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Journal of Virology, June 2000, p. 5486-5494, Vol. 74, No. 12
0022-538X/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.
A Yeast-Based Genetic System for Functional
Analysis of Viral mRNA Capping Enzymes
C. Kiong
Ho,
Alexandra
Martins, and
Stewart
Shuman*
Molecular Biology Program, Sloan-Kettering
Institute, New York, New York 10021
Received 14 February 2000/Accepted 20 March 2000
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ABSTRACT |
Virus-encoded mRNA capping enzymes are attractive targets for
antiviral therapy, but functional studies have been limited by the lack
of genetically tractable in vivo systems that focus exclusively on the
RNA-processing activities of the viral proteins. Here we have developed
such a system by engineering a viral capping enzyme
vaccinia virus
D1(1-545)p, an RNA triphosphatase and RNA guanylyltransferase
to
function in the budding yeast Saccharomyces cerevisiae in
lieu of the endogenous fungal triphosphatase (Cet1p) and
guanylyltransferase (Ceg1p). This was accomplished by fusion of
D1(1-545)p to the C-terminal guanylyltransferase domain of mammalian
capping enzyme, Mce1(211-597)p, which serves as a vehicle to target the
viral capping enzyme to the RNA polymerase II elongation complex. An
inactivating mutation (K294A) of the mammalian guanylyltransferase active site in the fusion protein had no impact on genetic
complementation of cet1
ceg1
cells, thus proving that
(i) the viral guanylyltransferase was active in vivo and (ii) the
mammalian domain can serve purely as a chaperone to direct other
proteins to the transcription complex. Alanine scanning had identified
five amino acids of vaccinia virus capping enzyme
Glu37, Glu39, Arg77,
Glu192, and Glu194
that are essential for
phosphate cleavage in
vitro. Here we show that the introduction of mutation E37A, R77A, or
E192A into the fusion protein abrogates RNA triphosphatase function in
vivo. The essential residues are located within three motifs that
define a family of viral and fungal metal-dependent phosphohydrolases
with a distinctive capacity to hydrolyze nucleoside triphosphates to
nucleoside diphosphates in the presence of manganese or cobalt. The
acidic residues Glu37, Glu39, and Glu192 likely comprise the
metal-binding site of vaccinia virus triphosphatase, insofar as their
replacement by glutamine abolishes the RNA triphosphatase and ATPase activities.
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INTRODUCTION |
Eukaryotic viruses have evolved
diverse strategies to acquire a 5' cap structure for their mRNAs
(4). RNA viruses that encode RNA-dependent RNA polymerases
to synthesize their mRNAs either steal the caps from cellular
transcripts, encode their own enzymes that cap and methylate the
plus-strand transcripts, or circumvent the capping problem by including
cis-acting elements in the plus strand that promote
cap-independent translation. The mRNAs of most DNA viruses are
synthesized by cellular RNA polymerase II (pol II) and are therefore
capped by the cellular capping and methylating enzymes. However,
vaccinia virus and other poxviruses, which replicate entirely in the
cytoplasm, encode and encapsidate their own DNA-dependent RNA
polymerase and mRNA capping apparatus (12, 16). African
swine fever virus, which has a cytoplasmic replication phase, also
encodes and encapsidates its own RNA polymerase and capping enzyme
(39). Baculoviruses, which replicate in the nucleus, use pol
II to transcribe early genes and then switch at late times to a
virus-encoded transcription system that includes RNA polymerase and
capping activities (14, 15, 26). Chlorella virus
PBCV-1 encodes a capping enzyme (25) but appears not to encode its own RNA polymerase.
Cap formation by the enzymes of DNA viruses, double-stranded RNA
viruses, and eukaryotic cells occurs via three sequential reactions:
(i) the 5' triphosphate end of the nascent pre-mRNA is hydrolyzed to a
diphosphate by RNA 5' triphosphatase, (ii) the diphosphate end is
capped with GMP by GTP:RNA guanylyltransferase, and (iii) the GpppN cap
is methylated by S-adenosylmethonine:RNA (guanine-N7) methyltransferase (48). This
"conventional" pathway of cap synthesis was defined using soluble
enzymes purified from vaccinia virus particles (12, 54). The
mechanisms and structures of cellular and DNA virus capping enzymes
have since been delineated through mutagenesis and crystallography
(10, 11, 17, 21, 28, 30, 33, 37, 42, 56, 57, 60-62).
Several single-stranded RNA viruses have evolved alternative cap
synthetic pathways, which entail unconventional chemistry and are less
well understood with respect to enzyme structure and mechanisms
(1-3, 47).
The genetic and physical organizations of the known virus-encoded mRNA
capping enzymes are significantly different from those of metazoan host
cells (48). Hence, the viral cap-forming enzymes are
potential targets for antiviral drugs that would interfere with capping
of pathogen mRNAs but spare the host capping enzymes. For any given
virus that provides its own caps, there are a number of questions that
need to be addressed before capping can be validated as a target, such
as (i) whether the viral gene encoding the capping enzyme is essential
for virus replication and (ii) whether the capping activity of the
viral gene product is essential for virus replication. These questions
have not been answered fully, even where the biochemistry of viral cap
formation is well understood. For example, vaccinia virus capping
enzyme is a multifunctional protein with RNA triphosphatase, RNA
guanylyltransferase, and RNA (guanine-7-) methyltransferase activities
(45, 54). The enzyme is a heterodimer of 95- and 33-kDa
subunits encoded by the vaccinia virus D1 and D12 genes, respectively.
The vaccinia virus D1 and D12 genes are essential for virus
replication, insofar as mutations that elicit temperature-sensitive
virus growth phenotypes have been mapped to the two capping enzyme
subunits (6, 18). However, the genetic landscape is
complicated, because vaccinia virus capping enzyme plays a larger role
in viral gene expression; it serves as a transcription termination
factor during the synthesis of viral early mRNAs (29, 50)
and as an initiation factor during the transcription of intermediate
genes (55). Amazingly, the D1 and D12 temperature-sensitive
mutant viruses display no gross defect in viral gene expression at the
restrictive temperature but are instead defective in resolving
concatemeric DNA replication intermediates into the hairpin telomeres
of the mature viral genome (6, 18). This mysterious
phenotype has no obvious connection to the known mRNA-processing or
transcription functions of the D1 and D12 proteins. Similar problems
arise in interpreting the essentiality of the baculovirus LEF-4 capping
enzyme, which is an intrinsic subunit of baculovirus RNA polymerase,
because it is not clear if the conditional phenotype of a
lef-4 mutant virus is a consequence of failure to transcribe
or failure to cap viral mRNAs (15, 26).
Genetic, and ultimately pharmacologic, analysis of viral capping
enzymes would be facilitated by the development of in vivo assays in
which the functional readout is clearly and exclusively dependent on
the capacity of the viral gene product to catalyze cap synthesis. Here
we explore the possibility of using the budding yeast
Saccharomyces cerevisiae as a genetic model for the study of
viral capping enzymes. S. cerevisiae encodes a
three-component capping system consisting of separate triphosphatase
(Cet1p), guanylyltransferase (Ceg1p), and methyltransferase (Abd1p)
gene products (22, 31, 43, 53). All three genes are
essential for yeast cell growth. Mutational analyses of Cet1p, Ceg1p,
and Abd1p have resulted in the delineation of minimal catalytic domains for each protein and the identification of catalytically important amino acid side chains that comprise the triphosphatase,
guanylyltransferase, and methyltransferase active sites (21, 27,
30, 37, 56, 57). By correlating mutational effects on catalysis
in vitro with effects on function in vivo, we have shown that the
triphosphatase, guanylyltransferase, and methyltransferase activities
are essential for yeast cell growth. The feasibility of using yeast
growth as a readout of the function of capping enzymes from
heterologous sources is underscored by the demonstration that the
entire three-component yeast capping apparatus can be replaced in vivo
by the two-component mammalian capping system, consisting of a
bifunctional triphosphatase-guanylyltransferase protein (Mce1p) and a
separate cap methyltransferase (Hcm1p) (41). This result is
remarkable because the structure and catalytic mechanism of the
mammalian RNA triphosphatase are completely different from those of the
yeast RNA triphosphatase (48).
The salient question here is whether a viral capping enzyme can
function in place of one or more of the yeast capping enzymes. To
address this issue, we tested the ability of the N-terminal triphosphatase-guanylyltransferase domain of the vaccinia virus D1
polypeptide [vD1(1-545)p] to complement the growth of yeast cet1
or ceg1
cells. We report that the
vaccinia virus enzyme is active in vivo, provided that it is targeted
to the pol II transcription complex by fusion to a cellular protein
that binds to pol II. Mutations of vD1(1-545)p that abrogate
triphosphatase activity in vitro abolish complementation of
cet1
. Additional mutational analysis of vD1(1-545)p
defines the triphosphatase active site and suggests a mechanism of
metal-dependent catalysis common to DNA viral and fungal capping
enzymes. Isogenic strains bearing vaccinia virus and human capping
enzymes can be used to screen for cytotoxic compounds that specifically
inhibit the poxvirus capping apparatus.
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MATERIALS AND METHODS |
Yeast expression plasmids for vaccinia virus capping enzyme.
The vD1(1-545) gene encoding the N-terminal
triphosphatase-guanylyltransferase domain of vaccinia virus capping
enzyme (35, 61) was excised from pET-D1(1-545) with
NdeI and HindIII and inserted between the
NdeI and HindIII sites of the customized yeast expression vector pYX1 (CEN TRP1), a derivative of
pYX132 (Novagen) that contains six tandem histidine codons and a unique NdeI site between the NcoI and BamHI
sites. The resulting yeast plasmid, pYX1-vD1(1-545), encodes vaccinia
virus D1(1-545)p fused in-frame with an amino-terminal 12-amino-acid
leader peptide (MGSHHHHHHSGH). An AatII-NheI
fragment containing the vD1(1-545) gene was excised from
pYX1-vD1(1-545) and inserted into the yeast multicopy expression plasmid pYX232 (2µm TRP1) to generate p232-vD1(1-545).
Expression of the vD1(1-545) gene is under the control of
the yeast TPI1 promoter.
Plasmids encoding a chimeric vaccinia virus-mammalian capping enzyme
with an N-terminal vD1(1-545)p segment fused to the C-terminal guanylyltransferase domain of the mouse capping enzyme Mce1(211-597)p were constructed as follows. The vD1(1-545) gene was PCR
amplified from a pET-D1(1-545) template using an antisense primer that
changed the vD1(1-545) stop codon to a His codon and
introduced an NdeI restriction site at a position
corresponding to the C-terminus. The PCR product was digested with
NdeI and then inserted into the NdeI site of
pYX1-MCE1(211-597) (CEN TRP1) to yield the fusion gene
plasmid pYX1-vD1(1-545)-MCE1(211-597). An
AatII-NheI fragment containing the fusion gene
was excised from pYX1-vD1(1-545)-MCE1(211-597) and inserted into pYX232
(2µm TRP1) to generate p232-vD1(1-545)-MCE1(211-597). Expression of the vD1(1-545)-MCE1(211-597) gene is under the
control of the yeast TPI1 promoter.
CEN TRP1 and 2µm TRP1 plasmids encoding mutated
versions of vD1(1-545)-Mce1(211-597)p with alanine substitutions at
residue Glu37, Arg77, or Glu192 were constructed as described above,
except that PCR amplification of the vaccinia virus component was
performed using pET-D1(1-545)-E37A, pET-D1(1-545)-R77A, or
pET-D1(1-545)-E192A as a template (60).
Plasmids encoding a mutated version of vD1(1-545)-MCE1(211-597)p in
which the active-site lysine nucleophile of the mouse guanylyltransferase domain (Lys294) was replaced by alanine were constructed as follows. The K294A mutation was introduced into the
MCE1(211-597) gene by PCR amplification with mutagenic
primers using the two-stage overlap extension method.
pYX1-MCE1(211-597) served as the template for the first-round PCR. The
product of the second-stage PCR was digested with StuI and
NsiI and then inserted into StuI- and
NsiI-digested pYX1-vD1(1-545)-MCE1(211-597) in lieu of the
wild-type gene fragment. An AatII-NheI fragment containing the fusion gene was excised from
pYX1-vD1(1-545)-MCE1(211-597)-K294A and inserted into pYX232 (2µm
TRP1) to generate p232-vD1(1-545)-MCE1(211-597)-K294A.
The presence of the desired mutations in the yeast plasmids was
confirmed in every case by DNA sequencing; the inserted fragments were
sequenced completely to exclude the acquisition of unwanted mutations
during the amplification and cloning procedure.
Yeast strains.
Strain YBS20 (MATa trp1
his3 ura3 leu2 ade2 can1 cet1::LEU2
p360-CET1) is deleted at the chromosomal CET1 locus encoding yeast RNA triphosphatase. Growth of YBS20 depends on maintenance of
plasmid p360-CET1 (CEN URA3 CET1). Strain YBS2
(MATa ura3 trp1 lys2 leu2
ceg1::hisG pGYCE-360) is deleted at the
chromosomal CEG1 locus encoding yeast RNA
guanylyltransferase. Growth of YBS2 depends on maintenance of plasmid
pGYCE-360 (CEN URA3 CEG1). Strain YBS50 (MATa
leu2 ade2 trp1 his3 ura3 can1 ceg1::hisG
cet1::LEU2 p360-CET1/CEG1) is deleted at the
chromosomal CET1 and CEG1 loci (41).
Growth of YBS50 is contingent on the maintenance of plasmid p360-CET1/CEG1 (CEN URA3 CET1 CEG1).
T7-based plasmids for expression of vD1(1-545)p in bacteria.
vD1(1-545) mutations E37D, E37Q, E39D, E39Q, E192D, E192Q,
E194D, and E194Q were programmed by synthetic oligonucleotides, using
the two-stage PCR-based overlap extension strategy.
NdeI-BglII restriction fragments of the
PCR-amplified mutated vD1(1-545) DNAs were inserted into the
T7-based expression plasmid pET16b that had been digested with
NdeI and BamHI. The resulting plasmids contained
the mutated vD1(1-545) coding sequence fused in frame with a
63-bp 5' leader sequence that encodes 10 consecutive histidine residues. The presence of the desired mutations was confirmed in each
case by sequencing the entire 1.7-kbp insert; the occurrence of
PCR-generated mutations outside the targeted region was thereby excluded.
Expression and purification of recombinant vD1(1-545)p.
The
recombinant His-tagged vaccinia virus proteins were purified by
nickel-agarose chromatography of soluble extracts of 1-liter cultures
of Escherichia coli BL21(DE3) bearing wild-type or mutated pET-His-D1(1-545) plasmids as described previously (61). The 200 mM imidazole eluate fractions of each preparation were dialyzed and
purified further by phosphocellulose chromatography (61). The polypeptide compositions of the column fractions were monitored by
sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis. Protein concentrations were determined using the Bio-Rad dye reagent with bovine serum albumin as a standard.
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RESULTS |
Engineering vaccinia virus capping enzyme to function in
yeast.
vD1(1-545)p is an autonomous trypsin-resistant domain with
RNA triphosphatase and RNA guanylyltransferase activities equivalent to
those of the native vaccinia virus capping enzyme (35, 36, 44,
61). The triphosphatase and guanylyltransferase active sites are
distinct, but the structural elements that comprise the active sites
are partially interdigitated within the primary structure, such that
vD1(1-545)p cannot be separated into catalytically active subdomains.
To express vaccinia virus triphosphatase-guanylyltransferase in yeast,
we cloned the vD1(1-545) gene into a yeast 2µm plasmid and
placed it under the transcriptional control of the strong constitutive
TPI1 promoter. The capacity of vD1(1-545)p to replace the
yeast RNA triphosphatase Cet1p was tested by plasmid shuffle in yeast
cet1
cells that contain CET1 on a
URA3 plasmid. The cet1
strain is unable to
form colonies on medium containing 5-fluoro-orotic acid (5-FOA), a drug
that selects against the URA3 plasmid, unless it is
transformed with a second plasmid bearing CET1 or a
functional homologue from another source. For example, transformation
with a TRP1 plasmid bearing the MCE1 gene, which
encodes the 597-amino-acid mammalian
triphosphatase-guanylyltransferase, allowed growth of cet1
cells on 5-FOA, whereas a plasmid expressing
Mce1(211-597)p, the C-terminal guanylyltransferase domain of mammalian
capping enzyme, did not (Fig. 1A). The
key finding was that expression of vD1(1-545)p did not complement the
cet1
mutation (Fig. 1A).

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FIG. 1.
Complementation of yeast cet1 and
ceg1 mutations by expression of a
vD1(1-545)-Mce1(211-597)p chimeric capping enzyme. Yeast strains YBS20
(cet1 ), YBS2 (ceg1 ), and YBS50
(cet1 ceg1 ) were transformed with 2µm
TRP1 plasmids containing either vD1(1-545) or
vD1(1-545)-MCE1(211-597). Control transformations were
performed with CEN TRP1 plasmids containing MCE1
or MCE1(211-597). Single Trp1+ transformants
were patched to agar plates lacking tryptophan and then streaked on
agar medium containing 5-FOA (0.75 mg/ml). The plates were photographed
after incubation for 4 days at 30°C.
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Similar tests of the ability of vD1(1-545)p to substitute for yeast
guanylyltransferase Ceg1p were performed by plasmid shuffle into a
ceg1
strain bearing a URA3 CEG1 plasmid (Fig.
1B). Cell expressing the full-length mammalian Mce1p grew on 5-FOA. So
did cells expressing the C-terminal guanylyltransferase domain
Mce1(211-5497)p, but as noted previously (24),
MCE1(211-597) cells formed smaller colonies than
MCE1 cells (Fig. 1B). We found that expression of vD1(1-545)p did not complement the ceg1
mutation (Fig.
1B). Thus, the vaccinia virus capping enzyme, by itself, was unable to
function in yeast, either as a triphosphatase or as a guanylyltransferase.
A plausible explanation for why vD1(1-545)p could not replace Cet1p or
Ceg1p is that the vaccinia virus capping enzyme failed to localize to
the intranuclear sites of pre-mRNA synthesis. We and others have shown
that specific capping of nascent pre-mRNAs is achieved via the binding
of the guanylyltransferase component of the cellular capping apparatus
to the phosphorylated carboxyl-terminal domain (CTD) of elongating pol
II (8, 9, 23, 24, 34, 46, 62). The CTD, consisting of tandem
repeats of a heptapeptide of the consensus sequence YSPTSPS, is
extensively phosphorylated in the context of the transcription
elongation complex. The guanylyltransferase domain Mce1(211-597)p of
mammalian capping enzyme binds specifically to the phosphorylated CTD
but not to unmodified CTD. The triphosphatase domain of mammalian
capping enzyme Mce1(1-210)p does not bind the CTD but is normally
brought along via its linkage in cis to the
guanylyltransferase. In yeast, the guanylyltransferase Ceg1p binds to
CTD-PO4, whereas the triphosphatase Cet1p does not.
Formation of a Cet1p-Ceg1p complex in trans allows the yeast
guanylyltransferase to chaperone the triphosphatase to the
transcription complex (20, 27). The reason why yeast
MCE1(211-597) cells grow slowly (Fig. 1B) is that mouse
guanylyltransferase has low affinity for the yeast triphosphatase
(20).
Vaccinia virus capping enzyme forms a binary complex in solution with
vaccinia virus RNA polymerase (16). This interaction facilitates the capping of nascent mRNA chains as soon as their 5' ends
are extruded from the RNA binding pocket on the elongating polymerase
(16). The poor efficiency of capping of RNAs transcribed by
T7 RNA polymerase in vaccinia virus-infected cells is likely a
manifestation of the vaccinia virus capping enzyme-vaccinia polymerase
interaction (13). Although several of the subunits of
vaccinia virus RNA polymerase are structurally homologous to those of
pol II, the viral enzyme has no equivalent of the CTD. In fact, the
vaccinia virus capping enzyme is unable to bind to CTD-PO4
in vitro under conditions permissive for CTD-PO4 binding by
cellular capping enzymes (34).
In light of these observations, we envisioned a scenario whereby
vaccinia virus capping enzyme might be made to function in yeast if it
could be correctly targeted to the pol II elongation complex. To
accomplish this targeting, we engineered a chimeric capping enzyme
gene, vD1(1-545)-MCE1(211-597), encoding a product in
which the vaccinia virus triphosphatase-guanylyltransferase is fused to
the C-terminal guanylyltransferase domain of the mammalian capping
enzyme. We showed recently that mammalian guanylyltransferase can act
as chaperone in cis for a catalytic domain of yeast
triphosphatase Cet1p that lacks the ability to bind to Ceg1p
(27). We also found that mammalian guanylyltransferase can
target Cth1p, an S. cerevisiae RNA triphosphatase not
normally involved in capping, and thereby convert it into a cap-forming
enzyme in vivo (37). These results suggested that the
mammalian guanylyltransferase can be used as a vehicle to deliver
heterologous proteins to the pol II transcription elongation complex in vivo.
The instructive finding was that either cet1
or
ceg1
cells transformed with the
vD1(1-545)-MCE1(211-597) fusion gene on a 2µm
TRP1 plasmid readily gave rise to 5-FOA-resistant colonies (Fig. 1A and B). Indeed, vD1(1-545)-MCE1(211-597)
complemented the growth of a yeast cet1
ceg1
strain in
which the yeast triphosphatase and guanylyltransferase were both
deleted (Fig. 1C). vD1(1-545)-MCE1(211-597) cells grew well
on rich medium at either 30 or 37°C (the latter being the natural
growth temperature for vaccinia virus in the mammalian host). The
colony size of vD1(1-545)-MCE1(211-597) cells on rich medium
was similar to that of MCE1 cells (not shown). We conclude
that vaccinia virus capping enzyme is functional in yeast when it is
targeted appropriately to the yeast transcription complex.
Vaccinia virus guanylyltransferase is active in yeast.
vD1(1-549)-MCE1(211-597) cells contain a single source of
RNA triphosphatase activity derived from the vaccinia virus component of the fusion protein, but they contain two potential
guanylyltransferase activities: one from the N-terminal vaccinia virus
domain and one from the C-terminal mammalian domain. In order to
determine whether the vaccinia virus guanylyltransferase could sustain
cell growth when it is the only guanylyltransferase present, we
introduced an inactivating missense mutation into the mouse
guanylyltransferase domain. RNA guanylyltransferases are structurally
and mechanistically conserved among fungi, mammals, and DNA viruses.
The signature features of the guanylyltransferases are a two-step
ping-pong reaction mechanism of nucleotidyl transfer through a covalent enzyme-(lysyl-N)-GMP intermediate (49). In the
first step, a lysine nucleophile on the enzyme attacks the
phosphorus of GTP to form the covalent intermediate and expel
pyrophosphate. In the second step, a nonbridging
phosphate oxygen
of diphosphate-terminated RNA attacks the covalently bound guanylate to
form the GpppN cap. A set of six conserved peptide motifs comprises the
active site (17, 48, 56). The lysine nucleophile that
becomes covalently attached to GMP is located within motif I (KxDG).
The active-site lysine of Mce1p is Lys294. Substitution of alanine for
Lys294 abrogates the guanylyltransferase activity and precludes
complementation of ceg1
cells by mammalian capping enzyme
(24, 59, 62).
A mutant chimeric capping enzyme gene,
vD1(1-545)-MCE1(211-597)-K294A, was cloned into the 2µm
TRP1 vector and tested for activity in yeast by plasmid
shuffle. Inactivation of the mammalian guanylyltransferase had no
effect on the ability of the fusion protein to support the growth of
cet1
cells (Fig. 2A),
ceg1
cells (Fig. 2B), or doubly deleted cet1
ceg1
cells (Fig. 2C). We conclude that (i) vaccinia virus
capping enzyme is functional in yeast as the sole source of RNA
triphosphatase and guanylyltransferase activities and (ii) the mutant
mammalian domain can serve as a vehicle for targeting of the viral
capping enzymes without playing a catalytic role in cap synthesis.

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FIG. 2.
Mutational analysis of the vD1(1-545)-MCE1(211-597)
fusion defines residues in vaccinia virus capping enzyme required for
cap formation in vivo in yeast. The polypeptides encoded by the
"wild-type" (WT) fusion gene vD1(1-545)-MCE1(211-597) and mutant
alleles vD1(E37A), vD1(R77K), vD1(E192A), and MCE1(K294A) are depicted
as horizontal bars with the N termini at the left and the C termini at
the right. The positions of residues mutated in the vaccinia virus RNA
triphosphatase subdomain (E37, R77, and E192) and the mouse
guanylyltransferase domain (K294) are indicated. Complementation of the
yeast cet1 , ceg1 , and cet1
ceg1 strains by the fusion genes on 2µm TRP1
plasmids was tested by plasmid shuffle as described for Fig. 1.
Trp1+ isolates were streaked on agar medium containing
5-FOA. The plates were photographed after incubation for 4 days at
30°C.
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In vivo effects of mutations in the putative active site of
vaccinia virus RNA triphosphatase.
Two distinct classes of
eukaryotic RNA triphosphatases have been described. The RNA
triphosphatases of mammals and other metazoan species belong to a
superfamily of phosphatases that act via formation and hydrolysis of a
covalent enzyme-(cysteinyl-S-)-phosphate intermediate (24, 52, 58). The metazoan RNA triphosphatase reaction
requires no metal cofactor. In fact, metazoan RNA triphosphatases are
inhibited by divalent cations. In contrast, the RNA triphosphatases of
DNA viruses (poxviruses and baculoviruses), the budding yeast S. cerevisiae, and the pathogenic fungus Candida albicans
are strictly dependent on a divalent cation cofactor (14, 21, 26,
38, 51). The viral-fungal triphosphatase family is defined by
three conserved collinear motifs (A, B, and C) that include clusters of
acidic and basic amino acids that are essential for catalytic activity (21, 37) (Fig. 3). Five
essential residues within these motifs were initially uncovered by
alanine scanning mutagenesis of the vaccinia virus RNA triphosphatase
(60, 61). Single alanine substitutions for residues Glu37,
Glu39, Arg77, Glu192, and Glu194 of vD1(1-545)p reduced triphosphatase
activity by two to three orders of magnitude without affecting the
guanylyltransferase activity of the mutant proteins (60).

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FIG. 3.
Purification of wild-type and mutated versions of
vaccinia virus D1(1-545)p. Conserved motifs A, B, and C of the RNA
triphosphatases of vaccinia virus (vD1), Shope fibroma virus (SFV),
molluscum contagiosum virus (MCV), Melanoplus sanguinipes
entomopoxvirus (EPV), Yaba monkey tumor virus (YMV), African swine
fever virus (ASF), Autographa californica baculovirus
(Lef4), S. cerevisiae (Cth1 and Cet1), and C. albicans (CaCet1) are aligned in the top panel. Vaccinia virus D1
residues that are conserved in the other proteins are shaded. The five
amino acids in vD1(1-545)p that were found by alanine scanning to be
essential for triphosphatase activity are indicated by asterisks.
Protein purification is shown in the bottom panel. Aliquots (0.5 µg)
of the phosphocellulose preparations of recombinant wild-type (WT)
vD1(1-545) and the indicated mutant proteins were electrophoresed
through a 10% polyacrylamide gel containing 0.1% SDS. Polypeptides
were visualized by staining with Coomassie Blue dye. The positions and
sizes (in kilodaltons) of marker proteins are indicated on the left.
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Three of the triphosphatase-inactivating mutations in motifs A, B, and
C (E37A, R77A, and E192A) were introduced into the chimeric capping
enzyme vD1(1-545)-Mce1(211-597)p, and their in vivo effects were tested
by plasmid shuffle (Fig. 2). The E37A, R77A, and E192A alleles were
incapable of complementing the growth of cet1
cells (Fig.
2A) but retained their activity in complementing the growth of
ceg1
cells (Fig. 2B). These results establish a correlation between the catalytic activity of vaccinia virus RNA triphosphatase in vitro and its function in vivo. The findings support
the hypothesis that motifs A, B, and C comprise the triphosphatase active site.
Conservative mutations of the active site of vaccinia virus RNA
triphosphatase.
We hypothesized previously that the glutamates in
vaccinia virus motifs A and C facilitate catalysis by coordinating the
essential divalent cation(s) (60, 61). The recently reported
crystal structure of the S. cerevisiae RNA triphosphatase
revealed that the glutamates in motif A and motif C do indeed comprise
the metal-binding site of Cet1p (28). Mutational analysis
showed that the glutamates are essential for Cet1p triphosphatase
activity, and other studies indicate that their equivalents in motifs A
and C of the C. albicans RNA triphosphatase CaCet1p
(38) and baculovirus LEF4 (26) are also essential
for catalysis.
The expectation is that if an acidic side chain is critical for metal
binding, then replacement of a metal-binding glutamate by glutamine
would have a significant effect on triphosphatase activity. Therefore,
we tested the effects of conservative substitutions in residues Glu37,
Glu39, Glu192, and Glu194 on vD1(1-545)p RNA triphosphatase activity in
vitro. Each position was changed to glutamine and aspartic acid. The
mutant proteins were expressed in E. coli as His-tagged
fusions and purified from soluble bacterial extracts by Ni-agarose and
phosphocellulose column chromatography. SDS-polyacrylamide gel
electrophoresis analysis of the phosphocellulose preparations revealed
a predominant 60-kDa polypeptide corresponding to vD1(1-545)p (Fig. 3).
The guanylyltransferase activity of each of the phosphocellulose
preparations was demonstrated by label transfer from
[
-32P]GTP to the enzyme to form a 60-kDa covalent
enzyme-GMP complex (not shown). The fact that the mutant enzymes
retained guanylyltransferase activity indicated that the conservative
mutations did not affect the global folding of the vaccinia virus protein.
The RNA triphosphatase activities of the phosphocellulose preparations
of wild-type and mutant vD1(1-545)p were assayed by the release of
32Pi from
-32P-labeled poly(A)
during a 5-min incubation in the presence of magnesium chloride. The
specific activities of the vD1(1-545)p mutants were calculated from the
slopes of the titration curves in the linear range of enzyme
dependence. The activities of the mutants were normalized to that of
the wild-type enzyme and are shown in Table
1. The salient findings were that the
E37Q, E39Q, and E192Q mutations abolished the RNA triphosphatase
activity of vaccinia virus capping enzyme, whereas the E194Q protein
displayed nearly wild-type specific activity (Table 1). Introduction of aspartic acid at positions 37 and 39 restored RNA triphosphatase activity to 29 and 10% of the wild-type level, respectively (Table 1).
We surmise that the negative charges on the two positions in motif A
are critical for catalysis and that shortening the distance from the
main chain to the carboxylate has a modest negative effect on activity.
Remarkably, the introduction of aspartic acid in lieu of Glu192 in
motif C elicited a twofold increase in RNA triphosphatase activity
compared to wild-type vD1(1-545)p. Thus, position 192 must be acidic,
but the shorter linker arm of aspartate is preferable to the native
glutamate. These data support a direct role for Glu37, Glu39, and
Glu192 in coordinating the metal, and they imply some steric
flexibility in the metal-binding site of vaccinia virus triphosphatase.
Note that RNA triphosphatase activity was also enhanced relative to
that of the wild type when Glu194 in motif C was replaced by aspartic
acid. Given that the E194A mutation abolished activity (60),
while the E194Q and E194D changes restored activity (Table 1), we infer
that hydrogen bonding rather than electrostatic interactions of this
residue are critical for catalysis.
Effects of conservative mutations on metal-dependent ATPase
activity.
The metal-dependent viral and fungal RNA triphosphatases
also have an intrinsic capacity to hydrolyze nucleoside triphosphates to nucleoside diphosphates and inorganic phosphate in the presence of a
divalent cation cofactor
either manganese or cobalt in the case of the
yeast and baculovirus enzymes and either manganese, cobalt, or
magnesium in the case of vaccinia virus capping enzyme (14, 21,
26, 37, 38, 45, 51). The nucleoside triphosphatase activities of
wild-type and mutant vD1(1-545)p proteins were assayed by the release
of 32Pi from [
-32P]ATP (1 mM)
during a 30-min reaction in the presence of 10 mM magnesium chloride
(the optimal magnesium concentration for ATP hydrolysis [data not
shown]). The relative specific activities of the vD1(1-545)p motif A
and C mutants (normalized to the wild-type activity) are shown in Table
1. The motif A mutational effects on magnesium-dependent ATPase
generally mirrored the effects on RNA triphosphatase, insofar as ATPase
activity was abolished by introducing glutamine in place of Glu37 and
Glu39. However, the extent of restoration of ATPase activity when
aspartic acid was introduced at positions 37 and 39 was about an order
of magnitude less than it was for RNA triphosphatase (Table 1). Thus,
ATP hydrolysis was more stringent in its dependence on glutamates in
motif A. In motif C, a glutamine at position 192 eliminated ATPase
activity, which was restored to greater-than-wild-type levels when an
aspartic acid was present at this position. This was the same
mutational effect seen for RNA triphosphatase. At position Glu194, the
level of residual activity with glutamine was much lower for ATPase
(9%) than for RNA triphosphatase (81%). Similarly, the E194D change,
although it restored activity compared to E194Q, had a relatively
greater impact on ATPase than on RNA triphosphatase.
Activation of the ATPase of vaccinia virus capping enzyme by manganese
and cobalt has not been well characterized. Optimal conditions for ATP
hydrolysis by vD1(1-545)p in the presence of MnCl2 or
CoCl2 were established by varying the divalent cation concentration and pH of the reaction mixture. ATPase activity at pH 8 was optimal at 1 mM MnCl2 or 2 mM CoCl2 (data
not shown). Remarkably, the pH optimum for ATP hydrolysis was strongly
influenced by the choice of divalent cation cofactor. We assayed ATPase
in bis-Tris-propane (BTP) buffers at pH 5.5 to 10 in the presence of 10 mM MgCl2, 1 mM MnCl2, or 2 mM CoCl2
(Fig. 4). Magnesium-dependent ATPase was
optimal at pH 8 to 8.5 and was virtually nil at pH 6 (Fig. 4A).
Manganese-dependent ATPase was optimal at pH 7.5 and minimal at pH 6. In contrast, cobalt-dependent ATPase peaked at pH 6.5 (Fig. 4C). Cobalt
supported considerable activity at pH 6 (unlike magnesium and
manganese) but was inactive in BTP buffer at pH 8 to 8.5, which is the
favored pH range of BTP buffer for magnesium and manganese cofactor
activity. We observed similar pH optima when Tris-acetate and Tris-HCl
buffers were tested in the range of pH 5.5 to 9.5, except that
cobalt-dependent ATPase was less sensitive to alkaline pH conditions in
Tris-HCl buffer than in BTP buffer (Fig. 4C). The molecular basis for
the distinctive acid shift in the pH dependence of ATP hydrolysis in
cobalt is unclear.

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|
FIG. 4.
Effect of pH on metal-dependent ATP hydrolysis by
vaccinia virus D1(1-545)p. Reaction mixtures (10 µl) containing 50 mM
buffer (either BTP [pH 5.5, 6.0, 6.5, 7.0, 7.5, 8.0, 8.5, 9.0, 9.5, or
10.0] or Tris [Tris-acetate at pH 5.5, 6.0, 6.5, or 7.0 or Tris-HCl
at pH 7.5, 8.0, 8.5, 9.0, or 9.5]), 5 ng of vD1(1-545)p, 1 mM
[ -32P]ATP, and either 10 mm MgCl2 (A), 1 mM MnCl2 (B), or 2 mM CoCl2 (C) were incubated
for 30 min at 37°C. The reaction products were analyzed by
polyethyleneimine-cellulose thin-layer chromatography (61).
ATPase activity is plotted as a function of pH.
|
|
The effects of motif A and C mutations on the manganese- and
cobalt-dependent ATPase activities of vD1(1-545)p at pH 8 and 6.5, respectively, are shown in Table 1. The vaccinia virus enzyme displayed
a stringent requirement for glutamate at positions 37 and 39 to support
ATP hydrolysis in cobalt and manganese; there was no recovery of
function when these positions were occupied by aspartic acid. In motif
C, the E194Q and E194D changes elicited more severe defects in
manganese- and cobalt-dependent ATPase than they did on activity in
magnesium (Table 1). The same was true of the E192D mutation.
 |
DISCUSSION |
Viral RNA capping enzymes are attractive targets for antiviral
drugs because the properties of the viral enzymes are often different
from those of the host cell enzymes. This is especially so for the
metal-dependent RNA triphosphatases of DNA viruses and double-stranded
RNA viruses (5, 14, 26, 35, 60), which are mechanistically
and structurally unrelated to the metal-independent cellular RNA
triphosphatase. The fact that metazoan species encode no obvious
homologues of the viral RNA triphosphatases suggests that an inhibitor
of viral RNA triphosphatase should have selectivity for the viral
pathogen and minimal effect on the host organism. The yeast-based
genetic system we describe here provides a valuable tool for basic and
applied studies of viral capping enzymes. We show that vaccinia virus
RNA triphosphatase and vaccinia virus guanylyltransferase can function
in lieu of the essential yeast enzymes Cet1p and Ceg1p, provided that
the vaccinia virus protein is fused to the mammalian capping enzyme,
which targets the viral protein to the pol II elongation complex.
Hence, the capping functions of the viral enzyme can be studied in vivo
independent of ancillary roles of the viral protein in the context of
virus replication. We have used this system to establish a concordance
between mutational effects on vaccinia virus RNA triphosphatase
activity in vitro and in vivo.
We have illuminated structure-activity relationships for four essential
amino acids of vaccinia virus RNA triphosphatase. Three essential
glutamates, Glu37 and Glu39 in motif A and Glu192 in motif C, cannot be
replaced by glutamine, suggesting that these side chains comprise the
metal-binding site of vaccinia virus triphosphatase. These results are
consistent with insights gained from the crystal structure of yeast RNA
triphosphatase Cet1p complexed with the divalent cation manganese.
Cet1p adopts a novel enzyme fold whereby an antiparallel eight-strand
barrel forms a hydrophilic "triphosphate tunnel" that is
topologically closed (28). Multiple acidic side chains point
into the tunnel cavity, including the essential glutamates of motifs A
and C. The interior of the tunnel contains a single sulfate ion
coordinated by basic side chains projecting into the tunnel. Insofar as
sulfate is a structural analog of phosphate, we surmise that the side
chain interactions of the sulfate reflect contacts made by the enzyme
with the
phosphate of the triphosphate-terminated RNA and
nucleoside triphosphate substrates. A manganese ion within the tunnel
cavity is coordinated with octahedral geometry to the sulfate, to the
side chain carboxylates of the two essential glutamates in motif A, and
to one of the glutamates in motif C. Glutamine substitutions for any of
the three Cet1p glutamates that directly coordinate the manganese result in a complete loss of catalytic activity (37). By
analogy with Cet1p, we propose that Glu37, Glu39, and Glu192 of
vaccinia virus capping enzyme interact directly with a divalent cation. The active site of Cet1p may be less flexible than that of vD1(1-545)p, insofar as none of the three metal-binding glutamates of Cet1p could be
functionally replaced by aspartic acid.
A second essential glutamate in motif C of Cet1p coordinates a water
molecule bound to manganese. We invoke a similar role for the Glu194 in
motif C of vaccinia virus capping enzyme. Coordination of solvent by
polar interactions of vaccinia virus side chain 194 would be consistent
with the retention of catalytic function by the E194Q mutant. Whereas
glutamine may suffice for coordinating solvent bound to magnesium,
phosphohydrolase activity in manganese and cobalt was strictly
dependent on a glutamate side chain. Spatial differences in the
coordination spheres of these metals may account for the distinct
mutational effects with different metal cofactors.
Motifs A and C are located within
strands of yeast Cet1p that are
widely separated in the primary structure but closely approximated in
the tertiary structure (28). Motifs A and C are located on
the tunnel "floor" that abuts the globular core of the protein. In
motifs A and C of the fungal RNA triphosphatases, alternating charged
side chains are interdigitated with alternating aliphatic or aromatic
side chains (Fig. 3). This sequence pattern is reprised in motifs A and
C of the poxvirus, African swine fever virus, and baculovirus RNA
triphosphatases, suggesting that the metal-binding residues of the
viral enzymes may also be located within
strands.
Although we propose that yeast and vaccinia virus RNA triphosphatases
share a common metal-binding site, we suspect that the active sites of
the yeast and viral enzymes may adopt different tertiary structures,
i.e., that the vaccinia virus active site does not residue within an
enclosed tunnel, because the motif A and C glutamates of vaccinia virus
D1(1-545)p are accessible to limited digestion with V8 protease
(60). A definitive assessment of the similarities between
fungal and viral RNA triphosphatases will hinge on successful
crystallization of vD1(1-545)p.
Finally, the availability of isogenic yeast strains containing
mammalian versus viral capping systems provides a means of drug
discovery aimed at blocking viral cap formation. For example, any
compound that is selectively cytotoxic to the
vD1(1-549)-MCE1(211-597)-K294A strain but not to the
MCE1 strain is a strong candidate for being a specific
inhibitor of vaccinia virus capping. Identification of effective
antipoxviral drugs is a reasonable goal in light of the high incidence
of molluscum contagiosum infection as a sequela of AIDS and the
potential threat of smallpox as a biological weapon. We anticipate
extending the yeast complementation approach to the methyltransferase
component of vaccinia virus capping enzyme (19, 32, 33) with
the goal of generating yeast strains in which the entire capping
apparatus is of viral origin. It will also be of interest to apply the
yeast complementation test to the capping enzymes of other viruses that
affect human health, e.g., rotavirus (7, 40). Genetic
complementation by viral polypeptides fused to the mammalian delivery
vehicle also provides a means to identify the capping enzymes of
viruses in cases where the biochemical activities are refractory to purification.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Molecular
Biology Program, Sloan-Kettering Institute, 1275 York Ave., New York,
NY 10021. Phone: (212) 639-7145. Fax: (212) 717-3623. E-mail:
s-shuman{at}ski.mskc.org.
 |
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Journal of Virology, June 2000, p. 5486-5494, Vol. 74, No. 12
0022-538X/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.
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