heme-binding region was designed to rescreen the cDNA library of C. elegans. Two new clones were obtained. Sequence comparison of the two oligo-screened clones and a previous antibody-screened 389-aa clone showed that the three clones were closely related but had different length cDNA inserts. They were also from the same mRNA of the C. elegans P450 gene. The presence of heme-binding regions in the oligo- and antibody-screened clones clearly indicated that the clones were closely related to cytochrome P450 (Fig. 1A). The truncated copies of the cytochrome P450 gene in some of the clones obtained from the cDNA library were probably due to incomplete reverse transcription from the mRNAs. The two oligo-screened clones contained the 389-aa coding sequence along with different length upstream sequences. One of the oligo-screened clones contained the same ORF for the 389 amino acids as the clone screened by the antibody, but had less of the 5′ end sequence. The other oligo-screened clone contained a large ORF encoding a protein of 473 amino acids with MW 54 958.60 and represented the full-length cytochrome P450 gene of C. elegans (Fig. 1B,C).

Figure 1

Comparison of the DNA sequences from the three clones (A), the deduced full C. elegans P450 sequence (B), and the clear picture of the DNA sequencing for the heme-binding region (C). The highly conserved heme-binding protein sequence, FxxGxxxCxG, is underlined in B. Clone 1, screened by antibody. Clones 2 and 3, screened by heme-oligo probe. Clone 3 contains the full C. elegans P450 gene. Dots indicate the same sequence as in the first line (clone 3). Dashes indicate that the sequence is lacking. The start locations for the 473 aa and 389 aa are indicated by underlines. The stop codon, TAA (underlined), is the same for the 473 and 389 aa. The 5′ ends of the three DNA sequences are the adapter sequence used for cDNA library preparation.

The full C. elegans P450 gene was successfully subcloned and overexpressed in a plasmid–E. coli system (pQE30). The overexpressed recombinant protein, upon analysis in SDS gels, migrated at 56 kDa (Fig. 2). Of the 56-kDa protein, 55 kDa was represented by the cloned gene and 1 kDa was represented by the 6×His tag. Three methods were used to demonstrate that the recombinant protein in E. coli was a P450. The amino acid sequence was an identical to the DNA-deduced P450 sequence. Western blot analysis with three antibodies (CYP1A1, CYP2E1, and CYP3A1) showed that the recombinant protein in E. coli was homologous to all the mammalian P450s tested (Fig. 3B). Benzidine staining to detect hemoproteins in SDS gels gave positive results, indicating that the heme group was present (Fig. 3C). Since the recombinant protein was found in the pellet and not in the supernatant fraction, it showed low P450 activity when tested with cyclobenzaprine and phenanthrene (data not shown). Therefore, achievement of significant enzyme activity may require other components of the P450 monooxygenase that are essential to transfer electrons for catalytic reactions which are not optimally expressed using the E. coli system.

Figure 2

SDS–polyacrylamide gel showing the overexpressed recombinant protein (56 kDa) from a subclone, pQE30-CE-P450 (473 aa) in E. coli. Lane M, molecular size marker. Lane 1, supernatant from 8 M urea buffer-treated cells. Lane 2, pellet from 8 M urea buffer-treated cells.

Figure 3

Immunostain and benzidine stain for P450. Lane M, molecular size marker. Lane 1, rat liver microsome preparation containing P450s at 50 kDa (positive control). Lane 2, E. coli proteins containing the overexpressed recombinant protein at 46 kDa from a subclone, pQE30-CE-389 aa, in E. coli. A: Coomassie blue-stained SDS gel for control to show the total proteins. B: Three P450 antibody-stained membranes with proteins transferred from the SDS gel. The three antibodies are CYP2E1, CYP1A1, and CYP3A1, which were described in Section 2. C: Benzidine-stained SDS gel.

A phylogenetic tree was constructed by comparison of the C. elegans P450 with other fungal P450 protein sequences published in the GenBank. The C. elegans P450 clustered close to the cyp51 family, which includes Candida albicans, Ustilago maydis, Penicillium italicum, and Schizosaccharomyces pombe (Fig. 4), and was named cyp509A1 by the International Committee on the Nomenclature for Cytochrome P450 Enzymes. Nelson [21] has suggested that a common ancestor to fungi and animals had only the cyp51 P450 gene, which encodes sterol 14α-demethylase. He also indicated that this enzyme may have been the first eukaryotic P450 [22]. Here we show for the first time that the zygomycete C. elegans P450 clusters with fungi in that cyp51 family and has immunological homology to some mammalian cytochrome P450s [23]. Our previous observations showed that the phase I reactions are catalyzed by cytochrome P450 in C. elegans[5,11]. The successful cloning and expression of the P450 gene described in this paper would further assist in understanding the mechanism of biotransformation and detoxification reactions in C. elegans.

Figure 4

Phylogenetic tree constructed by comparison of the C. elegans P450 (473 aa) with other fungal P450 protein sequences published in the GenBank. The scale indicates the amino acid difference.

In conclusion, a full-length cDNA clone of C. elegans cytochrome P450 was cloned and characterized. It was subcloned and overexpressed in a plasmid–E. coli system (pQE30). The C. elegans cytochrome P450 gene clustered close to cyp51 in a phylogenetic tree and was named cyp509A1. The results provide more evidence of the feasibility of using C. elegans for modeling the mammalian metabolism of pharmaceutically important compounds.


We appreciate Dr. David R. Nelson of the International Committee on the Nomenclature for Cytochrome P450 Enzymes for stimulating discussion and classifying the C. elegans P450 as cyp509A1. We also thank Drs. Saeed A. Khan and John B. Sutherland for critically reading the manuscript and Ms. Pat Fleischer for clerical assistance. A part of this work was supported by US Environmental Protection Agency Cooperative Agreement CR 820773.


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