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(Received for publication, October 11, 1995) From the
Human adenovirus contains a virion-associated proteinase
activity essential for the development of infectious virus. Maximal
proteinase activity in vitro had been shown to require three
viral components: the L3 23-kDa protein, an 11-amino acid cofactor
(pVIc), and the viral DNA. Here, we present a quantitative purification
procedure for a recombinant L3 23-kDa protein (recombinant
endoproteinase (rEP)) expressed in Escherichia coli and the
procedure that led to the purification and identification of pVIc as a
cofactor. The cofactors stimulate proteinase activity not by decreasing K
For many animal and plant viruses, a virus-coded proteinase
activity is vital for the synthesis of infectious virus (for review,
see (1) ). These virus-coded proteinases are appealing targets
for antiviral therapy. Human adenoviruses encode a proteinase activity
that is required for the maturation of infectious virions. Of the 12
major polypeptides from which adenovirus virions are assembled, six are
proteolytically processed. Weber (2) isolated a
temperature-sensitive mutant, H2ts-1 (ts-1), ( Recently, we developed a
specific, sensitive, and quantitative assay for the adenovirus
proteinase and used it to characterize the activity in disrupted
wild-type virus. ( We had previously shown
that when wild-type Ad2 virus was incubated with
(Leu-Arg-Gly-Gly-NH) Here, we present our purification
procedure for a recombinant L3 23-kDa protein expressed in E.
coli. Although others have published purification procedures for a
recombinant form of the L3 23-kDa protein from E. coli(9, 10) and insect cells(8) , none of the
purification procedures utilized a quantitative assay, so there is, for
example, no report of increases in specific activity or even yields. We
also present our procedure for the purification and identification of
pVIc as a cofactor for proteinase activity. We then show that the
cofactors stimulate proteinase activity not by decreasing K
Protein concentration was determined by the bicinchoninic acid
protein assay (Pierce) and/or for rEP with a calculated molar
absorbance coefficient at 280 nm of 26,510(11) . The
concentration of pVIc was determined by titration of its cysteine
residue with Ellman's reagent and confirmed by quantitative amino
acid analysis. The cysteine titration was done by adding 10 µl of
pVIc stock solution to 0.99 ml of Ellman's buffer (0.1 M
NaH
Figure 1:
Purification of
adenovirus rEP. Samples of lysates from bacteria induced with IPTG to
express rEP (lane a), the 10,000
The lysate
was clarified by centrifugation at 10,000 The
DEAE FT pool was fractionated on a 1.6 The SSEPH
pool was applied to a 1.6
The flow-through fraction from the second Centricon-30
centrifugation was evaporated to dryness, dissolved in 0.1%
trifluoroacetic acid, and applied to a C
Figure 2:
Processing of Ad2 ts-1 precursor proteins
by rEP. Twice banded Ad2 ts-1 virions were disrupted by two cycles of
freeze/thaw followed by heat treatment. Reactions of 0.18 ml contained
10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 10 mM octyl glucoside, 3
Figure 3:
Initial purification of the second
cofactor activity. Virus was disrupted by treatment with 10% pyridine.
The pellet and supernatant (Sup) were obtained after
centrifuging disrupted virus. The pellet was solubilized, placed in a
Centricon-30, and centrifuged to yield retentate-1 and flow-through-1.
Ammonium acetate to 1 M was added to retentate-1, and the
solution was recentrifuged to yield retentate-2 and flow-through-2.
Assays were performed in the presence of 3 nM rEP and in the
absence or presence of 778 ng/ml Ad2 DNA.
The final step in the purification of the second cofactor was
reverse-phase chromatography. The flow-through fraction from the second
Centricon-30 centrifugation was applied to a C
Figure 4:
Final step in the purification of the
second cofactor activity. The flow-through fraction from the second
Centricon-30 centrifugation was applied to a C
Figure 5:
Amino
acid sequence of the second cofactor and comparison with the amino acid
sequence of the precursor to adenovirus protein VI. The amino acid
sequences of the proteins in peaks a-c in Fig. 4(inset) were determined in a gas-phase sequencer.
The question mark at position 6 indicates a variable yield of
lysine, as described under ``Results.'' The amino acid at
position 10 was presumed to be a cysteine. The two adenovirus
proteinase consensus cleavage sequences in pVI are underlined,
and the location of the second cofactor sequence beginning at position
240 is in boldface. The amino acid sequence of pVI was from
Roberts et al.(14) .
The proteins in peaks a-c of Fig. 4were
also subjected to time-of-flight mass spectrometry. In peak a, there
was one major species with an M
Figure 6:
Reconstitution of proteinase activity in vitro with purified components and titration with the
second cofactor (A) and with Ad2 DNA (B). A,
assays in 400 µl contained 1.42 µg/ml Ad2 DNA, either 2 nM (open circles) or 4 nM (closed circles)
rEP, and the indicated volumes of cofactor activity purified as
described in the legend to Fig. 3. B, assays in 400
µl contained 2 nM rEP, 10 µl of cofactor activity
purified as described in the legend to Fig. 3, and the indicated
concentrations of Ad2 DNA. Rates are expressed as the difference in
rates between assays in the presence and absence of the cofactor (A) and Ad2 DNA (B).
Figure 7:
Optimization of assay conditions in the
absence (closed circles) and presence (open circles)
of Ad2 DNA: temperature (A), ionic strength (B),
octyl glucoside (C), and dithiothreitol (D). In A, complexes between rEP and pVIc were formed by incubating 70
nM rEP and 208 nM pVIc in 0.9 ml of 0.1 mM TAPS (pH 8.5), 10 mM octyl glucoside, 1 mM EDTA,
and 0.5 mM DTT for 5 min at 37 °C. The rEP
Based upon these and other observations, standard assay
conditions were adopted that included 37 °C, 10 mM buffer
at pH 8.5 for the absence of DNA and at pH 8.0 for the presence of DNA,
and 10 mM octyl glucoside. Occasionally, a preparation of rEP
was stimulated by DTT and/or EDTA, in which case, assays also included
0.5 mM DTT and/or 1 mM EDTA. EDTA at higher
concentrations was inhibitory; with rEP
Figure 8:
Maximal velocity as a function of pH for
rEP
The rEP protein was purified to apparent homogeneity using
three chromatographic steps with an overall yield of 66%. About 125 mg
of rEP were induced by IPTG in a 4-liter culture of cells grown to an
absorbance at 600 nm between 0.5 and 0.6 before induction by IPTG. rEP
does not bind to DEAE probably because of its high isoelectric point,
which was calculated to be 8.68. Also, the DEAE step was used to remove
nucleic acids because they bind to the column at NaCl concentrations
<0.3 M(15) . The S-Sepharose anion-exchange column
gave the largest increase in specific activity, from 67.7 to 485
units/mg. A chelating Sepharose column charged with zinc was used
because rEP contains eight free cysteines ( We were able to observe the
processing of most of the virion precursor proteins by adding purified
rEP to disrupted ts-1 virus. This established that rEP can find its
cofactors and become activated and that activated rEP can cleave in
vivo substrates. Furthermore, this indicated that rEP need not be
post-translationally modified, e.g. glycosylated, to become
activated and cleave in vivo substrates, unless such modifying
enzymes and their substrates are in the virion. These data also allow
one to conclude that the gene coding for the L3 23-kDa protein is
indeed the gene whose inactivation gives rise to the ts-1 phenotype.
The viral DNA was implicated as a cofactor because pretreatment of
disrupted ts-1 virus with DNase prevented processing after the addition
of rEP. The purification of the second cofactor, pVIc, was very
difficult, and, with hindsight, we now know why. We lost activity upon
column chromatography because it was so basic, it stuck to glass. We
lost activity upon dialysis because it was so small, it passed through
the pores in the tubing. Consistent with the second cofactor being a
small protein are the observations that boiling for 5 min did not
irreversibly denature it; at high ionic strength, it passed through a
Centricon-3 (3000-Da cutoff); and when incubated in 5 M urea,
it rapidly regained activity upon dilution of the urea (data not
shown). The amino acid sequence of the second cofactor is consistent
with the biochemical data. The second cofactor was sensitive to plasmin
because it contains one lysine and three arginines. The purification
data in Fig. 3implied that pVIc was bound to the viral DNA. At
each step before the second Centricon-30 centrifugation, cofactor
activity was not greatly stimulated by the addition of Ad2 DNA, but
after, enzyme activity was greatly stimulated by the addition of Ad2
DNA. The second cofactor was not in the flow-through fraction after the
first Centricon-30 centrifugation because it is a very basic protein
that was probably bound to the viral DNA. High ionic strength would
dissociate it from the viral DNA, and thus after the second
Centricon-30 centrifugation, it was in the flow-through fraction.
Cofactor activity in the flow-through fraction was greatly stimulated
by the addition of Ad2 DNA. The flow-through fraction from the
Centricon-30 centrifugation gave numerous peaks on a reverse-phase
C We were able to reconstitute maximal proteinase activity with
purified components: rEP, pVIc purified from wild-type virus, and Ad2
DNA. The cofactors stimulated proteinase activity by increasing k Other proteinases require cofactors for
activity, but none, so far, exhibits the requirements of the Ad2
proteinase. Several neutral proteinases need Ca The experiments on optimizing the assay
conditions for the proteinase activity of rEP Although we settled upon standard assay conditions, occasionally
they must be altered. We have found (data not shown) that with aged
disrupted virus, when compared with newly isolated, disrupted virus,
the degree of stimulation by low concentrations of DTT varied from zero
with newly isolated, disrupted virus to 4-5-fold with aged
disrupted virus. Purified rEP exhibits a similar pattern in that as it
ages during storage, 0.5 mM DTT will stimulate more and more
activity. This result can be interpreted as signifying the importance
of the oxidation states of certain cysteine residues. Similarly, the
presence of EDTA at concentrations <2 mM sometimes
stimulated proteinase activity (data not shown). Perhaps some zinc,
which is a potent inhibitor of enzyme activity, remained with the rEP
after chromatography on a chelating Sepharose column charged with zinc. The nature of the active site of the Ad2 proteinase is unclear. The
inhibitor profile of wild-type virus does not correspond to profiles
exhibited by classical serine or cysteine
proteinases(17, 18, 29, 30) . The requirement for DNA as a cofactor
for a proteinase activity is unprecedented. It is clearly required in
the Ad2 virion because proteinase activity is lost upon treatment with
DNase and restored upon addition of Ad2 DNA. In addition, the precursor
proteins in disrupted ts-1 virus are processed upon incubation with
rEP. However, no processing occurs if disrupted virions are pretreated
with DNase. Reconstitution of proteinase activity in vitro with purified components indicates that Ad2 DNA affects k The experiments on V The experiments on V
Volume 271,
Number 1,
Issue of January 5, 1996 pp. 536-543
©1996 by The American Society for Biochemistry and Molecular Biology, Inc.
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
FOOTNOTES
ACKNOWLEDGEMENTS
REFERENCES
, which changes by no more than 2-fold,
but by increasing k
. rEP alone had a small
amount of activity, the k
of which increased
355-fold with pVIc and 6072-fold with adenovirus serotype 2 (Ad2) DNA
as well. Curves of V
of rEPpVIc complexes
with the substrate (Leu-Arg-Gly-Gly-NH)
-rhodamine as a
function of pH in the absence and presence of Ad2 DNA indicate that the
pK values of amino acids that affect
catalysis are quite different from those that affect catalysis by the
cysteine proteinase papain. The pK
values
in the absence of Ad2 DNA are 5.2, 6.4, 6.9, 7.5, and 9.4, and those in
its presence are 5.2, 6.5, 7.4, and 8.8.
)of human
adenovirus serotype 2 (Ad2) that lacks proteinase activity at the
nonpermissive temperature. Virions of ts-1 assemble at the
nonpermissive temperature, but contain precursors in place of the
mature components present in wild-type virus. Such immature virions
attach to cells, but fail to initiate a productive
infection(3, 4) . The mutation in ts-1 was identified
as a single base pair change in a 204-codon open reading frame (L3
23-kDa protein) at the 3`-end of the L3 family of late
messages(5) . The nucleotides in the L3 23-kDa open reading
frame were cloned into plasmids that permitted efficient expression in Escherichia coli(6) .
)The assay is based upon the observation
that the adenovirus proteinase will cleave small peptides with
sequences that correspond to the sequences on the amino-terminal side
of the cleavage sites in virion precursor proteins. For example, the
substrate (Leu-Arg-Gly-Gly-NH)
-rhodamine is cleaved to
Leu-Arg-Gly-Gly-NH-rhodamine by the adenovirus proteinase; this is
accompanied by a 3500-fold increase in fluorescence that is
proportional to the amount of proteinase.
-rhodamine, significant hydrolysis of
the substrate was observed, and that when ts-1 virus was incubated with
(Leu-Arg-Gly-Gly-NH)
-rhodamine, no hydrolysis of the
substrate was observed(7) . Little or no hydrolysis was
observed with purified recombinant L3 23-kDa protein (recombinant
endoproteinase (rEP)) expressed in E. coli. However, when ts-1
virus and rEP were incubated together with
(Leu-Arg-Gly-Gly-NH)
-rhodamine, significant hydrolysis of
the substrate occurred. This implied that cofactors may be required for
maximal activity. The first cofactor we discovered was the viral DNA.
If disrupted wild-type virus is treated with DNase, proteinase activity
is lost, but can be restored upon addition of Ad2 DNA(7) . A
second cofactor was shown to be a plasmin-sensitive virion protein (7) that turned out to be the 11-amino acid peptide from the C
terminus of the precursor to virion protein VI,
pVIc(7, 8) ., which changes by no more than 2-fold,
but by increasing k
, which increases
>6000-fold. By measuring initial velocities as a function of pH, we
show that the enzyme activity is clearly different from that of papain.
Moreover, the pK
values of the amino
acids that affect catalysis are different in the presence and absence
of Ad2 DNA.
Materials
Tris, HEPES, dithiothreitol, and
5,5`-dithiobis(2-nitrobenzoic acid) (Ellman's reagent) were
purchased from Sigma. TSK-DEAE was obtained from Supelco Inc.
S-Sepharose and chelating Sepharose were from Pharmacia Biotech Inc.
Octyl glucoside was from Boehringer Mannheim. The pVIc peptide was
obtained from Multiple Peptide Systems (San Diego, CA).Cells and Viruses
The growth of HeLa cells,
infection by wild-type Ad2 and the mutant H2ts-1, and the purification
of viruses were carried out as described(6) . Twice CsCl-banded
virus was dialyzed against 10 mM Tris-HCl (pH 8.0) and 1
mM EDTA and centrifuged at 100,000 g for 1 h.
The pellet was suspended in 10 mM Tris-HCl (pH 6.8) containing
20% (v/v) glycerol and, after three 10-s bursts of sonication, was
stored at -20 °C. Disrupted virus prepared this way was used
as the source of in vivo or virion-associated proteinase
activity.
Assay for Proteinase Activity
For the purification
of rEP, activity assays contained, in 1 ml, 20 mM HEPES (pH
8.0), 10 mM octyl glucoside, saturating amounts of pVIc
peptide, 140 ng/ml Ad2 DNA, 2 µM
(Leu-Arg-Gly-Gly-NH)
-rhodamine, and rEP. Saturating levels
of pVIc were 100 nM when the rEP concentration was <50
nM and 350 nM for higher concentrations of rEP. The
assay mixtures were incubated at 37 °C, and the increase in
fluorescence was monitored as a function of time. The excitation
wavelength was 492 nm, and the emission wavelength was 523 nm, both
with a 5-nm slit width. Activity was defined as the change in
fluorescence of the assay containing rEP with cofactors minus the
change in fluorescence of an identical assay but without rEP.
PO
(pH 7.3) and 1 mM EDTA
containing 0.33 mM 5,5`-dithiobis(2-nitrobenzoic acid)) and
then monitoring the increase in absorbance at 412 nm. The moles SH/mol
of pVIc was calculated using a molar extinction coefficient at 412 nm
of 14,150 (12) for thionitrobenzoate.SDS-Polyacrylamide Gel Electrophoresis
SDS-PAGE
was performed using the Pharmacia Phast System. Proteins were
fractionated on either 10-15 or 8-25% gradient gels.
Protein bands were visualized with Coomassie Blue or silver staining.Expression of the Recombinant L3 23-kDa Protein in E.
coli
The adenovirus proteinase gene, the gene for the L3 23-kDa
protein, had been cloned into the pET expression vector pT7AD23k8 and
placed in E. coli strain BL21(DE3) under the control of the T7
expression system(6) . A glycerol stock was used to seed an
overnight culture in TB medium (1% Bacto-Tryptone and 0.5% NaCl)
supplemented with 50 µg/ml ampicillin, and this was then used at a
1:200 dilution to seed 4 liters of M9-TBY broth (0.1% NH
Cl,
0.3% KH
PO
, 0.6% Na
HPO
,
0.4% glucose, and 1 mM MgSO
/0.1% yeast, 1%
Bacto-Tryptone, and 0.5% NaCl) supplemented with 50 µg/ml
ampicillin. The cultures were grown with shaking at 30 °C until the
absorbance at 600 nm was between 0.5 and 0.6. At that time, the
cultures were induced by the addition of IPTG to 0.1 mM and
allowed to grow an additional 8-16 h (13) . SDS-PAGE of
the cells at various times after induction revealed that by 8 h, the
major protein in the cells was rEP (see Fig. 1). The cells were
harvested by centrifugation at 5000 g for 10 min. Cell
pellets were stored at -20 °C.
g supernatant of the lysate (lane b), the flow-through
fraction from the DEAE chromatography step (lane c), the rEP
activity pool from the S-Sepharose chromatography step (lane
d), rEP purified by passage over a zinc-iminodiacetic
acid-Sepharose column (lane e), and molecular mass markers (lane f) were separated by SDS-PAGE and stained with Coomassie
Brilliant Blue.
Purification of the Recombinant L3 23-kDa Protein
Expressed in E. coli
A bacterial cell pellet from 3 liters of
cells was suspended in 150 ml (0.05 volume) of 50 mM Tris (pH
8.0), 0.05% (v/v) Triton X-100, 15 mM NaCl, and 5 mM
-mercaptoethanol. The cells were lysed by incubation for 45
min at 4 °C with 100 µg/ml egg white lysozyme followed by three
cycles of freeze/thaw. DNA was digested upon adding 50 µg/ml DNase
and 5 mM MgCl
and incubating for 45 min at 4
°C. The resultant suspension was then subjected to three 30-s
bursts of sonication. This fraction was named the lysate. g for 10
min. This fraction, named the supernatant, was loaded onto a 2.5
25-cm TSK-DEAE column equilibrated in 50 mM Tris (pH
8.0), 15 mM NaCl, and 5 mM
-mercaptoethanol. The
column was washed with 300 ml of the equilibration buffer. rEP was
located in the flow-through fractions by SDS-PAGE and by activity
assays. The fractions with rEP were pooled and named DEAE FT. 15-cm S-Sepharose Fast
Flow column equilibrated in 50 mM Tris (pH 8.0), 15 mM NaCl, and 1 mM DTT. After loading, the column was washed
with 200 ml of 50 mM Tris (pH 8.0), 15 mM NaCl, and 1
mM DTT to remove the Triton X-100. Then, a 150-ml linear
gradient of 15-400 mM NaCl in 50 mM Tris (pH
8.0) was applied to the column. The fractions containing rEP were
identified and pooled and named SSEPH. rEP consistently eluted from
this column at an ionic strength of 0.1 M NaCl.
5-cm chelating Sepharose column
charged with zinc. Charging with zinc was accomplished by a thorough
washing of the resin with 0.05 M EDTA and 1 M NaCl,
followed by washing with water to remove the EDTA, and then followed by
washing with 0.2 M ZnCl
in 5 mM HCl.
Next, the column was equilibrated in 25 mM HEPES (pH 8.0) and
0.1 M NaCl. The column was loaded with the SSEPH pool and
washed with the equilibration buffer until the absorbance at 280 nm was
<0.02. Then, a series of solutions were applied in steps, each step
containing 25 mM HEPES (pH 8.0) and the indicated
constituents: 1 M NaCl; 0.1 M NaCl; 35 mM imidazole and 0.1 M NaCl; 0.1 M NaCl; 35
mM imidazole and 0.1 M NaCl; 0.1 M NaCl; 35
mM imidazole and 0.1 M NaCl; and 0.1 M NaCl.
rEP eluted in 25 mM HEPES (pH 8.0), 0.1 M NaCl, and
0.01 M EDTA. After dialysis against 20 mM HEPES (pH
8.0), 5 mM NaCl, and 0.1 mM EDTA, the purified enzyme
was stored at -70 °C.Purification of the Protein Cofactor pVIc
Twice
density gradient-purified wild-type Ad2 virus (5.8 10
virions) was suspended in 0.8 ml of 10 mM Tris-HCl (pH
8), 1 mM EDTA, and 10% pyridine. After 1 h at 25 °C, the
solution was centrifuged at 12,000
g for 6 min. The
pellet was resuspended in 0.8 ml of 0.01 M HEPES (pH 8) and
centrifuged at 12,000
g for 6 min. The pellet was
resuspended in 0.8 ml of 0.01 M HEPES (pH 8), 0.01 M octyl glucoside, and 0.001 M EDTA and then centrifuged at
5000
g in a Centricon-30 until 90% of the liquid
flowed through the membrane. The volume of the liquid that was retained
was increased to 0.8 ml with ammonium acetate such that its
concentration was 1 M. The solution in the Centricon-30 was
again centrifuged at 5000
g until >90% of the
liquid flowed through the membrane. Assays were performed in the
presence of the rEP protein and in the absence or presence of Ad2 DNA.
column (Aquapore
OD-300 7µ, 2.1 100 mm). The activity was eluted by a linear
gradient of 0-30% acetonitrile in 0.1% trifluoroacetic acid at a
rate of 1%/min. Assays of fractions from each peak were performed in
the presence of Ad2 DNA and rEP.
Comments on the Purification of rEP
A
description of the purification of rEP is given under
``Experimental Procedures,'' and the purification table is Table 1. Proteinase activity was measured using the fluorogenic
substrate (Leu-Arg-Gly-Gly-NH)
-rhodamine.
An
SDS-PAGE analysis of the various fractions during the purification
procedure is shown in Fig. 1. After clarification of the lysate
by centrifugation, the supernatant appeared to contain as much of the
mass migrating with rEP as was seen in the lysate. Also, the
supernatant contained 130% of the lysate activity. For these two
reasons, rEP was probably expressed in a soluble extractable form
within E. coli. After passing the supernatant through a DEAE
column, the specific activity increased 3-fold with an 87% recovery.
S-Sepharose chromatography resulted in a 7-fold increase in specific
activity with a 73% recovery. The enzyme eluted at low ionic strength.
Zinc column chromatography removed the remaining contaminants through
successive salt-imidazole steps. Once the contaminants were eluted, rEP
was eluted by applying EDTA to the column. The overall yield of rEP was
66%, and the specific activity increased 36-fold. SDS-PAGE analysis of
the zinc-iminodiacetic acid column pool indicated that rEP is
homogeneous (Fig. 1, lane e).
Complementation of the ts-1 Mutation by rEP
To
determine whether rEP was active with in vivo substrates and
to determine whether it is the protein whose inactivation gives rise to
the ts-1 phenotype, we investigated whether we could observe processing
of ts-1 precursor proteins upon incubation of rEP with ts-1 virions.
Disrupted ts-1 virions were incubated with purified rEP under
conditions optimal for assaying proteinase activity in disrupted
wild-type virus with our fluorogenic substrates.
As a
function of time, the reaction was monitored for processing of the
precursor proteins by SDS-PAGE (Fig. 2). After 30 min, the
profile (lane f) resembled that of wild-type virus (lanes
a and h) more than that of ts-1 virus (lane g).
pVI, pVII, and 11K were extensively processed, while pVIII and pIIIa
were less extensively processed. After 6 h, ts-1 virus incubated with
rEP (lane b) was identical to wild-type virus (lanes a and h), except for a band that is either pVIII or an
intermediate in pVI processing. An identical experiment but using
heat-inactivated rEP showed no processing, even after an 18-h
incubation (data not shown). If the same experiment was done but after
pretreatment of disrupted ts-1 virus with DNase and MgCl
,
no processing occurred, whereas processing was observed in the presence
of DNase and EDTA (data not shown). We could not see the processing of
the precursor to terminal protein because too few copies are present in
virions to be visualized even by silver staining.
10
virions, and 0.25
µM rEP. After the indicated times at 37 °C, aliquots
were removed from the reactions, and the proteins were fractionated by
SDS-PAGE on 8-25% gradient gels. Lanes a and h,
wild-type Ad2 virions; lane g, Ad2 ts-1 virions; lanes
b-f, Ad2 ts-1 virions incubated with rEP for 6, 4, 2, 1, and
0.5 h, respectively. The precursor proteins of the ts-1 virion and
their mature counterparts in the wild-type (wt) Ad2 virion are
labeled. The proteins were visualized by silver
staining.
Comments on the Purification and Identification of the
Second Cofactor, pVIc
A description of the purification of the
second cofactor is given under ``Experimental Procedures.''
Virions disrupted by 10% pyridine were centrifuged, and the pellet was
resuspended in octyl glucoside (Fig. 3). The solubilized
cofactor activity was placed in a Centricon-30 (30,000-Da cutoff) and
centrifuged until >90% of the liquid passed through the membrane.
The salt concentration in the liquid that was retained was increased to
1 M, and the solution in the Centricon-30 was again
centrifuged until >90% of the liquid passed through the membrane.
This time, the second cofactor activity passed through the membrane.
column, and
the cofactor activity was eluted with a linear gradient of 0-30%
acetonitrile (Fig. 4). Each peak from the column was assayed for
proteinase activity. Only the three peaks marked with arrows showed proteinase activity in the presence of rEP and Ad2 DNA. A
profile of the proteinase activity in each of the three peaks is shown
in the inset in Fig. 4. Of the total cofactor activity
applied to the C
column, 7% was recovered in peak a, 22%
in peak b, and 14% in peak c. The final yield was >49%.
column, and
the activity was eluted by a linear gradient of 0-30%
acetonitrile in 0.1% trifluoroacetic acid. Inset, assays of
fractions from peaks a, b, and c were performed in the presence of 778
ng/ml Ad2 DNA and 2.2 nM rEP. mAU, milli-absorbance
units.
Identification of the Second Cofactor as pVIc
The
amino acid sequences of the proteins in each of the three peaks that
contained cofactor activity were determined in a gas-phase sequencer.
The results (Fig. 5) indicated that the polypeptides in the
three peaks were homologous. The differences were in the yield of
lysine at position 6. In peak a, 5 pmol of lysine were detected,
whereas 15-30 pmol were expected. No amino acid was detected at
position 6 in peak b, and in peak c, 35 pmol of lysine were detected
where 40-80 pmol were expected. No amino acid was detected at
position 10, where a cysteine was expected. This 11-amino acid
polypeptide originated from the carboxyl terminus of the precursor to
band VI, pVI. That sequence is also shown in Fig. 5. There are
two proteinase consensus cleavage sequences in pVI, one beginning at
residue 29 (MSGG) and the other at residue 236 (IVGL). Cleavage of the
latter sequence at the Leu-Gly bond would liberate the 11-amino
acid cofactor.
of 1350. Thus,
there was mostly pVIc present. In peak b, there were two species
present at a ratio of 2:1, one with an M
of 1350
and the other with an M
of 2700. Thus, there was
mostly pVIc present, but also some pVIc dimer. In peak c, there was one
major species with an M
of 1350.Identification of the Proteins in the Other
Peaks
We also sequenced the proteins in the peaks in Fig. 4that did not show proteinase activity. Peak 1 contained
the sequence MRRAHHRRRRASHRRMRGG, which is the Mu peptide from the
11-kDa precursor(14) . The sequence in peak 2 was
FRHRVRSPGQGITHLKIR, which is the C-terminal fragment of pVIII. The
N-terminal sequence of the 11-kDa precursor, ALT-RLRFPVPGF, was found
in peak 3. The sequence in peak 4, GNPRA-LRP- -G, comes from the
C-terminal fragment of pIIIa; and the sequence GLRFPSKMFGG from peak 5
comes from the C-terminal fragment of the N-terminal fragment of pVII.Reconstitution of Proteinase Activity in Vitro with
Purified Components
Ad2 DNA and rEP were assayed in the presence
of increasing amounts of the second cofactor (Fig. 6A).
At low concentrations of the second cofactor, the amount of proteinase
activity was proportional to the amount of second cofactor. At higher
concentrations, saturation was approached. If the amount of rEP was
doubled, the amount of proteinase activity was doubled, and the
saturation limit appeared to double. Proteinase activity of
rEPpVIc complexes was stimulated by the presence of Ad2 DNA (Fig. 6B). As the Ad2 DNA concentration was increased
in the presence of a constant amount of rEP and second cofactor,
proteinase activity rose, reached a plateau, and eventually began to
decrease.
Optimization of Assay Conditions
The assay
conditions we used to monitor the purification of rEP and pVIc were
those we obtained from optimizing proteinase activity in vivo,
in disrupted wild-type virus.
With purified components, rEP
and pVIc, and the substrate (Leu-Arg-Gly-Gly-NH)
-rhodamine,
we varied the assay parameters to determine the optimal conditions for
maximal activity in vitro of rEPpVIc complexes in the
absence and presence of Ad2 DNA (Fig. 7). The optimal
temperature was 45 °C independent of the presence of Ad2 DNA (Fig. 7A). Proteinase activity was unusually sensitive
to ionic strength (Fig. 7B). Half the activity was lost
at NaCl concentrations of 10 mM in the absence of Ad2 DNA and
45 mM in the presence of Ad2 DNA. Addition of 10 mM octyl glucoside resulted in a 3-fold increase in activity in the
absence of Ad2 DNA; at 20 mM octyl glucoside, the activity
decreased to its level in the absence of octyl glucoside (Fig. 7C). In the presence of Ad2 DNA, 6-8 mM octyl glucoside increased activity slightly more than 50%. At
higher concentrations of octyl glucoside, activity decreased such that
at 18 mM it was half-maximal activity. With dithiothreitol, 5
mM increased the activity in the presence of Ad2 DNA by
slightly more than 50% (Fig. 7D). In the absence of Ad2
DNA, DTT was only inhibitory, with half-maximal activity at 1
mM.
pVIc
complexes were then assayed at pH 8.5 using TAPS buffer. Complexes
between rEP, pVIc, and Ad2 DNA were formed the same way, except that
the reactions contained 14 nM rEP, 200 nM pVIc, and
140 ng/ml Ad2 DNA. The rEP
pVIc
Ad2 DNA complexes were
assayed at pH 8.0 using Tris buffer. After the preincubations, 0.1 ml
of 0.1 M buffer, 30 µM
(Leu-Arg-Gly-Gly-NH)
-rhodamine, 10 mM octyl
glucoside, 1 mM EDTA, and 0.5 mM DTT was added; the
reactions were incubated at the indicated temperatures; and after 10
min, the increase in fluorescence was determined. In B-D, complexes were formed in 0.9 ml as described for A, except for the absence of the indicated variable. Then, 0.1
ml was added as described for A, except that it contained 10
times the final concentration of the indicated variable, and the
increase in fluorescence at 37 °C was monitored as a function of
time.
pVIc complexes,
half-maximal activity was lost at 50 mM EDTA (data not shown).
Under standard assay conditions, the increase in fluorescence as a
function of time with (Leu-Arg-Gly-Gly-NH)
-rhodamine as the
substrate was linear for >30 min.K
Once we had purified components and optimal assay
conditions, we determined the effects of the cofactors on the
macroscopic kinetic constants of the interaction of rEP with the
substrate (Leu-Arg-Gly-Gly-NH)
and k of rEP with the
Cofactors
-rhodamine (Table 2).
rEP alone had a small amount of activity. By incubating Ad2 DNA with
rEP, the K
increased 2-fold and the k 3-fold relative to those with rEP alone. By
incubating pVIc with rEP, the K
increased 2-fold
and the k 355-fold relative to those with rEP
alone. With all three components together, rEP plus Ad2 DNA plus pVIc,
the K
increased 2-fold and the k 6072-fold relative to those with rEP alone. Thus, the cofactors
increase proteinase activity by increasing the catalytic rate constant, k
.
V
Measurement of V
as a Function of pH
as a function of pH can reveal the
pK
values of the amino acids involved in
catalysis. With rEPpVIc complexes, in the absence and presence of
Ad2 DNA, we measured the rate of hydrolysis of
(Leu-Arg-Gly-Gly-NH)
-rhodamine in the pH range from 4.5 to
10 under conditions in which the substrate concentration was at least
5-fold greater than the K
. The data are shown in Fig. 8. In the absence of Ad2 DNA, the data can best be
characterized as the sum of four gaussian peaks with a correlation
coefficient of 98.1% (Fig. 8A). In the presence of Ad2
DNA, the data can best be characterized as the sum of three gaussian
peaks with a correlation coefficient of 96.9% (Fig. 8B). The curves of V
as a
function of pH implied that, in the absence of Ad2 DNA, there are at
least five amino acids with pK
values that can
affect catalysis. The pK
values are 5.2, 6.4, 6.9,
7.5, and 9.4. In the presence of Ad2 DNA, there are four amino acids
with critical pK
values: 5.2, 6.5, 7.4, and 8.8.
In the absence and presence of Ad2 DNA, the two gaussian curves between
pH 5 and 6 appear to be the same; the large, high pH gaussian curve in
the absence of Ad2 DNA appears in the presence of Ad2 DNA to have
shifted 0.5 pH units to the left. The gaussian curve in the presence of
Ad2 DNA with a pK
of 6.5 appears to have split
into two gaussian curves with pK
values of 6.4 and
6.9.
pVIc complexes (A) and for rEP
pVIc
Ad2 DNA
complexes (B). Complexes were formed by incubating 63 nM rEP and 200 nM pVIc (A) or 15.75 nM rEP, 200 nM pVIc, and 5.6 pM Ad2 DNA (B) for 5 min at 37 °C in 0.9 ml of 0.1 mM TAPS
(pH 8.5) containing 1.1 mM EDTA, 0.55 mM DTT, and 11
mM octyl glucoside. Then, 0.1 ml was added containing
components such that the final concentration of buffer was 10 mM and that of (Leu-Arg-Gly-Gly-NH)
-rhodamine was 3
µM, and the ionic strength was 16 mM. The
increase in fluorescence was then measured as a function of time. The
buffers used were sodium citrate (pH 4.0 and 4.6), sodium acetate (pH
5.0 and 5.5), MES (pH 6), sodium cacodylate (pH 6.0-6.8), HEPES
(pH 7-7.8), Tris (pH 8.0 and 8.5), CHES (pH 9.0 and 9.5), and
CAPS (pH 10.0 and 10.5). The curves were fitted using the program
Peakfit (Jandel Scientific) assuming merged gaussian peaks (dotted
lines).
)and three
histidines. rEP bound quite tightly to this column as it had to be
eluted with EDTA. The final step in the purification of rEP was
dialysis against 0.5 mM EDTA. This was done to remove all
traces of zinc, which is an inhibitor of enzyme activity. With
(Leu-Arg-Gly-Gly-NH)
-rhodamine as the substrate, the
specific activity increased from 22.4 to 815 nmol of substrate
hydrolyzed per s/mg of protein.
column. Three of the peaks contained cofactor activity.
Sequencing of the three peaks indicated that there was a variable yield
in lysine at position 6 and no amino acid was detected at position 10,
where we expected a cysteine. Time-of-flight mass spectrometry analysis
indicated that the major species in each peak had an M
of 1350, consistent with the presence of a monomer of pVIc.
Webster et al.(8) purified the cofactor by
solubilizing virions in 4 M guanidine HCl and fractionating by
fast protein liquid chromatography on a Superdex S-75 gel filtration
column. Two peaks of complementing activity were detected by subsequent
reverse-phase high pressure liquid chromatography. One peak was the
monomer of pVIc, and the other peak was the disulfide dimer of pVIc. >6000-fold. The K
changed by less than a factor of 3. Previous in vitro assays for the Ad2 proteinase activity were successful because
they utilized Ad2 precursor proteins in an extract from ts-1-infected
cells as substrate and disrupted wild-type virus (16) or rEP as
the source of proteinase (6) or synthetic peptides as substrate
and disrupted wild-type virus as the
proteinase(17, 18) . Hence, in those assays, both
cofactors were present. for
activity(19) . Some proteinases utilize ATP(20) . A
serine proteinase anchored to the membrane of Plasmodium falciparum by a covalently attached glycosylphosphatidylinositol moiety is
activated by phosphatidylinositol-specific phospholipase
C(21) . Many proteinases are synthesized as zymogens and must
be activated by proteolytic cleavage, e.g. the activation of
trypsinogen to trypsin by enterokinase or trypsin (22) or the
activation of plasminogen to plasmin by urokinase(23) . The
assembly and activation of some of the proteins of the blood
coagulation system require a negatively charged surface(24) .
The virus-coded proteinases from the human immunodeficiency virus and
avian sarcoma/leukosis viruses require themselves as cofactors as
homodimers are the active form(25, 26, 27) .
Although the E. coli RecA protein can facilitate the cleavage
of the LexA protein bound to DNA, RecA apparently does so as an
allosteric effector and not as a proteinase with an active-site
nucleophile(28) .
pVIc complexes in
the absence and presence of the viral DNA revealed an unusual
sensitivity to ionic strength. In the absence of the DNA, 10 mM NaCl inhibited 50% of the enzyme activity. In the presence of Ad2
DNA, 45 mM NaCl inhibited 50% of the enzyme activity. In
contrast to these results, in disrupted virions, 300 mM NaCl
was required for 50% inhibition of activity.
The latter
experiment implied that direct inhibition either of the binding of
substrate to the active site or, once bound, of the rate of catalysis
probably occurs at NaCl concentrations closer to 300 mM than
to 30 mM. Thus, NaCl concentrations of 10-45 mM must inhibit enzyme activity by interfering with formation of an
active complex, a complex already formed in a disrupted virus particle.
Examination of the L3 23-kDa gene sequence led Webster et al.(17, 18) to propose that the Ad2 proteinase may
be a member of a new subclass of cysteine proteinases described by
Brenner(31) , by Bazan and Fletterick(32) , and by
Gorbalenya et al.(33) . Based upon site-directed
mutagenesis studies, two groups have argued that the enzyme is a
cysteine proteinase and that Cys-104 is the active-site nucleophile (34, 35) . and not K
. Webster et
al.(36) found no stimulation of rEPpVIc complex
activity by Ad2 DNA.
as
a function of pH with rEPpVIc complexes in the absence and
presence of Ad2 DNA indicated that the enzyme is quite different from
the cysteine proteinase papain. Papain contains an active-site
thiolate-imidazolium ion pair between His-159 and Cys-25(37) .
The second-order acylation rate constant (k
/K
) as a function of pH
conforms to a bell-shaped curve. The two ionizing groups with
pK
values near 4 and 8.5 probably correspond to
His-159 and Cys-25, respectively, more appropriately to the formation
and decomposition of the ion pair. An active-site thiolate-imidazolium
ion pair in the adenovirus proteinase could have pK
values in the absence of Ad2 DNA of 5.17 and 9.43, whereas in the
presence of Ad2 DNA, the pK
values could be 5.15
and 8.78. These pK
values are similar to the
normal pK
values of 6.0 for histidine and 8.3 for
cysteine. Our thiol protection experiment at pH 5.0 in vivo with disrupted virus is consistent with the presence of a
thiolate-imidazolium ion pair.![]()
as a function of pH implied that rEPpVIc
complexes bind to Ad2 DNA. The profiles of rEP
pVIc complexes in
the absence and presence of Ad2 DNA are different: pK
values of 5.2, 6.4, 6.9, 7.5, and 9.4 versus 5.2, 6.5,
7.4, and 8.8, respectively. This indicates that Ad2 DNA does affect the
pK
values of some of the amino acids involved in
catalysis and therefore implies that the rEPpVIc complexes bind
to Ad2 DNA. In addition, the results of measuring the V
of rEPpVIc complexes in the presence of
Ad2 DNA are similar to those obtained with enzyme activity in disrupted
virus. The pK
values for disrupted virus are 5.2,
6.2, 7.2, and 8.4. This implied that in the virion, rEPpVIc
complexes are bound to the viral DNA.
)
-D-thiogalactopyranoside; DTT,
dithiothreitol; TAPS,
3-{[2-hydroxy-1,1-bis(hydroxymethyl)ethyl]amino}-1-propanesulfonic
acid; MES, 4-morpholineethanesulfonic acid; CHES,
2-(cyclohexylamino)ethanesulfonic acid; CAPS,
3-(cyclohexylamino)propanesulfonic acid.
)
)
We thank Dan Marshak for the time-of-flight mass
spectrometry analysis of the three peaks from the C
column. We also thank Suma Abraham for help in some of the
experiments.
©1996 by The American Society for Biochemistry and Molecular Biology, Inc.
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