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Phanerochaete chrysosporium NADPH-cytochrome P450reductase kinetic mechanism
Andrew G.S. Warrilow, David C. Lamb, Diane E. Kelly, and Steven L. Kelly*
Wolfson Laboratory of P450 Biodiversity, Institute of Biological Sciences, The University of Wales Aberystwyth, Aberystwyth SY23 3DA, UK
Received 10 October 2002
Abstract
The recently completed genome of the basidiomycete, Phanerochaete chrysosporium, revealed the presence of one NADPH-cyto-
chromeP450 oxidoreductase (CPR;EC1.6.2.4) gene and>123 cytochromeP450 (CYP) genes.Howa singleCPRcandrivemanyCYPs
is an important area of study. We have investigated this CPR to gain insight into the mechanistic and structural biodiversity of the
cytochrome P450 catalytic system. Native CPR and a NH2-terminally truncated derivative lacking 23 amino acids have been over-
expressed in Escherichia coli and purified to electrophoretic homogeneity. Steady-state kinetics of cytochrome c reductase activity
revealed a random sequential bireactant kinetic mechanism in which both products form dead-end complexes reflecting differences in
CPRkineticmechanisms evenwithin a single kingdomof life. Removal of theN-terminal anchor ofP. chrysosporiumCPRdid not alter
the kinetic properties displayed by the enzyme in vitro, indicating it was a useful modification for structural studies.
� 2002 Elsevier Science (USA). All rights reserved.
Keywords: NADPH-cytochrome P450 oxidoreductase; Cytochrome P450; Phanerochaete chrysosporium; Purification; Kinetics; Reaction mechanism
Eukaryotic cytochromes P450 (CYP) are membrane
proteins usually located in the endoplasmic reticulum [1]
and exhibit extraordinary diversity. Genome sequencing
projects have shown approximately 57 CYPs in humans,
90 in Drosophila melanogaster, 80 in Caenorhabditis
elegans, and 276 in Arabidopsis thaliana, but only 3 in
Saccharomyces cerevisiae [http://drnelson.utmem.edu/CytochromeP450.html]. The primary role of cytochromes
P450 is the monooxygenation of diverse substrates of
endogenous or exogenous origin [2]. NADPH-cyto-
chrome P450 oxidoreductase (CPR; EC 1.6.2.4) is a eu-
karyotic membrane-bound flavoprotein that is essential
for the transfer of electrons during theCYP catalytic cycle
in the endoplasmic reticulum. However, unlike CYP,
CPR is encoded by a single gene with the exception of A.thaliana, where two are present [3]. Amino acid sequence
homologies between CPRs from different organisms are
higher in contrast to CYPs where only three residues are
conserved. Hence, electron transfer from CPR to CYP is
thought to reside in the overall electrostatic and hydro-
phobic forces in the protein–protein interaction [4]. The
mechanism by which recognition and electron transfer
proceed is an important area needing clarification and
some biodiversity in this has already been observed [2,5].
In the present study, we have probed the kinetic
mechanism of CPR electron transfer in an organism with
a high CYP complement (Phanerochaete chrysosporium)and considered our results with the CPR kinetic mecha-
nism within a low CYP complement organism (S. cere-
visiae). The recently completed genome sequence of the
white rot fungusP. chrysosporium (as yet unpublished, see
http://drnelson.utmem.edu/CytochromeP450.html) re-
vealed the presence of one CPR gene, with a large pre-
dicted molecular mass (>80 kDa) and >123 CYP genes.
This is in contrast to the yeastS. cerevisiaewhere only oneCPR and three CYP genes were revealed. The present
data indicate that P. chrysosporium CPR follows a dif-
ferent kinetic mechanism from S. cerevisiae [6].
Materials and methods
Chemicals. All chemicals were obtained from Sigma Chemical
Company (Poole, UK), unless otherwise stated.
Biochemical and Biophysical Research Communications 299 (2002) 189–195
www.academicpress.com
BBRC
* Corresponding author. Fax: +44-1970-622350.
E-mail address: [email protected] (S.L. Kelly).
0006-291X/02/$ - see front matter � 2002 Elsevier Science (USA). All rights reserved.
PII: S0006 -291X(02 )02600 -1
Cloning of native and soluble P. chrysosporium CPRs for expression
in E. coli. A Lambda ZAP II cDNA library for P. chrysosporium
ATCC24725 was constructed from total RNA extracted from 3-day-
old cultures of P. chrysosporium ATCC24725 and reagents from
Stratagene (LaJolla, California). PCR primers against the CPR gene
sequence [7] incorporated a NdeI site in the forward primers and a 4-
His tag and HindIII site in the reverse primer. Forward primers F1 (50-
CAT CGC CAT ATG GCC GTA TCT TCG TCT TCG-30) and F2
(50-CAT CGC CAT ATG CGC GAG CAA ATC TTC T-30) were used
to isolate CPR genes that were full-length (native) and D23 amino acid
residues, respectively. The reverse primer used, R1, was 50-ACT GCT
AAG CTT CTA GTG ATG GTG ATG CGA CCA GAC ATC CAA
CAA-30. PCR used an annealing temperature of 56 �C for both CPR
genes. CPR products were first cloned into pGEMT-Easy vector
plasmid and sequenced. Authentic CPR genes were excised using di-
gestion with NdeI/HindIII and then cloned into pET17b vector.
Heterologous expression in E. coli, purification of native, and soluble
P. chrysosporium CPRs. Expression was undertaken in E. coli
BL21DE3 (pLysS). An overnight culture (5ml) was used to inoculate
500ml of Terrific-Broth (TB) containing ampicillin (100lg/ml).
Following growth for 6 h at 37 �C, 170 rpm, heterologous protein
expression was induced with addition of 0.5mM isopropyl-b-DD-thiogalactopyranoside (IPTG) and incubated for 18 h, 120 rpm, at
29 �C. The cells were harvested by centrifugation at 5000g for 10min.
All following procedures were carried out at 4 �C. The cell pellet was
resuspended in 25ml of 100mM potassium phosphate, pH 7.5 buffer.
Cells were broken by passage through a C5 Emulsiflex high pressure
homogeniser operating at 170,000 kPa (Glen Creston, Stanmore,
Middlesex). The cell lysates were centrifuged 10min at 5000g to re-
move cell debris and then at 180,000g for 90min to separate membrane
fractions (pellet) from cytosolic fractions (supernatant). The mem-
brane fractions were suspended in 50mM potassium phosphate buffer,
pH 7.5, 20% glycerol. CPR activity was monitored by the reduction of
cytochrome c. Background levels of reductase activity were determined
using the cytosolic and membrane extracts from control cultures of
E. coli that contained just the empty pET17b plasmid and these were
then subtracted from the activities obtained with the CPR clones.
Protein concentration was determined by the bicinchoninic acid
method (BCA) using bovine serum albumin standards.
Purification and characterisation of native and soluble CPR. Mem-
brane bound full-length CPR was solubilised with 2% (w/v) sodium
cholate as described previously [8] prior to purification. His4-tagged
native and soluble D23 CPRs were purified by a single-step using
nickel-chelating affinity chromatography as previously described [9].
Fractions containing purified native and soluble CPRs (monitored by
cytochrome c reduction assay) were pooled, dialysed overnight against
20mM potassium phosphate buffer, pH 7.5, 20% glycerol, and stored
at )80 �C until use. SDS–PAGE was performed as essentially described
by Laemmli [10] using an 8% resolving gel. A set of SDS–protein
standards (MW-SDS-200, Sigma) were used for calibration and Coo-
massie blue R250 to visualise protein bands. The absolute absorption
spectra were determined between 300 and 700 nm using native CPR
(75lM) and D23 CPR (80 lM) in 1M Tris–HCl, pH 8.1. NADPH-
reduced absorption spectra of the two CPRs were determined in the
presence of 0.2mM NADPH. These spectral determinations were
made using a Hitachi U-3310 UV/Vis spectrophotometer (San Jose,
California).
Substrate saturation kinetics of native and soluble P. chrysospo-
rium CPRs. Kinetics assays relied on the change in absorbance at
550 nm at 25 �C when oxidised cytochrome c is converted into re-
duced cytochrome c with an extinction coefficient of 21mM�1 cm�1
[11] and contained an enzymatic NADPH regeneration system
consisting of 0.2M Tris–HCl, pH 7.8, 2mM glucose-6-phosphate,
and 3U glucose-6-phosphate dehydrogenase in a total volume of
1ml. Protein contents of 1.55 and 0.128lg were used per assay for
the native and soluble D23 enzyme, respectively. Substrate satura-
tion experiments were performed varying the cytochrome c con-
centration at five different fixed NADPH concentrations (1.5, 3, 6,
12.5, and 50lM) and by varying the NADPH concentration at
seven different fixed cytochrome c concentrations (2.5, 5, 10, 20, 30,
40, and 50 lM). Velocities are expressed as nmoles reduced cyto-
chrome c produced per minute. Kinetic parameters were determined
by non-linear regression using the Michaelis–Menten equation to
determine Km and Vmax values. Linear regression was used to analyse
the Eadie–Scatchard and Lineweaver–Burk plots constructed. A plot
of (Km/Vmax) against the reciprocal of substrate concentration was
constructed to determine Kd values for both NADPH and cyto-
chrome c. Analyses were performed using ProFit 5.01 (Quantum-
Soft, Zurich, Switzerland).
Inhibition studies with NADPþ and reduced cytochrome c. Inhibition
assays were performed without the presence of the NADPH regener-
ation system. Substrate saturation studies varying cytochrome c con-
centration at a constant 50 lM NADPH were performed in the
presence and absence of 75 lM NADPþ using the two P. chrysospo-
rium CPR enzymes. Substrate saturation studies varying NADPH
concentration at a constant 50 lM oxidised cytochrome c were per-
formed in the presence and absence of 45lM reduced cytochrome c
and 75 lM NADPþ. Each kinetic determination was made in triplicate
at a constant 25 �C in 0.2M Tris–HCl, pH 7.8. The relative reactivity
of the two CPR enzymes towards NADH was determined by replacing
the 50 lM NADPH in the non-regenerative assay system with 50lMNADH in the presence of 50lM oxidised cytochrome c.
Immobilisation of the cytochrome cox–D23 CPR complex and its
reduction by NADPH. Conjugation of oxidised cytochrome c to D23CPR was performed as by Nisimoto [12]. The cytochrome cox–CPRconjugation protein was purified by using Sephadex G50SF and re-
duced with 0.1mM NADPH in 0.1M Tris–HCl, pH 8.1. Five micro-
litres containing 1mM oxidised cytochrome c and 40lM D23 CPR was
applied to PVDF membrane equilibrated in 0.1M Tris–HCl, pH 8.1.
On adsorption the membrane was washed with quenching buffer
(0.1M Tris–HCl, pH 8.1, 0.2M NaCl, and 0.05% Tween 20) for 20min
prior to blocking with 5% w/v dried skimmed milk powder in
quenching buffer for 30min. The membrane was washed again in
quenching buffer prior to equilibration in 0.1M Tris–HCl, pH 8.1, for
20min. Solid NADPH was added to a final concentration of 2mM and
the membrane was incubated at room temperature for a further 4 h.
Control reactions in which NADPþ was used instead of NADPH and
oxidised cytochrome c bound to the PVDF membrane instead of the
cytochrome cox–CPR mixture were also performed.
Results and discussion
Since there is only one CPR gene in eukaryotes with
the exception of some plant species [13], CPR must be
able to interact with and reduce the widely divergent
cytochromes P450 that exist in each organism. Kinetic
mechanisms and their diversity between and within or-
ganisms is an important area of investigation, particu-larly where a huge number of CYPs are encountered in
one organism as has been discovered in P. chrysospo-
rium. There have been only limited previous investiga-
tions of this type with rat liver CPR [14], housefly CPR
[15], and yeast CPR [6] and we have initiated this work
as a beginning for biochemical studies on this P. chry-
sosporium system. Here we describe the successful use of
pET-based techniques for the expression of this type ofmembrane protein and the successful generation of full-
length CPR and a soluble version that is currently the
subject of crystallization trials.
190 A.G.S. Warrilow et al. / Biochemical and Biophysical Research Communications 299 (2002) 189–195
Expression, purification, and characterisation of native
and soluble P. chrysosporium CPRs
Both CPRs were successfully expressed in E. coli
without the need for modification of the N-terminus as
is frequently undertaken for CYP expression. The NH2-
terminal truncation site was chosen from a plot of polar
free energies [16] of the amino acid residues (data notshown). The main N-terminal membrane anchor region
appeared to be residues 2–24. Primers were designed so
that full-length (native) and truncated cytosolic D23CPRs would be obtained and results confirmed the
membrane anchor prediction with 96% of the overex-
pressed D23 CPR being localised in the cytosolic frac-
tion in contrast to the full-length CPR that was localised
in the membrane. The D23 soluble CPR protein
expressed at a higher level, of 4.7 lmol/L, compared to
the native CPR protein at just 0.84 lmol/L. Chroma-
tography of the native P. chrysosporium and D23 trun-
cated CPRs on Ni2þ-NTA–Agarose resulted in 20-fold
increases in purity being obtained (Table 1) and were
over 99% pure when analysed by SDS–PAGE. The native
enzyme and D23 CPRs had apparent Mr values of 88.2
and 85.9 kDa, respectively, compared to the theoreticalMr values of 81.6 and 79.3 kDa. The purified native and
D23 CPRs were both yellow in colour after elution from
the Ni2þ-NTA–Agarose column, indicating the presence
of flavin. Further confirmation was obtained through
UV/visible spectral analysis (Fig. 1). Both the native and
D23 CPRs produced spectra that were typical of micro-
somal CPRs [17,18] and were reduced in vitro by 0.2mM
NADPH to form the �air-stable� neutral flavin semi-qui-none, characterised by the broad absorbance peak at
585 nm (Fig. 1). The specific activities of the purified
native and D23 CPRs in reducing cytochrome c were
3.3 and 14.8 lmol/min/mg protein, respectively.
Kinetic mechanism determination for native and soluble
P. chrysosporium CPRs
Both native and D23 P. chrysosporium CPRs obeyedMichaelis–Menten kinetics with respect to both cyto-
chrome c and NADPH (Fig. 2) and gave similar kinetic
parameters (Table 2). The Km values for cytochrome c
were 11 and 12 lM and the Km values for NADPH were
nearly identical at 1.9 and 2.2 lM. The maximum
turnover numbers were determined to be 19 and 42 for
the native and D23 CPR enzymes, respectively. This
compares with Km values for cytochrome c of 1.6 lM foryeast CPR [6], 4.6 lM for housefly CPR [15], and 3.4 lMfor rat CPR [14]. P. chrysosporium CPR has an 8-fold
lower affinity for cytochrome c than yeast CPR [6]. The
Km values for NADPH were 1–2lM for yeast [6], rat
[14], and housefly [15] CPRs. Eadie–Scatchard plots of
the substrate saturation data (Fig. 2) gave a distinctive
pattern of converging lines that met behind the ½S�=v-axis. This result excludes the possibility that the CPRenzyme mechanism was bi bi ping pong, as such a
mechanism would give a convergence of the lines at the
½S�=v-axis at ½S� ¼ 0. This kinetic pattern suggests a bi-
reactant sequential mechanism in which both substrates
must bind to the enzyme to form a ternary complex
before the products can be formed and released. Such a
Table 1
The specific activties and yields of native and soluble CPR enzymes following heterologous expression in Escherichia coli
CPR enzyme Specific activity (lmol/min/mg protein) Increase in purity
(Fold)
Amount
(lmol/L)aCytosol Membranes Nickel column
Native 0.034 0.162 3.265 20.2 0.84
D23 0.746 0.169 14.76 19.8 4.67
a Litre of culture.
Fig. 1. The absorption spectra of purified P. chrysosporium native CPR
(A) and cytosolic D23 (B) CPR. Absorption spectra of the native CPR
((A) 75 lM) and the cytosolic D23 CPR ((B) 80 lM) were determined
both in the absence (solid line) and presence of 0.2mM NADPH
(dashed line).
A.G.S. Warrilow et al. / Biochemical and Biophysical Research Communications 299 (2002) 189–195 191
pattern of intersecting lines behind the ½S�=v-axis indi-
cates that the Km is greater than the Kd and has been
characterised for mechanisms that involve �sticky�susbstrates [19]. The Kd values were 1.5- to 2-fold lower
than the Km values (Table 2). Inhibition studies using45 lM reduced cytochrome c proved unsuccessful in
significantly inhibiting the CPR reaction when NADPH
was the variable substrate. The presence of 45 lM of
reduced cytochrome c in an assay containing 37.5 lMNADPH and 50 lM oxidised cytochrome c caused ob-
served inhibitions of 8% and 11% for the native and D23CPRs, respectively. Substrate saturation experiments
varying oxidised cytochrome c and NADPH concen-trations individually in the presence or absence of 45 lMreduced cytochrome c gave no discernable inhibition
(data not shown). The lack of inhibition of CPR by
Fig. 2. Initial velocity patterns obtained from enzyme mechanism substrate saturation experiments. Substrate saturation experiments using
P. chrysosporium native and soluble D23 CPRs with increasing cytochrome c concentrations were performed at five fixed NADPH concentrations of
50lM (d), 12.5lM (j), 6lM (N), 3lM (�), and 1.5 lM (s). Eadie–Scatchard plots of these data were constructed for native (A) and soluble D23(B) CPRs. Substrate saturation experiments with increasing NADPH concentrations were performed at seven fixed cytochrome c concentrations of
50lM (d), 40lM (j), 30 lM (N), 20lM (s), 10 lM (�), 5lM (M), and 2.5 lM ( ). Eadie–Scatchard plots of these data were constructed for
native (C) and soluble D23 (D) CPRs. The data points at 50mM have been omitted to aid clarity in interpreting the kinetic pattern but these data
points were used in the kinetic fitting process. Velocities (v) are expressed as nmoles reduced cytochrome c produced per minute. All data points are
means of three replicates.
192 A.G.S. Warrilow et al. / Biochemical and Biophysical Research Communications 299 (2002) 189–195
reduced cytochrome c prevents the identification of theorder of substrate binding by traditional kinetic meth-
ods. Therefore both ordered and random sequential
kinetic mechanisms can be considered for P. chrysos-
porium CPR.
If substrate binding to CPR is random, oxidised cy-
tochrome c should be able to bind to both oxidised and
reduced forms of CPR and NADPH should be able to
bind to the free CPR enzyme and to the cytochrome cox–CPR complex. To establish the absolute binding order
of substrates to CPR a conjugated cytochrome cox–CPRprotein was generated. The isolated conjugated protein
was reduced by 0.1mM NADPH, giving an absorbance
Table 2
Kinetic constants derived for the P. chrysosporium CPR enzymes
Kinetic constant Native D23
Vmax (nmol/min) 4:08� 0:12 4:01� 0:16
Km for NADPH (lM) 1:92� 0:03 2:20� 0:13
Km for cytochrome c (lM) 11:31� 0:34 11:54� 0:29
Kd for NADPH (lM) 1.5 1.2
Kd for cytochrome c (lM) 8.3 5.8
Ki for NADPþ (lM) 22:2� 0:9 20:6� 1:2
Turnover number (s�1)
(NADPH)
18.6 41.5
Turnover number (s�1)
(NADH)
0.12 0.89
Fig. 3. Initial velocity patterns obtained by inhibition of P. chrysosporium CPR enzymes with NADPþ. Substrate saturation experiments were
performed using native (A) and soluble D23 (B) CPR enzymes with increasing cytochrome c concentrations in the absence () and the presence (s)
of 75lM NADPþ. Substrate saturation experiments were also performed using native (C) and soluble D23 (D) CPR enzymes with increasing
NADPH concentrations in the absence (d) and the presence (s) of 75 lM NADPþ.
A.G.S. Warrilow et al. / Biochemical and Biophysical Research Communications 299 (2002) 189–195 193
peak at 550m. The cytochrome cox–D23 CPR compleximmobilised on PVDF membrane was also reduced by
NADPH, resulting in a colour change from red to pink
after 2 h and eventually to a pinkish yellow after 4 h. The
two controls remained in dark red colour after 4 h of
incubation. Therefore, NADPH can bind to and reduce
the cytochrome cox–D23 CPR complex as well as binding
to the free D23 CPR enzyme (Fig. 1). The D23 CPR
enzyme behaved in an identical fashion to the full-lengthCPR. The rapid reduction of free CPR with NADPH
(Fig. 1) indicates that NADPH can bind to the free CPR
enzyme. Preincubation of CPR with NADPH prior to
the addition of oxidised cytochrome c resulted in no
reduction in the observed CPR activity. This indicated
that oxidised cytochrome c can bind to the reduced CPR
enzyme (CPR–NADPH complex). A similar preincu-
bation of the CPR enzyme with oxidised cytochrome cprior to the addition of NADPH also resulted in no
reduction of the observed CPR activity. Therefore the
binding of both substrates of P. chrysosporium CPR is
random. There was no difference in the kinetic mecha-
nism between the native and D23 soluble CPRs, indi-
cating that the N-terminal membrane anchor did not
modulate the kinetic activity of P. chrysosporium CPR
towards cytochrome c or NADPH in vitro. ThereforeD23 CPR can be used as a valid model for future
structural studies of P. chrysosporium CPR.
If such a random bireactant sequential mechanism
involved no dead-end complexes then each product
would behave as a competitive inhibitor of each sub-
strate [19]. This was not the case with P. chrysosporium
CPR as the product NADPþ was a competitive in-
hibitor of NADPH, but was a mixed-type inhibitor ofoxidised cytochrome c (Fig. 3). Such an inhibition
pattern can be obtained if the CPR enzyme can form
dead-end complexes with one or both of its products.
Such dead-end complexes would be (CPR–Cyt.cox–NADPþ) and (CPR–NADPH–Cyt.cred) [19]. This in-
hibition pattern is not encountered with bireactant ping
pong mechanisms. Native and D23 CPR enzymes had
similar affinities for NADPþ with KiNADP values of 22and 21 lM and had a 5-fold lower affinity for NADPþ
than for the substrate NADPH. Both CPR enzymes
were insensitive to inhibition by reduced cytochrome c,
suggesting an extremely low affinity (high Km values)
for the reduced form. Therefore the rate of formation
of the (CPR–NADPH–Cyt.cred) dead-end complex
would be significantly lower than the rate of formation
of (CPR–Cyt.cox–NADPþ).Both P. chrysosporium CPR enzymes could utilise
NADH to reduce cytochrome c, however, at much re-
duced rates of 0.6% and 2.1% of those observed when
NADPH was the substrate for the native and D23 CPRs,
respectively. The observed rates with NADH were too
low to perform the same kinetic experiments that had
been previously performed with NADPH.
Rat liver CPR [14] was found to obey a two-site ping-pong kinetic mechanism, with site one responsible for
the NADPH/NADPþ half-cycle and site 2 responsible
for the Cyt.cox/Cyt.cred half-cycle. At high ionic strength
(0.85M) the cytochrome c half-cycle is a tetra uni ping-
pong mechanism and at lower ionic strength (0.20–
0.75M) it becomes a random sequential mechanism in
which NADPþ release occurs before the binding of cy-
tochrome c. Therefore rat liver CPR appears to be ahybrid between a traditional ping-pong mechanism and
a random sequential mechanism. Yeast CPR [6] was
found to display the kinetic characteristics of a standard
random bi bi ping-pong mechanism with a Lineweaver–
Burk plot of the substrate saturation experiments at
different fixed concentrations of the second substrate
resulting in a series of parallel lines. Housefly CPR [15]
was found to obey a bireactant random sequential ki-netic mechanism with both substrates having to bind to
the CPR enzyme to form a ternary complex prior to
product formation and release. Therefore the P. chry-
sosporium CPR kinetic mechanism is closer to that de-
scribed for housefly [15], and unlike yeast [6] or rat CPR
[14]. As the CPR kinetic mechanism varies between
different species this suggests that divergent evolution
has taken place, even within the fungi. The present workon the purification and characterisation of P. chrysos-
porium CPR has paved the way for the investigation of
activity of the remarkable CYP complement (CYPome)
of this organism.
Acknowledgment
We are grateful to the Biotechnology and Biological Science Re-
search Council of the United Kingdom for support.
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