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(Received for publication, August 7, 1996, and in revised form, September 24, 1996)
From the Department of Biochemistry, Cornell University Medical
College, New York, New York 10021
5-Oxoprolinase (EC 3.5.2) catalyzes
a reaction in which the endergonic cleavage of
5-oxo-L-proline to form L-glutamate is coupled
to the exergonic hydrolysis of ATP to ADP and inorganic phosphate.
Highly purified preparations of the enzyme have been obtained from rat
kidney and Pseudomonas putida. The rat kidney enzyme is
composed of two strongly interacting, apparently identical subunits
(Mr = 142,000), whereas that from P. putida is composed of two functionally different protein
components that can readily be dissociated. Here we report the cloning
of rat kidney 5-oxoprolinase with preliminary expression studies.
cDNA clones encoding the enzyme were isolated by screening a
5-Oxo-L-prolinase
(5-OPase)1 catalyzes the
ATP-dependent cleavage of 5-oxoproline to
L-glutamate:
Volume 271, Number 50,
Issue of December 13, 1996
pp. 32293-32300
©1996 by The American Society for Biochemistry and Molecular Biology, Inc.
and
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
FOOTNOTES
Acknowledgments
REFERENCES
gt11 cDNA library beginning with a degenerate oligonucleotide
probe based on peptide sequence data obtained from the purified enzyme.
The whole cDNA clone was completed by amplifying its 5
end from a
premade library of rat kidney Marathon-ReadyTM cDNAs
using polymerase chain reaction methodology. The composite cDNA
(4,016 bases) revealed an uninterrupted open reading frame encoding
1,288 amino acid residues (Mr = 137,759). The
deduced amino acid sequence contains all four of the peptide sequences that were independently found in peptide fragments derived from the
enzyme. Expression of the full-length clone in Escherichia coli yielded a product of the same size as the rat kidney enzyme and which reacted with antibodies directed against the rat kidney enzyme. The predicted amino acid sequence is almost 50% identical throughout its entire length to that of a hypothetical yeast protein YKL215C. It is also 26% identical in half its length to the bacterial hydantoinase HyuA and 26% identical in the other half to the bacterial hydantoinase HyuB. The results suggest unexpected evolutionary relationships among the hydantoinases and rat kidney 5-oxoprolinase which share the common property of hydrolyzing the imide bond of
5-membered rings but which do not all require ATP.
This reaction is highly unusual in that hydrolysis of ATP is
required for the cleavage of a specific peptide bond (1). 5-OPase has
been found in mammalian tissues (2), plants (3), and microorganisms (4,
5). Apparently homogeneous preparations of 5-OPase from rat kidney (6)
and Pseudomonas putida (7) had been obtained in this
laboratory and were used for physical characterization and for studies
of catalytic mechanism. 5-OPase from rat kidney is composed of two
apparently identical subunits that exhibit a molecular mass of 142 kDa
on SDS-polyacrylamide gel electrophoresis (6). The enzyme is evidently
a "sulfhydryl enzyme" (8) and has a number of sulfhydryl
groups/monomer (6). The relationship between the essential sulfhydryl
groups of the enzyme and its various catalytic activities have been
probed (6). Unlike rat kidney 5-OPase, P. putida 5-OPase is
composed of two different, reversibly dissociable protein components, A
and B (7). Component A catalyzes an initial step in the reaction that
involves 5-oxoproline and ATP (9). Component B may function as a
catalyst that converts a phosphorylated form of 5-oxoproline to
glutamate, or it might alter the conformation of Component A so as to
facilitate the reaction (10, 11). Data are lacking, however, on the
amino acid sequence of the enzyme from any source. Knowledge of the
amino acid sequence of the enzyme and the cloning of the encoding
cDNA are essential for further studies on the structure, mechanism
of action, and physiological function of the enzyme.
This study was undertaken to elucidate the primary structure of rat kidney 5-OPase as preparation for the analysis of relationships between its structure and function. Peptides obtained from the purified rat kidney enzyme by enzymatic cleavage with Lys-C were used to design oligonucleotide probes that permitted cloning and sequencing of the cDNA encoding the complete protein. Protein representing the composite whole cDNA and truncated cDNA clones of the enzyme was also expressed in Escherichia coli, as confirmed by immunodetection with the rabbit antiserum against isolated rat kidney 5-OPase.
Frozen rat kidneys were obtained from Pel-Freez.
Ultrogel AcA34 was from LKB. Phenyl- and aminohexyl-Sepharose were
obtained from Pharmacia Biotech Inc.. DEAE-cellulose (DE-52) was from
Whatman. The rat kidney
gt11 cDNA library, premade rat kidney
Marathon-ReadyTM cDNAs and Taq-start
antibody were purchased from Clontech. DNA polymerase for PCR
amplification (LD-PCR system) was from Boehringer Mannheim. Restriction
endonucleases were from New England Biolabs Inc.. All radioisotopes
were obtained from Amersham Corp. All chemicals and biologicals were
purchased from Sigma unless noted otherwise.
Standard molecular biology techniques were
used (12). Recombinant
DNA purification was performed as described
(13). cDNA clones were subcloned into a Bluescript II KS vector
(Stratagene) and sequenced by the dideoxy chain termination method (14)
with Sequenase (United States Biochemical Corp.) using T3, T7 primers or specific internal primers. Automated DNA sequencing was carried out
at the Cornell University DNA Synthesis and Sequencing Facility.
Enzyme activity was determined (6) in reaction mixtures containing (final volume, 0.5 ml) 100 mM Na-Hepes buffer (pH 8.0), 2 mM 5-oxo-L-proline (containing 100 cpm/nmol 5-oxo-L-[U-14C]proline), 5 mM ATP, 8 mM MgCl2, 2 mM P-enolpyruvate, 150 mM KCl, 2 mM dithiothreitol, pyruvate kinase (5 units), and 5-OPase. After incubation at 37 °C for 30 min, the reaction mixtures were treated with 0.1 volume of 1 M HCl and placed at 0 °C for 5 min; an equal volume of 1 M Tris was then added. Denatured proteins were removed by centrifugation. Portions of the neutralized reaction mixtures were then analyzed for [14C]glutamate by liquid scintillation counting after removal of unreacted 5-oxoproline by chromatography on Dowex 50 (H+) as described (6). One unit of activity is defined as the amount of enzyme needed for the production of 1.0 µmol of glutamate/h under standard assay conditions.
Purification of 5-OPaseRat kidney 5-OPase was isolated from rat kidney homogenates using a procedure developed by Williamson and Meister (6). The homogenate was first centrifuged (16,200 × g for 90 min), and the proteins in the supernatant solution were fractionated by ammonium sulfate precipitation. The fraction containing the enzyme activity was then processed by a series of column chromatography steps, which sequentially involved DEAE-cellulose (DE-52), Ultrogel AcA34, phenyl-Sepharose, AH-Sepharose, and a second Ultrogel AcA34 step, as described (6). The preparation of the enzyme was further processed by a second DE-52 step and a third Ultrogel AcA34 chromatography step. An almost homogeneous (>90% pure) preparation of the enzyme with a specific activity of 72 units/mg was obtained in about 20% yield. Every step of the purification was followed by SDS-PAGE analysis. Quantitative assay for protein was done by the method of Bradford (15).
Preparation of Antibody against Rat Kidney 5-OPaseThe 5-OPase (300 µg) was dialyzed for 24 h against two changes of phosphate-buffered saline and was concentrated to a final volume of 600 µl by vacuum dialysis against phosphate-buffered saline. An equal volume of complete Freund's adjuvant was added to the enzyme and mixed vigorously until the solution became very viscous. Two anesthetized New Zealand White rabbits (~1.8 kg) were injected intradermally at 20 sites (20-25 µl of emulsion each). A test bleed was performed 2 weeks after the primary immunization. The titer and specificity of the antibodies were determined by enzyme-linked immunosorbent assay and Western blot analysis, respectively.
Amino Acid Sequences of Peptides from 5-OPaseApproximately 5 µg (1.5 pmol) of the protein isolated from rat kidney was electrophoresed on a 7.5% SDS-polyacrylamide gel and electrotransferred to a polyvinylidene difluoride membrane (16). The membrane was stained with Amido Black, and the protein band corresponding to 5-OPase (~140 kDa) was cut out for solid phase enzymatic digestion (endopeptidase Lys-C, enzyme/substrate, 1:10) (17). The microbore high performance liquid chromatography purification and sequencing of the peptides were carried out at the Rockefeller University Protein & Peptide Sequencing Facility.
cDNA Cloning of Rat Kidney 5-OPaseA 29-mer degenerate
oligonucleotide, oligonucleotide 1, (GTITTC(T)CAA(G)GAA(G)GAA(G)GCIGTIACIGAA(G)GC) was synthesized
based on the peptide sequence VFQEEAVTEA in peptide 1 (Table I),
end-labeled with [
-32P]ATP, and used to screen a
gt11 rat kidney cDNA library. The probe is a mixture of 32 different 29-mer oligonucleotides corresponding to all codon
combinations derived from peptide 1. Deoxyinosine (I) was substituted
at the wobble positions in four of the codons. Duplicate filters were
prehybridized at 42 °C for 3 h in prehybridization solution
(6 × SSC, 5 × Denhardt's solution, 0.5% SDS, 0.01%
sodium pyrophosphate, and 100 µg/ml denatured fragmented salmon sperm DNA), followed by hybridization at 50 °C for 18 h in the same solution containing 1.6 × 105 cpm of
32P-labeled probe/ml of hybridization buffer. The filters
were washed with 2 × SSC containing 0.5% SDS for 20 min at room
temperature with one change of the wash buffer, followed by washing
with 2 × SSC and 0.2% SDS at 50 °C for 40 min with one change
of the buffer. Of the ~5 × 105 clones that were
screened, three positives were identified, plaque-purified, and
subcloned into Bluescript II KS (Stratagene). These three clones,
designated as CL33, CL91, and CL99, contained inserts of 1.3, 1.5, and
0.8 kb, respectively; CL91 also contained a poly(A) tail. CL33 and CL91
were sequenced completely. The position of these clones in the
ultimately derived sequence and that of the relevant clones described
below are shown in Fig. 1.
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A 0.39-kb PstI/EcoRI fragment was prepared from
the 5
end of CL33 and labeled with [
-32P]dCTP by nick
translation (1 × 108 cpm/µg) for use as a probe for
the second screening of the same library. Duplicate filters were
hybridized at 55 °C in 6 × SSC hybridization solution (same as
above) with 1.0 × 105 cpm of 32P-labeled
probe/ml of hybridization solution. After rinsing briefly in 2 × SSC, 0.5% SDS at room temperature, the filters were washed in 0.4 × SSC, 0.1% SDS for 40 min at 55 °C with one change of the wash
buffer. Of the ~5 × 105 clones that were screened,
32 positives were identified, plaque-purified, and DNA prepared. Their
insert sizes ranged from 1.1 to 3.2 kb. Southern blot analysis revealed
that 14 of them hybridized with an oligonucleotide probe (17 mer) which
is close to the 3
end of CL33 and CL91. This result indicated that
these 14 clones overlapped completely with CL33 and CL91. One of these
14 clones, CL241, was chosen for subcloning and 5
and 3
end
sequencing analysis because it represented a relatively large insert
(~2.0 kb). Another four clones (all contain inserts >2.0 kb), CL222,
CL252, CL273, and CL282, were chosen from the 18 clones that did not
hybridize with the oligonucleotide probe. CL273 and CL282, the two
apparently most 5
-extended clones, as well as CL241, were subjected to
restriction mapping and complete sequencing. CL273 proved to be an
artifact, as described further under "Results."
An 0.8-kb EcoRV/XbaI fragment was prepared from
the 5
end of CL282 and used as a probe for further screening of the
library. Fourteen positive clones were obtained. In order to quickly
screen the most 5
-extended clones, a 24-mer primer (antisense primer) complementary to nucleotides 100-123 of CL282 (nucleotides 744-764 in
Fig. 2), was synthesized and used to amplify the
5
-extended region of the 14 positive clones with PCR according to the
manufacturer's instructions. The sense primer used here was one of the
two primers of the
gt11 cDNA insert Amplifier (Clontech). Three
positive clones, CL341, CL342, and CL361, seemed to contain relatively longer sequences in the 5
-end region and were subjected to subcloning, restriction mapping, and sequencing, although CL341 proved to be
another artifact (see under "Results").
end is
indicated by a triple asterisk. Independently determined
internal peptide sequences are double underlined. Single
asterisks indicate the potential N-glycosylation sites.
The potential polyadenylation signal (AATAAA) is boxed. The
entire cDNA was sequenced on both strands. Sequence analysis was
carried out with the Genetics Computer Group (GCG) package at the
Rockefeller University Computer Service.
In order to obtain a complete cDNA clone, three antisense gene-
specific primers (GSP1, GSP2, and GSP3, which are complementary to
nucleotides 254-277, 744-764, and 1414-1434, respectively; Fig. 2)
were designed and used to amplify the 5
-cDNA end of 5-OPase from a
premade library of rat kidney Marathon-Ready cDNAs (Clontech) with
the provided adapter specific primer AP1 (18). PCR (30 cycles) was
performed according to the manufacturer's instruction with the LD-PCR
System (Boehringer Mannheim) in a Perkin-Elmer DNA Thermal Cycler 480 using the following program: 94 °C for 1.0 min, then 30 cycles of
94 °C for 30 s, 63 °C for 45 s, and 68 °C for 1.5 min. 5 µl of the PCR products were subjected to electrophoretic
examination on a 1.2% agarose-EtBr gel. A secondary PCR reaction was
performed following the same procedure described above except that 5 µl of the diluted (1:10) primary PCR product were used in place of
the Marathon-Ready cDNAs as template, and 25 cycles were applied.
After the secondary PCR amplification, the products were gel-purified,
digested with ApaI/NotI (for CGSP2) or
HincII/NotI (for CGSP3), subcloned into
Bluescript II KS which had been previously digested with
ApaI/NotI or HincII/NotI,
and sequenced.
A charged nylon membrane containing
mRNA from various rat tissues (Clontech) was used. The membrane was
incubated in prehybridization buffer (5 × SSPE containing 10 × Denhardt's solution, 50% formamide, 2% SDS, and 100 µg/ml
denatured fragmented salmon sperm DNA) at 42 °C with CL33, which was
labeled with 32P by nick translation (5 × 108 cpm/mg). The membrane was washed twice for 10 min each
with 2 × SSPE and 0.05% SDS at room temperature and twice for 40 min at 50 °C in 0.1 × SSPE and 0.1% SDS. Autoradiography was
performed at
79 °C for 3 days.
An N-terminal truncated cDNA clone
of 5-OPase was constructed by joining the overlapped clones of CL361,
CL282, and CL241 using the unique restriction sites of
HincII and AgeI (Fig. 1). The assembled 3.8-kb
cDNA clone, which contains a stop codon at its 3
end, was excised
from the recombinant Bluescript II KS by EcoRI digestion and
ligated to pT7-7 (19) which had been digested with EcoRI.
The resulting clone, pFCL361-241, which is truncated at the N-terminal
of 5-OPase by 54 residues, is in the proper reading frame in the
EcoRI site of pT7-7 and would subsequently be translated as
a fusion protein linked through its amino terminus to the first 4 amino
acids of the gene 10 protein.
Another N-terminal deleted clone (truncated by 850 residues at the N terminus of 5-OPase), pFCL33, was constructed directly by joining the cDNA insert of CL33 into pT7-7 at the EcoRI site. The resulting clone, pFCL33, would also subsequently be translated as a fusion protein linked through its amino terminus to the first 4 amino acids of the gene 10 protein.
Creation of the NdeI site at the start codon of 5-OPase was
achieved by PCR amplification from rat kidney Marathon-Ready cDNAs using 5
-CTCCAGCTTCAACCATATGGGCAGC-3
as the gene-specific primer. The
LD-PCR amplification resulted in a full-length cDNA clone of
5-OPase (4.0 kb, as shown in Fig. 3B). This
clone was digested with NdeI/PstI, yielding a
2.9-kb cDNA fragment that was truncated at the C-terminal region of
5-OPase by 302 amino acid residues and was ligated to pT7-7 which had
previously been digested with NdeI/PstI. For
subsequent expression as a fusion protein, the resulting clone (pFCPCR)
was linked at its 3
end to the DNA sequence encoding the hexapeptide
AQAYHR followed by a stop codon.
and 3
Marathon RACE of 5-oxoprolinase
from rat kidney Marathon-Ready cDNAs. 5
and 3
Marathon RACE
were performed using the provided adapter-specific primer (AP1) and the
indicated gene-specific primer. A, 5
RACE products.
Lanes 1, 2, and 3 are 5
RACE products using
GSP1, GSP2, and GSP3 as the gene-specific primers, respectively (see
under "Experimental Procedures"). B, 3
(lanes
1 and 2) and 5
(lane 3) Marathon RACE
products. Cycling parameters: 1 min at 94 °C followed by 30 cycles
(25 cycles for secondary PCR amplification) of 30 s at 94 °C,
45 s at 62 °C, and 5 min at 68 °C. The gene-specific primers
used were: lane 1, nucleotides 92-114, containing an
NdeI restriction site introduced at the start codon in this
primer; lane 2, nucleotides 1067-1084, and lane
3, an antisense primer complementary to nucleotides 2581-2599. The expected size of the products can be deduced by the position of the
gene-specific primer used in each case. For example, the expected size
of the products in B are: lane 1, ~4.0 kb;
lane 2, 2.95 kb (4016-1066); lane 3, 2.599 kb.
The full-length clone was constructed by ligation of the
NdeI/KpnI fragment of pFCPCR to pFCL361-241
which had been digested with NdeI/KpnI. The
constructed full-length clone, pROPASE, is immediately downstream from
the T7 promoter (
10). Sequences representing the full-length and
truncated recombinant 5-OPase were expressed in E. coli
(BL21:DE3) as described (20).
The enzyme preparation obtained from step 9 of the purification procedure yields, as monitored by SDS-polyacrylamide gel electrophoresis, a dominant band of 140 kDa that comprises >90% of the protein and two minor bands of lower molecular weight. Approximately 600 µg of protein could be obtained from 500 g of frozen rat kidney with a specific activity of 72 units/mg. Table I shows the sequences of four Lys-C enzymatic peptides obtained from the purified enzyme. The amino acid sequences corresponding to these four peptides were subsequently found in the cDNA clone (Fig. 2).
Isolation of cDNA Clones Coding for 5-OPaseFig. 1
outlines the position in the cDNA sequence of the relevant clones
used for sequence determination. By screening a rat kidney cDNA
library with the end-labeled degenerate oligonucleotide probe encoding
the partial sequence of peptide 1, three positive clones were initially
obtained. Two of them, CL33 and CL91, were found to contain the longest
sequence of the 3
-untranslated region. CL91 also included a poly(A)
tail. Screening of the same library using the 0.39-kb
32P-labeled EcoRI/PstI fragment
prepared from the 5
end of CL33 gave 32 positives. Of these, CL241,
CL222, and CL282 were completely sequenced. Though CL273 was the
largest (3.2 kb) and the most 5
-extended, this clone was found to be
an artifact at its 5
region on the basis of restriction mapping and
sequencing; i.e. about two-thirds of the 5
terminal region
of CL273 was from an unknown cDNA clone, as judged in part by the
presence of a poly(A) tail in this region. CL341, the most 5
-extended
cDNA clone (2.4 kb) from the third screening (which used a probe
from the 5
end of CL282), was also found to be incorrect; restriction
mapping and sequencing of this clone indicated that a fragment of 0.6 kb at its 5
end was an artifact, as evidenced by the presence of a
number of internal stop codons. CL324 and CL361 from the third sequence
allowed determination of most of the remaining sequence.
The complete cDNA clone for the enzyme was obtained by LD-PCR
amplification using the premade rat kidney Marathon-Ready cDNAs as
templates. After secondary PCR amplification as described under "Experimental Procedures," the resulting PCR product generated a
band of the predicted size after electrophoresis on a 1.2%
agarose-EtBr gel (Fig. 3A). Sequencing of the clones of
CGSP2 and CGSP3 revealed two completely overlapping cDNA fragments
of the 5
end of 5-oxoprolinase, in which CGSP3 was more 5
-extended
than CGSP2 by 4 bases.
The sequence of the assembled 4.016-kb cDNA for rat kidney 5-OPase
is shown in Fig. 2. It revealed an uninterrupted open reading frame
encoding 1288 amino acid residues with a calculated molecular weight of
137,759, which agrees well with that previously estimated by SDS-PAGE
(Mr = 142,000) (6). The 5
-untranslated region of 105 nucleotides contains an in-frame stop codon. The first ATG
(position 106) is presumed to be the initiation codon and conforms to
the consensus sequence for an initiation codon context (21). The coding
sequence ends with a termination codon (TGA) at position 3969, followed
very closely by the polyadenylation signal AATAAA beginning at position
3981 and a 14-nucleotide poly(A) tail (Fig. 2).
All four independently determined peptide sequences are found in the deduced amino acid sequence (Fig. 2). The sequence also indicates five potential sites for N-glycosylation (N-X-S/T), although actual glycosylation has not been demonstrated. The calculated amino acid composition is in fair agreement with the amino acid analysis of the isolated protein (6), except for Asx, Glx, and Lys (data not shown). The predicted protein sequence was found to be unique when compared with the protein sequences given in the GenBank and SwissProt data bases, but strong sequence similarities to three other proteins were found (see under "Discussion").
Tissue mRNA ExpressionNorthern blot hybridization
studies with nick-translated probe prepared from a fragment of 5-OPase
(CL33) showed that the mRNA for the enzyme is well expressed in
testis, kidney, and liver, whereas the mRNA levels in other tissues
examined (brain, heart, lung, spleen, and muscle) were about 10% or
less of that found in testis or kidney (Fig. 4). These
findings are in general agreement with determinations of the activities
of 5-OPase in these tissues (8). The size of the transcript in kidney
(~4.4 kb) is a little smaller than that found in testis and liver
(~5.0 kb). Minor bands of smaller size, particularly evident in the
testis sample, probably arise from mRNA degradation or from
nonspecific hybridization. It should be noted that the rat multiple
tissue Northern blot (Clontech) used in this study had been probed
several times before, so the strength of the hybridization signal does
not represent the real level of the mRNA.
79 °C for 3 days. Lanes 1-8
were mRNAs from rat testis, kidney, skeletal muscle, liver, lung,
spleen, brain, and heart, respectively.
Expression of Recombinant 5-OPase
The expressed recombinant
rat kidney 5-OPase and the expressed N-terminal and C-terminal
truncated proteins gave bands of the predicted sizes when analyzed by
SDS-gel electrophoresis and Western blot using the antibodies against
the purified 5-OPase (Fig. 5, A and
B). Also, recombinant 5-OPase and the 5-OPase isolated from
rat kidney homogenate gave bands of apparently same size when detected
by Western blot. These data provide further evidence that the cDNA
clone obtained in this study corresponds to that of rat kidney 5-OPase.
The C-terminal truncated recombinant 5-OPase (missing a C-terminal
peptide of 243 residues) encoded by pFCPCR gave no detectable band on
the Western blot (Fig. 5B), but its expression was readily
seen when gels were stained with Coomassie Blue (Fig. 5A).
This result suggests that the polyclonal sera principally contain
antibodies that recognize denaturation-resistant epitopes within the
C-terminal region of 5-OPase. Enzymatic activity analysis of the
expressed recombinant rat kidney 5-OPase in the lysate of E. coli using standard procedures (see under "Experimental Procedures") indicated no significant increase in activity above the
control.
The present work is the first carried out on the cloning and expression of 5-oxoprolinase. The deduced amino acid sequence of the rat kidney enzyme consists of 1288 residues with a calculated molecular weight of 137,759, which is close to the weight of 142,000 previously estimated from SDS-PAGE analysis of the isolated enzyme (6). Previous work (4, 6) in this laboratory also suggested that the native enzyme (Mr = 325,000, estimated by gel filtration) is composed of two subunits of identical molecular weight that are not held together by disulfide bonds. Since all of the four independently determined peptide sequences were found within the predicted protein sequence and the calculated amino acid composition was in fair agreement with the amino acid analysis of the isolated rat kidney enzyme, the data support the suggestion that the two subunits are identical.
Most of the cDNA sequence of 5-OPase presented here represents the
overlapping cDNA clones that were obtained from successive screening of a
gt11 rat kidney cDNA library. However, further screening of the same library with probes directed to the 5
-terminal region failed to produce positive results. Accordingly, to determine the 5
-terminal sequence of the enzyme, we turned to the rat kidney Marathon-Ready cDNAs. Marathon-Ready cDNAs are premade
libraries of adapter-ligated double strand cDNA ready for use as
templates in Marathon cDNA amplification, a unified method for
performing rapid amplification of both 5
- and 3
-cDNA ends (RACE)
from the same template (18) with the LD-PCR method (22). In the present studies, we completed the cDNA of rat kidney 5-OPase by amplifying its 5
end from a library of rat kidney Marathon-Ready cDNAs. Three
primers, which were complementary to the known sequences at various
regions of the cDNA, were designed and used as gene-specific primers to perform the 5
RACE. They each gave the product of the
predicted size (Fig. 3A). Sequencing of CGSP2 and CGSP3
revealed that they were completely overlapped except for a several base extension at the 5
end of CGSP3. Sequencing of the 5
end of another
5
RACE product (Fig. 3B, lane 3) gave the same results as
CGSP3.
The full-length (beginning just before the start codon; Fig. 3B,
lane 1) and the 3
end cDNA of 5-OPase (Fig. 3B, lane
2) have also been amplified from Marathon-Ready cDNAs and
their sequences confirmed by restriction mapping and DNA sequencing,
giving the same results as obtained from the conventional screening of
the
gt11 cDNA library. This indicates that the library of rat
kidney Marathon-Ready cDNAs contains the full-length cDNA of
5-OPase and that the cDNA clones from conventional screening of the
gt11 cDNA library are consistent with those obtained from
Marathon-Ready cDNAs by LD-PCR amplification. Thus, the cDNA
clone of rat kidney 5-OPase obtained in this study has been checked by
two different methods.
Western blot and standard SDS-PAGE analysis of the proteins encoded by the recombinant 5-OPase clones demonstrated that the full-length recombinant 5-OPase expressed in E. coli migrates at a position identical to that of endogenous rat kidney 5-OPase (Fig. 5), further demonstrating that the isolated cDNA corresponds to that encoding the rat kidney enzyme. Similar analysis of proteins encoded by the truncated recombinant cDNA clones revealed that recombinant proteins with intact C-terminal regions are specifically detected by the antiserum against the isolated rat kidney 5-OPase, whereas the C-terminal truncated recombinant proteins were not detected by the antiserum. The results indicate that the C-terminal 243 residues of 5-OPase contain the reactive denaturation-resistant epitopes for the anti-5-OPase serum and that other regions of the enzyme either do not contain such epitopes or that their epitopes are unreactive in the absence of the C-terminal region.
It is perhaps not surprising that expression of the rat kidney 5-OPase cDNA in E. coli did not result in a detectable increase in 5-OPase activity. The rat kidney enzyme is a very large homodimer in which the two subunits interact tightly without any disulfide bonds and might well not fold to give an enzymatically active protein in E. coli, at least under the conditions used here. Obtaining functional recombinant 5-OPase is clearly a prerequisite for mechanistic and further structural studies of this enzyme.
The unexpected result from this study is the demonstration of strong
sequence similarities among rat kidney 5-OPase, the two bacterial
hydantoinases, and the yeast protein YKL215C (Fig. 6). YKL215C is a hypothetical protein of 1287 residues encoded by the
URA1-RSD1 intergenic region (23). The similarity between this sequence
and that of the rat kidney enzyme is sufficiently strong (48.4%
identity) to suggest that the yeast protein is also a 5-oxoprolinase.
To understand the similarity to the bacterial hydantoinases, a
comparison of the 5-oxoprolinase reaction and that catalyzed by the
hydantoinases indicates the relationship between the chemical reactions
involved (Fig. 7). Both reactions involve the hydrolysis
of 5-membered rings via hydrolysis of their internal -CO-NH- bonds.
HyuA is specific for D-5-substituted hydantoins, while HyuB
is specific for the corresponding L isomers (24, 25). The
amino-terminal half of rat kidney 5-oxoprolinase shows 26.6% identity
with the amino-terminal region of HyuA, while the carboxyl-terminal
half of the rat kidney enzyme shows 25.9% identity with the
amino-terminal region of HyuB. These somewhat surprising relationships
partially reflect the fact that HyuA and HyuB show no significant
sequence similarities to each other (24, 25). Thus it is possible that
the rat kidney enzyme evolved from an evolutionary fusion of these
functionally similar but structurally different enzymes, or that the
hydantoinases arose from an enzyme related to rat kidney
5-oxoprolinase. However, it is relevant that neither HyuA nor HyuB
require ATP for ring hydrolysis, in contrast not only to 5-OPase, but
also to a different bacterial hydantoinase that cleaves 5-substituted
hydantoins (26) as well as to one that cleaves
N-methylhydantoins (27). The difference among the bacterial
hydantoinases in their requirement for ATP is surprising, and it will
clearly be of interest to learn the structural relationship of rat
kidney 5-OPase to the ATP-requiring hydantoinases.
The above raises the question of bacterial 5-oxoprolinase. 5-OPase from bacteria (P. putida) (4, 7), unlike that from rat kidney, is composed of two functionally different protein components, Component A and Component B. Neither component alone catalyzes the 5-OPase reaction, but the reaction is effectively catalyzed when the components are mixed. Component A is composed of two subunits, Mr = 65,500 and 50,000, and exhibits 5-oxo-L-proline-dependent ATPase activity, indicating this component can interact with both ATP and 5-oxo-L-proline. The role of Component B (Mr = 80,000) is uncertain, since it does not exhibit ATPase activity, and there is no evidence that it binds 5-oxo-L-proline. Of relevance here is the fact that the antiserum directed against the rat kidney enzyme strongly reacts with an E. coli component of ~60 kDa (Fig. 5B), suggesting that this component might be a subunit of E. coli 5-OPase Component A and raising the question of homology between the rat kidney and bacterial 5-oxoprolinases and the relationship of the bacterial 5-oxoprolinases to the bacterial hydantoinases. The sequence of bacterial 5-oxoprolinase will be an important clue in this evolutionary puzzle.
The nucleotide sequence(s) reported in this paper has been submitted to the GenBankTM/EMBL Data Bank with accession number(s) U70825[GenBank] (BankIt69326).
To whom correspondence should be addressed: Dept. of Biochemistry,
Cornell University Medical College, 1300 York Ave., New York, NY 10021. Tel.: 212-746-6428. Fax: 212-746-8875.
and 3
RACE, 5
and 3
rapid
amplification of cDNA ends; PCR, polymerase chain reaction; LD-PCR,
long distance polymerase chain reaction; IPTG,
isopropyl-
-D-thiogalactopyranoside; PAGE, polyacrylamide gel electrophoresis; kb, kilobase(s); SSPE, a 1× solution represents 0.18 M NaCl, 10 mM sodium phosphate, pH 7.7, and 1 mM EDTA.
We thank Dr. Stanley W. Tabor for a gift of pT7-7 expression vector, Ms. Hui-Qing Zhu for help with DNA sequencing and other preliminary experiments, Drs. Mary E. Anderson and Chin-Shiou Huang for helpful discussions, and Dr. S. S. Tate for constructive criticism of the manuscript.
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