Trypanosoma brucei RNA Triphosphatase: Anti-Protozoal Drug Target

and Guide to Eukaryotic Phylogeny

C. Kiong Ho and Stewart Shuman*

Molecular Biology Program

Sloan-Kettering Institute

New York, NY 10021 USA

*Corresponding author Tel: (212) 639-7145 Fax: (212) 717-3623

E-mail: s-shuman@ski.mskcc.org

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ABSTRACT

The mRNA capping apparatus of the protozoan parasite Trypanosoma brucei consists of

separately encoded RNA triphosphatase and RNA guanylyltransferase enzymes. The

triphosphatase TbCet1 is a member of a new family of metal-dependent phosphohydrolases that

includes the RNA triphosphatases of fungi and the malaria parasite Plasmodium falciparum. The

protozoal/fungal enzymes are structurally and mechanistically unrelated to the RNA

triphosphatases of metazoans and plants. These results highlight the potential for discovery of

broad-spectrum antiprotozoal and antifungal drugs that selectively block the capping of

pathogen-encoded mRNAs. We propose a scheme of eukaryotic phylogeny based on the

structure of RNA triphosphatase and its physical linkage to the guanylyltransferase component of

the capping apparatus.

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INTRODUCTION

Kinetoplastid protozoan parasites of the genus Trypanosoma are major zoonotic pathogens of

humans. T. cruzi is the cause of Chagas disease, endemic in South America and affecting some

20 million people (1, 2). T. brucei causes seeping sickness in Africa, which has been resurgent in

recent years and is estimated to affect 500,000 people (3, 4). The drugs currently in use to treat

trypanosomiasis are old, ineffective and toxic. There is an acute need for new therapeutic

approaches, and it is anticipated that candidate drug targets will be uncovered by sequencing

Typanosoma genomes. The most promising targets are gene products or metabolic pathways that

are essential for all stages of the parasite life cycle, but either absent or fundamentally different

in the human host. Such targets can be identified either by whole-genome comparisons or by

directed analyses of specific cellular transactions.

Here we analyze the mRNA capping apparatus of T. brucei. The m7GpppN cap structure (cap

0) is a defining feature of eukaryotic mRNA and is required for mRNA stability and efficient

translation. The cap is formed by three enzymatic reactions: the 5' triphosphate end of the

nascent pre-mRNA is hydrolyzed to a diphosphate by RNA triphosphatase; the diphosphate end

is capped with GMP by RNA guanylyltransferase; and the GpppN cap is methylated by RNA

(guanine-N7) methyltransferase (5). Each of the mRNA capping enzymes is essential for cell

growth in budding yeast.

Although the three capping reactions are universal in eukaryotes, there is a surprising

diversity in the genetic organization of the cap-forming enzymes in different taxa as well as a

complete divergence in the structure and catalytic mechanism of the RNA triphosphatase

component as one moves from lower to higher eukaryotic species (5). Metazoans and plants

encode a two-component capping system consisting of a bifunctional triphosphatase-

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guanylyltransferase polypeptide and a separate methyltransferase polypeptide, whereas fungi and

the microsporidian parasite Encephalitozoon cuniculi encode a three-component system

consisting of separate triphosphatase, guanylyltransferase, and methyltransferase gene products

(5, 6). The primary structures and biochemical mechanisms of the fungal and mammalian

guanylyltransferases and cap methyltransferases are conserved. However, the atomic structures

and catalytic mechanisms of the fungal and mammalian RNA triphosphatases are completely

different (7, 8). Thus, it has been suggested that RNA triphosphatase is a promising target for

antifungal drug discovery (7).

Relatively little is known about the organization of the mRNA capping apparatus in the many

other branches of the eukaryotic phylogenetic tree, especially the protozoa. We recently

identified the guanylyltransferase and triphosphatase enzymes from the malaria parasite

Plasmodium falciparum and we showed that the Plasmodium triphosphatase is structurally and

mechanistically similar to the metal-dependent fungal enzymes (9). An evolutionary connection

between Plasmodia and fungi had not been appreciated in previous schemes of molecular

taxonomy.

Trypanosome mRNAs contain a unique hypermodified “cap 4” structure, which is derived

from the standard m7GpppN cap by cotranscriptional methylation of seven sites within the first

four nucleosides of the spliced leader RNA (10, 11). Although cap formation is (in principle) an

attractive target for drug treatment of trypanosomiasis, the pathway of cap synthesis has not been

fully determined. An RNA guanylyltransferase has been characterized in Trypanosoma and

Crithidia (12), but the triphosphatase and several methyltransferase components have not been

identified. The T. brucei guanylyltransferase is mechanistically and structurally related to the

guanylyltransferases from all other eukaryal species (and thus is not an especially attractive drug

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target). However, the 586-amino acid T. brucei guanylyltransferase contains a 250-amino acid

N-terminal extension not found in fungal or metazoan guanylyltransferases; it has been

speculated that this extra domain (also present in Crithidia guanylyltransferase) might contribute

the triphosphatase activity during cap synthesis (12).

Here we report the identification of the triphosphatase component of the T. brucei capping

apparatus as the product of a separate gene, which we named TbCET1. The TbCet1 enzyme is

structurally and mechanistically related to the fungal and Plasmodium RNA triphosphatases.

Indeed, TbCet1 is active in cap formation in vivo when expressed in budding yeast. We discuss

the pharmacological and evolutionary implications of these results.

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EXPERIMENTAL PROCEDURES

Yeast expression vector for T. brucei RNA triphosphatase

A DNA fragment containing the TbCET1 ORF was amplified by polymerase chain reaction

from T. brucei genomic DNA (a gift of Vivian Bellofatto, UMDNJ) using oligonucleotide

primers designed to introduce an NcoI restriction site at the predicted translation start codon and

a BamHI site 3' of the predicted stop codon. The PCR product was digested with NcoI and

BamHI and cloned into the yeast vector pYX132 (CEN TRP1). TbCET1 expression is under the

transcriptional control of the yeast TPI1 promoter. The nucleotide sequence of the T. brucei

DNA insert was determined and was found to be identical to the genomic sequence (Genbank

AC091330).

Expression and purification of recombinant TbCet1.

The TbCET1 ORF was excised from pYX-TbCET1 with NcoI and BamHI, and the 5’

overhangs were filled in with T4 DNA polymerase. The blunt DNA fragment was inserted into

the filled-in BamHI site of pET28-His/Smt3 (a gift of Chris Lima, Cornell Medical College) so

as to fuse the ORF in-frame to N-terminal His6/Smt3. pET-His/Smt3-TbCet1 was transformed

into Escherichia coli BL21-CodonPlus(DE3). A 200-ml culture amplified from a single

transformant was grown at 37°C in Luria-Bertani medium containing 60 µg/ml kanamycin and

100 µg/ml chloramphenicol until the A600 reached 0.5. The culture was adjusted to 2% ethanol

and 0.4 mM IPTG and then incubated at 17˚C for 18 h. Cells were harvested by centrifugation

and the pellet was stored at -80°C. All subsequent procedures were performed at 4°C. Thawed

bacteria were resuspended in 10 ml of buffer A (50 mM Tris-HCl [pH 7.5], 0.25 M NaCl, 10%

sucrose). Cell lysis was achieved by addition of lysozyme and Triton X-100 to final

concentrations of 100 µg/ml and 0.1%, respectively. The lysate was sonicated to reduce viscosity

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and insoluble material was removed by centrifugation. The soluble extract was applied to a 1-ml

column of Ni-NTA-agarose resin (Qiagen) that had been equilibrated with buffer A containing

0.1% Triton X-100. The column was washed with 5 ml of the same buffer and then eluted step-

wise with 2-ml aliquots of buffer B (50 mM Tris-HCl [pH 8.0], 0.25 M NaCl, 10% glycerol,

0.05% Triton X-100) containing 5, 50, 100, 200, and 500 mM imidazole. The polypeptide

compositions of the column fractions were monitored by SDS-PAGE. The 45 kDa recombinant

His/Smt3-TbCet1 polypeptide was recovered in the 50 and 100 mM imidazole fractions. The 100

mM eluate fraction (containing 3 mg of protein) was used to characterize the triphosphatase

activity of TbCet1.

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RESULTS

Identification of a candidate T. brucei RNA triphosphatase TbCet1

Metazoan and plant RNA triphosphatases belong to the cysteine phosphate enzyme

superfamily, which is defined by the conserved phosphate-binding loop motif HCxxxxxR(S/T).

Mammalian RNA triphosphatase catalyzes a two-step ping-pong phosphoryl transfer reaction in

which the conserved cysteine of the signature motif attacks the γ phosphorus of triphosphate-

terminated RNA to form a covalent protein-cysteinyl-S-phosphate intermediate and expel the

diphosphate RNA product (8). The covalent phosphoenzyme intermediate is hydrolyzed to

liberate inorganic phosphate. The reaction does not require a divalent cation cofactor.

In contrast, the RNA triphosphatases of fungal species such as Saccharomyces cerevisiae,

Candida albicans, and Schizosaccharomyces pombe are strictly dependent on a divalent cation.

The fungal enzymes belong to a new family of metal-dependent phosphohydrolases that

embraces the triphosphatase components of the poxvirus, baculovirus, phycodnavirus, and P.

falciparum mRNA capping systems (13-20). The signature biochemical property of this enzyme

family is the ability to hydrolyze nucleoside triphosphates to nucleoside diphosphates and

inorganic phosphate in the presence of either manganese or cobalt. The defining structural

features of the metal-dependent RNA triphosphatases are two glutamate-rich motifs (β1 and β11

in Fig. 1) that are required for catalysis by every family member and which comprise the metal-

binding site. The crystal structure of the S. cerevisiae RNA triphosphatase Cet1 revealed a novel

tertiary structure in which the active site is situated within a topologically closed hydrophilic

tunnel composed of 8 antiparallel β strands (7). The β strands comprising the tunnel walls are

displayed over the Cet1 protein sequence in Fig. 1. Each of the 8 strands contributes at least one

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functional constituent of the active site (13, 16, 21). The 15 individual side chains within the

tunnel that are important for Cet1 function in vitro and in vivo are denoted by dots in Fig. 1.

We searched for a candidate RNA triphosphatase in T. brucei by querying the Microbial

Genomes Database (www.ncbi.nlm.nih.gov/Microb_blast) for proteins related to the S. pombe

RNA triphosphatse Pct1. We thereby identified a putative RNA triphosphatase gene on T. brucei

chromosome III (DNA sequence in Genbank accession AC091330) that encodes a 252-amino

acid polypeptide (shown in Fig. 2A) with primary structural similarity to the catalytic domains of

fungal, viral, and Plasmodium RNA triphosphatases (Fig. 1). We named this T. brucei gene

product TbCet1 (Capping Enzyme Triphosphatase). TbCet1 is slightly larger than the “minimal”

RNA triphosphatases of Chlorella virus PBCV-1 (cvRtp1; 193-amino acids) and

Encephalitozoon cuniculi (EcCet1; 221-amino acids), but is smaller than the RNA

triphosphatases of P. falciparum (Prt1; 596-amino acids), S. cerevisiae (Cet1; 549-amino acids),

C. albicans (CaCat1; 520 amino acids), and S. pombe (Pct1; 303 amino acids). Cet1 and CaCet1

contain large non-essential N-terminal extensions (22, 23) that are missing from the T. brucei

protein.

TbCet1 includes the two glutamate-rich metal-binding motifs characteristic of the fungal,

viral, and Plasmodium triphosphatases, plus putative homologs of all of the other β strands that

comprise the active site tunnel of Cet1 (Fig. 2). Indeed, all of the fifteen hydrophilic amino acids

that are essential for catalysis by Cet1 are conserved in the T. brucei polypeptide, which

suggested strongly that TbCet1 is the RNA triphosphatase component of the trypanosome

mRNA capping apparatus.

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Metal-Dependent Triphosphatase Activity of TbCet1

The TbCET1 gene was cloned into a T7 RNA polymerase-based pET vector so as to fuse the

protein in-frame with an N-terminal His6-Smt3 tag (24). The recombinant TbCet1 protein was

purified from a soluble bacterial extract by adsorption to Ni-agarose and elution with 50 and 100

mM imidazole (Fig. 1B). We found that recombinant TbCet1 catalyzed the release of 32Pi from

[γ32P]ATP in the presence of manganese and that the extent of ATP hydrolysis was proportional

to enzyme concentration; the reaction proceeded to completion at saturating enzyme (Fig. 1C).

We calculated a specific activity of 1.3 nmol 32Pi formed per ng of TbCet1 during a 15 min

reaction, which corresponded to a turnover number of 65 s-1. There was no detectable ATPase

activity in the absence of a divalent cation (Fig. 3A). Hydrolysis of 0.2 mM ATP was optimal at

2 mM MnCl2 and declined slightly at 5-10 mM MnCl2 (Fig. 3A). Activity with magnesium (10

mM) was 6% of that observed at 2 mM managanese (Fig. 3A). Specificity for NTP hydrolysis in

the presence of manganese is characteristic of the fungal-type RNA triphosphatase family.

Triphosphatase activity was optimal at pH 7.5 in Tris buffer and declined sharply as the pH

was lowered to 5 or increased to 9 (Fig. 3B). The rate of release of 32Pi from [γ32P]ATP was

nearly identical to the rate of conversion of [α32P]ATP to [α32P]ADP in a parallel reaction

mixture containing the same concentration of TbCet1 (Fig. 3C). We detected no formation of

[α32P]AMP during the reaction. Hence, we conclude that TbCet1 catalyzes the hydrolysis of

ATP to ADP and Pi. TbCet1 also converts [α32P]GTP to [α32P]GDP (not shown).

RNA triphosphatase activity of TbCet1 in vivo

We cloned the TbCET1 gene into a yeast CEN TRP1 plasmid under the transcriptional

control of the constitutive yeast TPI1 promoter. The function of the TbCET1 gene was first tested

by plasmid shuffle in yeast cet1 cells that contain CET1 on a CEN URA3 plasmid. The cet1

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strain is unable to form colonies on medium containing 5-fluoroorotic acid (5-FOA), a drug that

selects against the URA3 plasmid, unless it is transformed with a second plasmid bearing CET1

or a functional homolog from another source. We found that TbCET1 was unable to complement

growth of cet1 on 5-FOA (Fig. 4A). This negative result was not surprising, given that TbCet1

lacks an essential domain of Cet1 that mediates its binding to the yeast guanylyltransferase Ceg1

(25). Ceg1 is exquisitely labile and stabilized against inactivation by binding to Cet1 (26). The

requirement for the guanylyltransferase binding and stabilization functions of Cet1 can be

circumvented in vivo by replacing the endogenous S. cerevisiae guanylyltransferase with an

inherently stable guanylyltransferase, e.g., Mce1(211-597), the guanylyltransferase domain of

mammalian capping enzyme (26, 27).

Thus, the function of the TbCET1 gene was tested again by plasmid shuffle in yeast cet1

ceg1 cells that contain CET1 on a CEN URA3 plasmid and MCE1(211-597) on a CEN ADE2

plasmid. We found that TbCET1 now supported growth on 5-FOA, whereas cells transformed

with the TRP1 vector alone did not (Fig. 4B). The cells expressing TbCET1 plus MCE1(211-597)

grew as well as MCE1 cells on rich medium (YPD agar) at 25, 30, and 37˚C (not shown). These

results show that TbCET1 encodes a biologically active RNA triphosphatase.

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DISCUSSION

Kinetoplast mRNAs acquire their 5’ caps via trans-spicing of an RNA leader sequence

containing the hypermethylated cap 4 structure (10, 11). The presence of a distinctive N-terminal

domain in the RNA guanylyltransferases of T. brucei and C. fasciculata, which contains a

putative nucleotide-binding motif, raised the possibility that the N-terminal segment comprises

the triphosphatase component of the capping apparatus (12), but there is as yet no biochemical

evidence for a triphosphatase activity associated with the T. brucei guanylyltransferase. Here we

demonstrated that T. brucei encodes a separate RNA triphosphatase TbCet1, which is structurally

and mechanistically akin to the metal-dependent RNA triphosphatases of fungi and the malaria

parasite P. falciparum. The finding that TcCet1 complements the cet1 mutation in budding

yeast confirms that the T. brucei protein can function as a cap-forming enzyme in vivo.

TbCet1 is an attractive therapeutic target for trypanosomiasis because: (i) the active site

structure and catalytic mechanism of TbCet1 is completely different from the RNA

triphosphatase domain of the metazoan capping enzyme and (ii) metazoans encode no

identifiable homologs of the fungal or protozoal RNA triphosphatases. Thus, a mechanism-based

inhibitor of TbCet1 should be highly selective for the kinetoplastid parasite and have minimal

effect on the human host. Given the central role of the mRNA cap in eukaryotic gene expression,

a drug that targets TbCet1 would presumably be effective at all stages of the parasite’s life cycle.

Also, the structural similarity between T. brucei, P. falciparum, and fungal RNA triphosphatases

raises the exciting possibility of achieving antitrypansosomal, antimalarial and antifungal activity

with a single class of mechanism-based inhibitors.

We have suggested that capping enzymes are a good focal point for considering eukaryotic

evolution because: (i) the mRNA cap structure is ubiquitous in eukarya, but absent from the

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bacterial and archaeal domains and (ii) differences in the capping apparatus between taxa will

reflect events that post-date the emergence of ancestral nucleated cells (9). We proposed a

heuristic scheme of eukaryotic phylogeny based on two features of the mRNA capping

apparatus: the structure and mechanism of the triphosphatase component (metal-dependent

“fungal” type versus metal-independent cysteine-phosphatase type) and whether the

triphosphatase is physically linked in cis to the guanylyltransferase component. By these simple

criteria, relying on fundamental differences in the same metabolic pathway, one arrives at

different relationships among taxa than those suggested by comparisons of sequence variations

among proteins that are themselves highly conserved in all eukaryotes (28).

For example, the capping-based phylogeny would place metazoans in a common lineage with

Viridiplantae (exemplified by the metaphyta Arabidopsis and the unicellular alga

Chlamydomomas reinhardtii) because all of these organisms have a cysteine-phosphatase type

RNA triphosphatase fused to their guanylyltransferase (Fig. 5). Fungi, microsporidia, Plasmodia

(which are classified as Apicomplexa along with other pathogenic parasites Toxoplasma and

Cryptosporidia), and now Trypanosoma (which are classified as Euglenozoa along with the

human parasite Leishmania) fall into a different lineage distinguished by a “Cet1-like” RNA

triphosphatase that is physically separate from RNA guanylyltransferase. In contrast, the protein

sequence variation-based scheme proposed by Baldauf et al. (28) places fungi in the same

supergroup as metazoa and puts the Apicomplexa nearer to plants.

Assuming that multicellular animals evolved from unicellular ancestors, we envision that the

three component capping system with a metal-dependent triphosphatase is the ancestral state

from which other eukarya (and their viruses) evolved (Fig. 5). We see evidence of evolution in

two directions. Certain viruses (poxviruses, baculoviruses, African swine fever virus) and fungal

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cytoplasmic episomes have acquired bifunctional capping enzymes by fusion of the ancestral

triphosphatase and guanylyltransferase genes (14, 15, 18, 19, 29). Metazoans and plants have

experienced a different gene rearrangement event that transferred a cysteine-phosphatase domain

into the same transcription unit as the guanylyltransferase, leading to creation of the

triphosphatase-guanylyltransferase fusion protein that we see today. A plausible pathway of

evolution could entail the appearance of a new cysteine phosphatase enzyme (e.g., via

duplication and mutation of one of the protein phosphatase genes present in lower eukarya) that

gained the capacity to hydrolyze an RNA 5’ phosphate instead of, or in addition to, a

phosphoprotein (Fig. 5). The model implies a “transition state” wherein an organism contained

both a metal-dependent and a cysteine-phosphatase type triphosphatase. The fusion of the

cysteine phosphatase to the guanylyltransferase presumably allowed for the loss of the Cet1-like

enzyme from the genome of the common metazoan/plant ancestor or else the divergence of the

protein to a point that it is no longer discernable as Cet1-like. The alternative explanation would

be that plants and metazoans independently experienced this gene fusion in distant branches of

the phylogenetic tree, a prospect that seems less appealing to us.

The scheme is useful in that it raises some interesting questions about missing links and the

order of events in the progression from fungal and protozoal-type to metazoan and plant-type

capping systems. It is surely oversimplified because it is based on knowledge of only a fraction

of eukaryal taxa. As more genomes are sequenced, we may encounter species that have a Cet1-

like triphosphatase fused to a guanylyltransferase, others with a cysteine-phosphatase-type RNA

triphosphatase that participates in cap formation but is physically separate from the

guanylyltransferase, and yet others that encode a novel class of RNA triphosphatase enzyme. Of

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particular interest will be to characterize the mRNA capping apparatus in the most primitive

protozoan and metazoan organisms.

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FIGURE LEGENDS

Fig. 1. Structural conservation among fungal, viral, microsporidian, and protozoan RNA

triphosphatases. The amino acid sequence of the catalytic domain of S. cerevisiae RNA

triphosphatase Cet1 is aligned to the sequences of C. albicans CaCet1, S. cerevisiae Cth1, S.

pombe Pct1, P. falciparum Prt1, E. cuniculi Cet1, Chlorella virus cvRtp1 and the newly

identified RNA triphosphatases from T. brucei (TbCet1). Gaps in the alignment are indicated by

dashes. Poly-asparagine inserts in Prt1 are omitted from the alignment and are denoted by ∆. The

β strands that form the triphosphate tunnel of ScCet1 are denoted above the sequence. Peptide

segments with the highest degree of conservation in all nine proteins are highlighted by the

shaded boxes. Hydrophilic amino that comprise the active site within the ScCet1 tunnel are

denoted by dots.

Fig. 2. Triphosphatase activity of recombinant TbCet1. (A) Sequence of the TbCet1 polypeptide.

(B) Purification of TbCet1. Aliquots (10 µl) of the soluble bacterial lysate (L), the Ni-agarose

flow-through (FT), wash (W), and the indicated imidazole eluates were analyzed by SDS-PAGE.

The fixed gel was stained with Coomassie brilliant blue dye. (C) Triphosphatase activity.

Reaction mixtures (10 µl) containing 50 mM Tris-HCl (pH 7.5), 5 mM DTT, 2 mM MnCl2, 0.2

mM [γ32P]ATP, and TbCet1 as specified were incubated for 15 min at 30°C. The reactions were

quenched by adding 2.5 µl of 5 M formic acid. Aliquots of the mixtures were applied to a

polyethyleneimine–cellulose thin layer chromatography plate, which was developed with 1 M

formic acid, 0.5 M LiCl. 32Pi release was quantitated by scanning the chromatogram with a Fujix

phosphorimager and then plotted as a function of input protein.

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Fig. 3. Characterization of T. brucei triphosphatase. (A) Divalent cation dependence. Reaction

mixtures (10 µl) containing 50 mM Tris-HCl (pH 7.5), 0.2 mM [γ32P]ATP, 2 ng of TbCet1, and

either MnCl2, or MgCl2 as specified were incubated for 15 min at 30°C. 32Pi release is plotted as

a function of divalent cation concentration. (B) pH dependence. Reaction mixtures (10 µl)

containing 50 mM Tris buffer (either Tris-acetate pH 4.5, 5.0, 5.5, 6.0, 6.5, or Tris-HCl pH 7.0,

7.5, 8.0, 8.5, 9.0, 9.5), 5 mM DTT, 2 mM MnCl2, 0.2 mM [γ32P]ATP, and 2 ng TbCet1 were

incubated for 15 min at 30°C. 32Pi release is plotted as a function of pH. (C) Kinetics. Reaction

mixtures (100 µl) containing 50 mM Tris–HCl (pH 7.5), 5 mM DTT, 2 mM MnCl2, 0.2 mM

[γ32P]ATP or [α32P]ATP, and 100 ng of TbCet1 were incubated at 30°C. Aliquots (10 µl) were

withdrawn at the times indicated and quenched immediately with formic acid. The reaction

products were analyzed by TLC. The extent of 32Pi or [32P]ADP formation (from 2 nmol of input

ATP per sample) is plotted as a function of time.

Fig. 4. TbCet1 functions as an RNA triphosphatase in vivo. (A) Yeast strain YBS20 (cet1 ) was

transformed with CEN TRP1 plasmids bearing the MCE1 or TbCET1 genes or with the CEN

TRP1 vector alone. Individual Trp+ isolates were selected and streaked on agar medium

containing 0.75 mg/ml of 5-FOA. (B) Yeast strain YBS50 (cet1 ceg1 ) was cotransformed

with a CEN ADE2 plasmid bearing MCE1(211-597) under the control of the TPI1 promoter and

a CEN TRP1 plasmid bearing either MCE1 or TbCET1 or no insert (vector). Individual Trp+

Ade+ isolates were selected and streaked on agar medium containing 0.75 mg/ml of 5-FOA. The

plates were photographed after incubation for 3 days at 30˚C.

Fig. 5. Capping enzyme-based scheme of eukaryotic phylogeny. The ancestral capping system

consists of a separately encoded metal-dependent RNA triphosphatase (TPase, blue) and

guanylyltransferase (GTase, yellow) enzymes. The metazoan and plant capping systems,

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consisting of a cysteine phosphatase-type RNA triphosphatase (TPase, red) fused to a

guanylyltransferase (GTase yellow) may have evolved via a series of intermediate steps

highlighted in the shaded boxes.

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β1 β5

β6 β7 β8 β9

β10 β11

• • •ScCet1 IELEMKFGVIIDAKGPDRVNPPVSSQCVFTE-LDAHLTPNIDASLFKELSKYIRGISE-------VTENTGKFSIIESQTRDSVYR-CaCet1 VELELKFGKIIDKRSGNRIDLNVVTECIFTDHSSVFFDMQVEEVAWKEITKFLDELEK----SFQEGKKGRKFKTLESDNTDSFYQ-ScCth1 IEIEMKFGVITDKRTHRRMTPH-NKPFIVQN-RNGRLVSNVPEQMFSSFQELLRSKSE-----NPSKCAPRVVKQVQKYTKDSIYNCSpPct1 VEIEAKLGTLIDLETQNRFEFPVMNETILNP--EFNLRTRFESDMTASEHKYLNEFLNQAFRDSQ-KPGRLPFAYKHTKQVDLFYE-PfPrt1 IEIEGRVGLVIDKN-KNRIKLPINTDAIIEN----NY-SDFQAGIDRESFEYLLDYFHNMTLKKRLS ∆ FLELKTTKSIDKYYV-cvRtp1 VELEFRLGFQAPGEFITNINKHVWTTA----------------------------------------KEKLGTPAQELVMVDKYIR-EcCet1 KELEIRLGKIVSKEDGSRMKVDTVAPIVFRN---IPVDYRFESAVDPGDFKVLKKQFS---------------FCKGESTNDVVII-TbCet1 MELEARLCRRAEVSDKSGSTSSEREWKGRRARK----------------------TRTEVMPGVAEEDYKRIEEFCLDKGKEGSVT-

• • • • • • ScCet1 -VGLSTQRPRFLRMSTDI--KTGRVG-QFIEKRHVAQLLLYSPKDSYDVKISLNLELPVPDNDPPEKYKSQSPISERTKDRVSYIHCaCet1 -LGRKGEHPKRIRVTKDNLLSPPRL--VAIQKERVADLYIHNPGSLFDLRLSMSLEIPVPQGNIESIITKNKPEMVREKKRISYTHScCth1 NNASKVGKLTSWRCSEDL--RNKELKLTYIKKVRVKDFLIRYPQSSLDAKISISLEVP--EYETSAAFRN-GFILQRTKSRSTYTFSpPct1 ---TEDNSRDKIRVSKNQ--SDNQV-LACVKKRRVADLFLYCPNDAFDIRISISDELPV-----SMPSGNQQPSLTRLKDRVGYVHPfPrt1 ----IKNNNSRIRTTTYLN ∆ NNTHGLTTSKSQHIYNNLVDKNDSIDYRISINIEYTKP--ISKLYLSKNTPVHERLKERTTFINcvRtp1 ----ST-PGESSRYVVFP---DGQ-G-YWEHKKKVAKETTTGGK--YGVRSAFSLERR--ENGKPPV----SFRMQRTKYRTTFVKEcCet1 --------NEDGRETYEN----DELK-KVEKKTRSQKLDIYIPGKRYDVRLVLNEENEM-----FKRPSKKKAIVKRVRRRETYFITbCet1 RSTTRDVSFGQWRYTYTS--GKPSECIACIRKERLFVLDVPVPSGAYDIRFSACTEITG---ELPSPNFAPTRGYTRHKDRLSVTD

• • • • • • ScCet1 NDSC-TRIDITKVENHNQNSKSRQSETTHEVELEINCaCet1 PPTI-TKFDLTRVIGN-------KTEDKYEVELEAGScCth1 NDKMPLHLDLTKVTTTRRNS---HQYTSHEVEVEMDSpPct1 QE---IKIDLTKTTQN---DPVYDTTERHELEVEFG PfPrt1 TY-LGLQVDMTKIKT--------KNNELYEVEIEIPcvRtp1 GP---WKIDFTRVESI--PATDRDCESTYEIEVELYEcCet1 EP---YGFDFTEVVLSGEKDE--KEKRKFEIEVEVF TbCet1 GL---FRYDLTRVRD--------KHTTGYEVEVEFL

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0.0

0.5

1.0

1.5

2.0

5 6 7 8 9 10

pH

0.0

0.5

1.0

1.5

2.0

0 10 20 30 40

Time (min)

0.0

0.5

1.0

1.5

2.0

0 2 4 6 8 10

Divalent cation (mM)

Mn

Mg

A B C

[γ32P]ATP → 32Pi

[α32P]ATP → [α32P]ADP

Trip

ho

sph

ata

se (

nm

ol)

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FungiMicrosporidia

NematodaArthropodaChordata

Apicomplexa (Plasmodium)Euglenozoa (Trypanosoma)

Metazoa

Viridiplantae

TPaseGTase

TPase GTaseArabidopsisChlamydomonas

?TPaseGTase

TPase TPase GTase

TPaseTPase GTase

TPase

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C. Kiong Ho and Stewart Shumaneukaryotic phylogeny

Trypanosoma brucei RNA triphosphatase: Anti-protozoal drug target and guide to

published online September 11, 2001J. Biol. Chem. 

  10.1074/jbc.M108706200Access the most updated version of this article at doi:

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  When a correction for this article is posted• 

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