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Research Communications |
-amidating enzyme precursor that generates five distinct enzymes
a Department of Molecular and Cellular Neurobiology, Graduate School Neurosciences Amsterdam, Research Institute Neurosciences Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; and
b Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| ABSTRACT |
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-amidation in
individually identifiable Lymnaea neurons that synthesize
multiple proproteins, yielding complex mixtures of structurally diverse
peptide substrates. The
-amidation of these peptide substrates is
efficiently controlled by a multifunctional Lymnaea
peptidyl glycine
-amidating monooxygenase (LPAM), which contains
four different copies of the rate-limiting Lymnaea peptidyl
glycine
-hydroxylating monooxygenase (LPHM) and a single
Lymnaea peptidyl
-hydroxyglycine
-amidating lyase.
Endogenously, this zymogen is converted to yield a mixture of
monofunctional isoenzymes. In vitro, each LPHM displays a
unique combination of substrate affinity and reaction velocity,
depending on the penultimate residue of the substrate. This suggests
that the different isoenzymes are generated in order to efficiently
amidate the many peptide substrates that are present in molluscan
neurons. The cellular expression of the LPAM gene is
restricted to neurons that synthesize amidated peptides, which
underscores the critical importance of regulation of peptide
-amidation.Spijker, S., Smit, A. B., Eipper, B. A.,
Malik, A., Mains, R. E., Geraerts, W. P M. A molluscan peptide
-amidating enzyme precursor that generates five distinct enzymes.
Key Words: posttranslational modification neuropeptide
-amidation PAM mono-oxygenase mollusk Lymnaea stagnalis
| INTRODUCTION |
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In this study, we examine the process of peptide
-amidation, a
posttranslational modification that is critical for generating
bioactive peptides. Peptide
-amidation protects peptides from
degradative enzymes and is often required for high-affinity interaction
with cognate receptors (3)
. It is a final step in a series
of enzymatic events in which neuropeptides mature from proproteins
within the endoplasmic reticulum, trans-Golgi network
(TGN),1
and secretory granules. It involves the sequential conversion of a
peptidylglycine substrate into peptidyl-
-hydroxyglycine and
conversion of the latter into an amidated peptide (4
,
5
). Of the two reactions, the first, catalyzed by
peptidylglycine
-hydroxylating monooxygenase (PHM), is rate limiting
and dependent on the penultimate position of the substrate (Xxx-Gly)
(3
, 6
, 7
). The second reaction
is catalyzed by peptidyl-
-hydroxyglycine
-amidating lyase (PAL).
In vertebrates, PHM and PAL are synthesized together as the
bifunctional protein peptidylglycine
-amidating monooxygenase (PAM)
8-10)
, whereas in Drosophila
(11)
and Calliactis (12)
PHM is
encoded by a distinct gene.
As a model in our study, we chose the central nervous system (CNS) of
the mollusk Lymnaea stagnalis, because molluscan neurons
often coexpress multiple proproteins yielding different amidated
peptides that are colocalized in a single subset of large dense-core
vesicles (13)
. Moreover, a molluscan proprotein often
yields peptides having different carboxy-terminal amidated residues
(e.g., Ile-NH2, Val-NH2,
Leu-NH2/Met-NH2) (A. B. Smit, unpublished
observations; 14). We reasoned that the cocktails consisting of many
different peptide substrates produced by molluscan neurons may place
high demands on the performance of the peptide
-amidating enzyme in
the molluscan brain.
Here, we examined the specific structural characteristics of the
molluscan
-amidating enzyme from the Lymnaea CNS (LPAM)
and performed a functional analysis of the enzyme(s) toward different
Xxx-Gly substrates. Using the advantage offered by the
Lymnaea CNSnamely, of large neurons that are identifiable
according to shape, function, and chemical characteristicswe examined
the cellular coexpression of LPAM and neuropeptides by single-cell
reverse transcriptase polymerase chain reaction (RT-PCR) on cDNA
generated from individual neurons of the Lymnaea CNS.
| MATERIALS AND METHODS |
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-N-Ac-Tyr-Gly-Gly was obtained from the Dutch Cancer
Institute (NKI, The Netherlands).
-N-Ac-Tyr-Phe-Gly and
-N-Ac-Tyr-Val-Gly were synthesized as described by Husten
and Eipper (15)
. The peptidyl-
-hydroxyglycine substrate
was prepared as described by Eipper et al. (16)
.
Protein extraction
Total brain extracts of 100 snails were made in 1 ml TM [20 mM
NaTES, 10 mM mannitol, and the inhibitor mix (final concentrations): 5
µg/ml aprotinin, 50 µg/ml lima bean trypsin inhibitor, 2 µg/ml
pepstatin, 16 µg/ml benzamide-HCl, 2 µg/ml leupeptin, 0.3 mg/ml
phenyl methyl sulfonyl fluoride, and 0.6 mg/ml Pefabloc]. Debris was
removed by a 5 min centrifugation at 1000 x g. The
soluble fraction was frozen, thawed, and separated from the particulate
fraction by 15 min centrifugation at 435,000 x g. The
membrane pellet was resuspended in TMT (TM with 1% Triton X-100). All
solutions contained protease inhibitors as above. Linear gradients were
520% sucrose (1.8 ml) in TMT containing 150 mM NaCl. Aggregated
material in the samples (0.117 ml soluble mixed with 0.133 TMT or 0.25
ml particulate) was pelleted at 8500 x g for 5 min.
Supernatant was loaded on the gradient and centrifuged for 3 h at
200,000 x g in a swinging bucket rotor at 4°C. In
total, 13 0.15 ml fractions (17)
were collected from the
top. Protein standards were analyzed simultaneously. Aliquots of these
fractions were analyzed by sodium dodecyl sulfate-polyacrylamide gel
electrophoresis to locate the marker proteins.
Cloning of LPAM
Poly(A)+ RNA was isolated from dissected CNS of
L. stagnalis using magnetic beads (Dynal A.S., Oslo, Norway)
and reverse transcribed into hexanucleotide primed cDNA. Two degenerate
oligonucleotides (Isogen Bioscience, Maarssen, The Netherlands)
directed to sequences that are conserved among the vertebrate PHM
enzymes, namely, Ala-Trp-Ala-Arg-Asn-Ala-Pro-Pro (sense,
OL1:
5'-CTCAAGCTTCITG(T/C)GCI(A/C)GNAA(C/T)GCNCCNCC-3') and
Pro-Gln-Ala-Phe-Tyr-Pro-Val-Glu (antisense, OL2:
5'-CGGGAATTC(T/C)TCIACIGG(A/G)TA(A/G)AANGC (T/C)TGNGG-3'), were
used to amplify PHM-like sequences. PCR was performed on one animal
equivalent of CNS cDNA using 150 pmol of OL1 and OL2 under standard
conditions for 45 cycles (94°C, 20 s; 53°C, 30 s; 72°C,
1 min). Amplified cDNA of the expected size was cloned and sequenced.
The cloned LPAM PCR product was used as a random primed
[
-32P]dATP-labeled probe (specific activity
>109 cpm/µg) to screen approximately 200,000 clones of
an amplified
ZAP II cDNA library, as described previously
(18)
. To obtain the partial cDNA sequence of LPAM-2, total
RNA isolated from the CNS was treated with DNase-I to remove traces of
genomic DNA and reverse transcribed into hexanucleotide primed cDNA.
Amplification of cDNA was performed in a 100 µl PCR in triplicate
using a primer combination (sense, PAM S8:
5'-CGCGGATCCACTACCCCCCAACCCTG-3'; antisense, LPAL AS1:
5'-CGCGGATCCACGCCCCAA TCTGAC-3') that covers the noncatalytic exon A
domain. Three ~140 bp products obtained were cloned into M13mp19 and
sequenced.
Subcloning and nucleotide sequence analysis
The insert of the pBluescript II PAM cDNA was excised by
digestion with Bam HI and further digested with either
Mbo I, Rsa I, Hpa II, or
Taq I. The fragments obtained were randomly cloned into a
Bam HI-, Sma I-, or Acc I-cut M13mp18,
respectively. LPAM PCR products, LPAM cDNA fragments subcloned in
M13mp18, pBluescript II LPAM cDNA, and LPAM constructs for expression
(see below) were sequenced in both orientations according to the
dideoxy chain termination method (19)
, by using T7 DNA
polymerase, universal primers, and internal primers continued by primer
walking. Sequence alignments were performed using the program Clustal
W1.5.
5'-Rapid amplification of cDNA ends (5'-RACE)
Poly(A)+ RNA was isolated from the CNS using
magnetic beads. 5'-RACE was carried out as described by Frohman et al.
(20)
, with the following modifications: 0.5 µg mRNA, 400
pmol hexanucleotide primers in 30.5 µl water were heated at 90°C
for 1 min, quenched on ice, 10 U of RNAsin (Promega, Madison, Wis.) was
added, and reverse transcription was performed using Superscript II and
the manufacturers protocol (Gibco BRL, Grand Island, N.Y.). After
incubation, the cDNA was size-separated on a Pasteur pipette Sephadex
G-50 column to remove nucleotides and hexanucleotide primers. Fractions
of 150 µl were collected and fractions 3 to 7 were pooled,
precipitated and resuspended in 5 µl water. For dATP tailing, the
cDNA was heated at 90°C for 2 min and snap-cooled, then terminal
deoxynucleotidyl-transferase components were added as described by the
manufacturer (Boehringer Mannheim, Mannheim, Germany). The mixture was
incubated at 37°C for 30 min and heat-inactivated at 65°C for 2
min, precipitated, and dissolved in 10 µl water. Aliquots (3 µl)
were used for a first round of amplification with Super Taq polymerase
(Boehringer Mannheim, Germany), by using 50 pmol PAM-specific antisense
primer in combination with 50 pmol RoRi-(dT17)
[5'-ATCGATGGTCGACGCATGCGGATCCAAAGCTTGAATTCGAGCTC(T)17-3']
or with ADA-(dT20)
[5'-GACTCGAGTCGACATCGA(T)20-3'] for 10 cycles (94°C,
30 s; 34°C (RoRi) or 40°C (ADA), 45 s; 72°C, 2 min) in
a volume of 50 µl. Then, 2% of this PCR reaction mixture was
reamplified by using 50 pmol of the first set of adaptor primers Ro
(5'-ATCGATGGTCGACGCATGCGGATCC-3') or ADA-I
(5'-CGCTCTAGAGACTCGAGTCGACATCGA-3') in combination with 50 pmol
PAM-specific antisense primer in a volume of 100 µl. We used Ro for
40 cycles (94°C, 30 s; 63°C, 45 s; 72°C, 2 min) or
ADA-I for 5 cycles (94°C, 30 s; 56°C, 45 s; 72°C, 2
min), followed by 35 cycles (94°C, 30 s; 63°C, 45 s;
72°C, 2 min). To increase specificity, a second round of
amplification was carried out on 1% of the previous PCR reaction
mixture by using 50 pmol of a nested PAM-specific antisense primer in
combination with 50 pmol nested adaptor primers Ri
(5'-GGATCCAAAGCTTGAATTCGAGCTCT-3') or ADA-II
(5'-CGCGAGCTCGAGTCGACATCGATTT-3') under conditions identical to those
described above. Three sets of nested antisense PAM primers were used,
OL4 (5'-CTTTTTATGAGTTGTATGGATCATG-3') and OL5
(5'-AGAGGATCCGATCTGGAGCTTCTGAAATCTTC-3');
OL6(5'-CACTGACTGGATGTGTCATAGAA-3') and OL7
(5'-GTGGGATCCGTCGATCGAGCAGCCAGTTTG-3'); OL8
(5'-GCACAAGAGTTTTAATGGTGGTC-3') and OL9
(5'-GCGAAGCTTCACCTTCTGGGAGAACTGTG-3'). Amplified cDNA was digested
with BamHI and SacI or with Bam HI and
HindIII, and separated on an agarose gel. In each cycle of
5'-RACE, both the RoRi set as well as the ADA-set were used in
duplicate; at least three fragments were cloned from each individual
PCR, both in M13mp18 and mp19, and sequenced in order to avoid the
introduction of sequence errors arising from individual PCRs.
Size determination of LPAM mRNA
Total RNA from the CNS was isolated (21)
, and two
CNS equivalent to RNA (~20 µg) were fractionated on a 0.8%
agarose-formamide gel and transferred to charged nylon membranes. The
inserts of the LPHM-1, -2, -3, -4 and LPAL pCI.neo-plasmids (see below)
and a subclone containing the exon A domain (bp 4221-4531) of the LPAM
cDNA were used to make individual random primed
[
-32P]dATP-labeled probes (specific activity
>109 cpm/µg). Only the exon A domain probe or a mixture
of equal activities of each LPHM and the LPAL probe were used for
hybridization (conditions as described above).
Single-cell RT-PCR
Individual neurons were isolated using a fine glass pipette (tip
diameter, ~100 µm), washed in culture medium, and transferred to a
glass plate. After removal of superfluous medium, 11 µl water
containing 200 pmol hexanucleotides was added, mixed, and transferred
to a tube; the sample was heated at 90°C for 1 min, quenched on ice,
10 U of RNAsin was added, and reverse transcription was performed using
M-MLV reverse transcriptase and the manufacturers protocol (Promega) in
a total volume of 25 µl. Amplification of cDNA (1 µl) was performed
in a 100 µl PCR using LPAM- or neuropeptide-specific primers. LPAM
primers (sense, OL10: 5'-TGTCTGTGTGCACCCAGCC-3'; antisense, PALC2:
5'-GCG-GATCCTGAAGGTGTGAAATCACTGC-3') or
primersspecific for the presence (sense, Ex-ASI:
5'-GGAAACATCACAGAGAGAATC-3') or absence (sense, LPHM4/PALSI:
5'-GGGATGAAAGCAGCATCCA-3') of the exon A domain were used in
combination with the LPAL primer (antisense, LPALAS1) as well as
primers specific for neuropeptide transcripts for MIP-I, LYCP, ELH-I
(CDCH-I), SCP, CP, and APGWa (data not shown). After 35 cycles of
amplification, 10 µl of each PCR reaction was separated on an agarose
gel and Southern blotted. After hybridization to individual random
primed [
-32P]dATP-labeled probes (specific activity
>109 cpm/µg), the filters were washed and
autoradiographed. Autoradiograms were scanned by using a flatbed
scanner.
Phylogenetic analysis
The various PHM, rat dopamine ß-monooxygenase and
Drosophila tyramine ß-hydroxylase amino acid sequences,
analogous to rat PHM Ile66 to Pro347, i.e.,
from the first identical amino acid residue between LPHM and rat PHM to
the end of the PHM catalytic core, were aligned by using the program
Clustal W1.5. Bootstrap analysis was then performed to generate 100
resampled data sets (with a 10-fold jumble of input order) using
Seqboot. Protdist was used to compute distance between the protein
sequences using the Dayhoff PAM001 matrix, followed by Fitch to
calculate a distance matrix. The Consense program generated a consensus
tree. Confidence limits were calculated by using the data obtained from
bootstrapping. Programs used were made and distributed by Felsenstein
(22)
.
Plasmid construction for functional expression
pCI.neo-plasmids encoding the separate domains of LPHM-1, -2,
-3, -4 and LPAL were created using amplification of cDNA by PCR. To
ensure correct synthesis, routing, and secretion, each enzyme domain
was preceded by the consensus Kozak sequence (23)
and rat
PAM signal and prosequence, followed at the carboxyl terminus by a
rhodopsin epitope tag (GSGATETSQVAPA; 24) to visualize expression, and
a stop codon. Constructs contained the following sequences: LPHM-1,
Thr22-Pro344; LPHM-2,
Ile353-Ser675; LPHM-3,
Thr690-Gly1013; LPHM-4,
Gly1019-His1333 LPAL,
Phe1496-Ser1865 (numbers refer to LPAM-1).
Specific primers for each catalytic domain were used in PCR
amplification. PCR products were cloned in-frame into a pBluescript
vector containing the rhodopsin epitope tag (pBS.rhodopsin). The
Kozak/signal sequence/pro sequence was amplified from pBS.rPHMs
(23)
using a specific primer, Koz-proA1 (antisense,
5'-GCGGAGCTCAAATGATCTGGTAGTTTCTTTAAAC-3', containing a SacI
site at the 5'-end) in combination with a universal pBS primer and
cloned into pBluescript II KS (Stratagene) to yield pBS.rKoz/ss/pro.
cDNA regions derived from PCR were verified by sequencing. Finally,
fragments of pBS.rhodopsin-LPHM/LPAL cDNA and the fragment of
pBS.rKoz/ss/pro were ligated together in the pCI.neo-expression vector
(Promega).
Cell culture and transfection
hEK-293 cell lines were maintained as described
(25)
. pCI.neo-plasmids containing LPHM-1, -2, -3, and -4
and LPAL were transfected into hEK-293 cells using lipofectin and G-418
selection (25)
and screened by PHM or PAL assay
(10)
, Western blot, and immunostaining with a mouse
anti-rhodopsin antibody (24)
, as described
(23)
. Clones secreting the highest amount of PHM or PAL
activity were selected for collection of the medium.
PHM and PAL assays
Aliquots of fractions collected from the sucrose gradients (see
section on protein extraction) and aliquots of spent medium were
assayed as described (10)
by using 0.5 µM substrate and
mono-125I-
-N-acetyl-Tyr-Val-Gly (PHM) or
mono-125I-
-N-acetyl-Tyr-Val-
-hydroxyglycine.
In addition,
mono-125I-
-N-acetyl-Tyr-Phe-Gly and
mono-125I-
-N-acetyl-Tyr-Gly-Gly (PHM)
were used in kinetic studies. Assays were performed in duplicate or
triplicate.
| RESULTS |
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The LPAM-1 cDNA sequence predicts a bifunctional peptide
-amidating enzyme with four PHM domains and a single PAL domain
To identify the structural organization of the LPAM precursor, PCR
using degenerate primers directed to conserved regions of vertebrate
PHM (5)
was performed on cDNA from the Lymnaea
brain. A PCR product of the expected size (360 bp) (Fig. 2A
) encodes a protein fragment with 38% amino acid sequence
identity to rat PHM. To identify the full sequence of the LPAM cDNA, we
used the PCR fragment to screen 200,000 clones of a cDNA library from
the cerebral ganglia of the Lymnaea brain (18)
,
yielding one positive clone of ~5 kb. Sequencing of the 5'-end of
this clone, named LPAM clone 2.11, revealed that the longest open
reading frame contains a partial PHM amino acid sequence, but no start
codon. It is flanked by a 603 bp 3' untranslated region. A short
poly(A) stretch is present at the 3' end of the cDNA clone, but a
consensus sequence for polyadenylation is absent. To obtain the 5' part
of the cDNA encoding the start codon, three cycles of 5' rapid
amplification of cDNA ends (5'-RACE) were required (20)
.
The assembled sequences (Fig. 2A
) gave rise to a cDNA of
6615 nucleotides (LPAM-1). The open reading frame consists of 5853
nucleotides and encodes a protein of 1951 amino acids with a predicted
mass of 215.6 kDa. The coding region is flanked by a 156 bp 5'
untranslated sequence containing several in-frame stop codons.
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The predicted LPAM-1 protein is a putative multifunctional peptide
-amidating enzyme. Surprisingly, it is organized differently from
vertebrate PAM (Fig. 2B
). LPAM-1 contains a signal peptide,
which is predicted to be cleaved after residue Ala21
(29)
. An adjacent propeptide, present in rat PAM-1, is
absent in LPAM-1. In contrast to rat PAM-1, the LPAM-1 protein contains
four distinct putative monooxygenase domains, LPHM-1 to -4, each of
which exhibits 3740% sequence identity to vertebrate PHM. In
addition, a domain with 36% sequence identity to vertebrate PAL is
present. This putative Lymnaea PAL domain (LPAL) is followed
by a predicted transmembrane domain and a cytoplasmic domain with 39%
sequence identity to the cytoplasmic domain of rat PAM-1. The LPAL
domain is separated from the four LPHM domains by a putative exon A
domain, which shows no significant homology to the corresponding region
of rat PAM-1. A single consensus site for N-linked
glycosylation is present in rat PAM-1, whereas one to four consensus
sites for N-linked glycosylation are present in each LPHM
domain and in the LPAL domain (Fig. 2B
).
Rat PAM-2 and PAM-3 arise via alternative
splicing in the pre-PAM RNA of small exons, representing
either the exon A domain or the transmembrane domain and/or part of the
cytoplasmic domain (5
, 30
, 31
).
Rat PAM-4 arises via alternative use of an alternative
polyadenylation addition site, generating a soluble monofunctional PHM
protein. To explore the possibility that the LPAM gene gives
rise to different splice variants, we first performed Northern blot
analysis of RNA from the CNS (Fig. 2C
). LPAM
transcripts of ~7.0 kb and ~6.5 kb were detected. Taking into
account the length of the LPAM-1 cDNA and the absence of a
polyadenylation site, we concluded that the ~7.0 kb transcript
represents the LPAM-1 cDNA. To identify the putatively
alternatively spliced region in the 6.5 kb transcript
(LPAM-2, see below), RT-PCR was performed on CNS cDNA by
using the primer combinations indicated in Fig. 2B
. Only the
primer combination that covers the noncatalytic exon A domain yielded
two products, a prominent band of ~140 bp in addition to the 630 bp
product predicted by the LPAM-1 transcript (Fig. 2D
). Cloning and sequencing of the 140 bp PCR product
revealed that it contains the LPAM-1 cDNA sequence, but lacks the exon
A domain (bp 4169-4633). The exon A domain is not a retained intron,
since it does not disrupt the open reading frame and exon/intron
consensus sequences are absent at the boundaries (Fig. 2D
).
To determine whether the 6.5 kb LPAM-2 transcript lacks the
sequence of the exon A domain, Northern blot analysis was performed
with RNA prepared from Lymnaea CNS, by using the exon A
domain as a probe. Only the 7.0 kb LPAM-1 transcript was
detected (Fig. 2E
). Together, these results strongly suggest
that LPAM-1 and LPAM-2 are generated by
alternative splicing of exon A. Further transcript diversity is absent.
LPAM expression is restricted to neurons that express amidated
peptides
To address the question whether LPAM is strictly coexpressed with
amidated peptides, we performed single-cell RT-PCR on cDNA, generated
from identifiable neurons of the Lymnaea CNS. Neurons were
selected for which the complement of peptides synthesized is known from
previous studies, by using mass spectrometric methods applied to single
neurons 32-34)
. We selected three cell types that are
representative of neurons expressing amidated peptides: 1)
the caudo-dorsal cells (32)
; 2) the
visceral-dorsal neuron 1, (34)
; and 3) neurons
from the right anterior lobe cluster 35-38)
. As examples
of neurons that exclusively produce no
-amidated peptides, only two
cell types could be selected because most identifiable neurons in the
Lymnaea CNS produce amidated peptides. These cell types are
light green cells (39)
and the light yellow cells
(33)
.
For each cell type, at least three neurons were isolated and cDNA was
synthesized from each individual cell. PCR reactions on this cDNA were
performed for the neuropeptide transcripts and for LPAM. We found that
LPAM expression was restricted to neurons that express
amidated peptides (Fig. 3A
), indicating that peptide
-amidation gene expression is
indeed tightly regulated.
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To examine the cellular localization of the LPAM-1 and
LPAM-2 transcripts in more detail, RT-PCR was performed on
the same cDNA from neurons that were shown to express the
LPAM gene (see above). Primer sets specific for the presence
of the exon A domain (LPAM-1) and specific for the absence
of exon A (LPAM-2) were used. PCR products representing the
LPAM-1 transcript were detected only in a subset of neurons of the
right anterior lobe cluster (Fig. 3B
, upper panel), whereas
the PCR product representing the LPAM-2 transcript is
present in all neurons analyzed (Fig. 3B
, lower panel).
LPAM-1 and LPAM-2 proteins are structurally multifunctional PAM
zymogens
LPHM and LPAL characteristics
The interspecies sequence identity between LPHM-1 to LPHM-4 and
rat PHM varies between 37% and 40% (Fig. 2B
and Fig. 4A
). Identical amino acid residues and conserved substitutions
are restricted to a number of small regions, which form the core of the
enzyme and are essential for catalytic activity (40)
. The
eight conserved Cys residues, which form four intrachain disulfide
bondstwo in the amino-terminal and two in the carboxy-terminal domain
of the catalytic core of rat PHM (41)
are conserved in
the other type 2 copper monooxygenase, dopamine ß-monooxygenase (EC
1.14.17.1; DßM), as well as in all LPHM domains. In addition, the
five essential His residues (rat PHM residues 107, 108, 172, 242, and
244) and Met314, which are involved in copper binding, are
present in all four LPHM domains (23
, 40
,
42
). Arg240, Asn316, and
Tyr318, which are involved in substrate binding, and
Tyr79, whose mutation affects the Km
for the peptidylglycine substrate, are also conserved.
|
The amino acid sequence identity in the LPAL domain (Fig. 4B
) is also restricted to short stretches of residues, and
four Cys and six His residues are conserved. PAL is a metalloenzyme,
requiring divalent ions for optimal activity (16)
. As in
PHM, the conserved His residues in PAL may be involved in metal ion
binding and the conserved Cys residues may be important for protein
folding (23
, 41
, 42
).
The cytoplasmic domains of LPAM and rat PAM exhibit 39% sequence
identity, indicating the presence of functionally important residues in
this domain. In the cytoplasmic domain of rat PAM, residues
Ser937 and Tyr936 are crucial for intracellular
routing of PAM and for internalization of integral PAM protein after
exocytosis (25
, 43
). In LPAM-1,
Ser1915 corresponds to rat PAM Ser937, but
Tyr936, critical to internalization, is replaced by an Asn
(Fig. 4C
). The cytoplasmic domain of LPAM is shorter by 18
residues, indicating the lack of an exon equivalent to rat exon
Bb (5
, 30
, 31
). As
in rat PAM, LPHM has a high percentage of acidic and charged residues
near its carboxyl terminus, including several putative casein kinase II
phosphorylation sites. The Pro-Glu-Ser-Thr sequence at the
carboxy-terminal of rat PAM-1 is only weakly represented in LPAM.
Phylogenetic relatedness of PHM domains
We determined the phylogenetic relatedness of the LPHM domains to
other type 2 copper monooxygenases, including Drosophila and
vertebrate PHM, rat DßM, and Drosophila tyramine
ß-hydroxylase (TßH), using a protein distance matrix to compute the
phylogenetic distance between the protein sequences (Fig. 4D
). It demonstrates that the LPHM domains and DPHM are
related to the PHM proteins of vertebrates. Bootstrap analysis of the
tree and the data set shows that the assignment of the LPHM domains to
the vertebrate PHM class is supported with 100% confidence.
The extensive branch lengths of the four LPHM domains indicate that
after multiplication of the LPHM domains, considerable structural
diversification occurred, as delineated in Fig. 4E
. The
shared sequence identity of the PHM domains in Lymnaea
(55%) is even lower than that of the PHM domains of the various
vertebrate species (63%; human, bovine, rat, and Xenopus;
5).
The four LPHM domains and the LPAL domain display enzyme activity
The high sequence divergence among the LPHM domains might reflect
random mutations and consequent loss of function or, alternatively,
mutations that allow diversification of the catalytic properties of
each LPHM domain. Because the endogenous LPHM and LPAL forms are single
enzyme entities, we could address this issue and evaluate the four LPHM
domains and the LPAL domain for their individual activity.
We made expression constructs of each putative domain of LPAM and
created five sets of hEK-293 cell lines, each set stably expressing one
of the four LPHM domains or the LPAL domain. Spent medium from each
cell line was assayed for protein production by Western blot analysis
(data not shown) and for hydroxylating (PHM) or peptide
-amidating
lyase (PAL) activity by using the synthetic tripeptide substrates
-N-Ac-Tyr-Val-Gly or
-N-Ac-Tyr-Val-
-hydroxyglycine, respectively
(10)
. The pH dependence of the reactions as well as the
copper and ascorbate dependence of the LPHM domains were determined.
Spent medium from cells expressing recombinant rat PHM and PAL served
as controls. All four LPHM proteins and LPAL were active (Fig. 5
). Because all four LPHM domains behaved similarly with respect to
pH, copper, and ascorbate, only the results obtained with LPHM-3 are
shown. As with rat PHM (44)
, the LPHM domain showed
maximal activity at acidic pH; activity at pH 5 was about threefold
higher than at pH 7 (Fig. 5A
). The pH range of LPAL was even
broader than that of rat PAL (16)
. As rat PHM
(23)
, each LPHM domain showed a similar dependence on
ascorbate (Fig. 5B
), with optimal activity observed with
0.51 mM ascorbate. Also, each LPHM domain showed dependence on copper
(Fig. 5C
), with optimal activity observed with 0.52 µM
CuSO4. As shown for rat PHM (45)
, addition of
diethyl-dithiocarbamate, a copper chelator, abolished nearly all LPHM
activity, showing that the LPHM proteins require copper for catalytic
activity. Thus, despite sequence divergence, each LPHM domain displays
catalytic activity and shows pH and cofactor requirements similar to
rat PHM.
|
The LPHM enzymes display distinct substrate specificities
Rat PHM hydroxylates peptidylglycine substrates with different
amino acid residues at the penultimate position, with different
affinities and at different rates (3
, 6
,
7
, 23
). Therefore, we examined the
possibility that each LPHM domain might show a distinctive pattern of
kinetics toward different synthetic tripeptide substrates. Three
substrates were chosen, for which rat PHM displays a high, a medium,
and a very low affinity, respectively. For each LPHM domain and for
each substrate, the data could be fit to Michaelis-Menten kinetics. The
data obtained with each LPHM domain using the
ga-N-Ac-Tyr-Val-Gly and ga-N-Ac-Tyr-Phe-Gly
substrates are shown as Eadie-Hofstee plots (Fig. 6
A). The values obtained with
ga-N-Ac-Tyr-Gly-Gly are presented together with the
substrate affinity (Km) (Fig. 6B
) and
Vmax (Fig. 6C
) for the other
substrates, showing that each LPHM domain yielded a distinct set of
values for Km and Vmax
(Table 1
).
|
|
| DISCUSSION |
|---|
|
|
|---|
-amidation in molluscs. In this paper,
we set out to identify the peptide
-amidating enzymes from the
snail, L. stagnalis.
Using a PCR amplification and cDNA cloning strategy, we identified a
PAM sequence from the Lymnaea CNS. Many structural features
uniquely identify LPAM as a true PAM homologue, having both PHM and PAL
catalytic domains. LPAM and vertebrate PAMs share this type of
organization, in contrast to Drosophila and
Calliactis (11
, 12
). In
vertebrates, PHM and PAL are synthesized as a bifunctional protein on a
single gene. In the fruit fly Drosophila, both PHM and PAL
activities were demonstrated. The PHM and PAL enzymes do not form a
bifunctional enzyme and are encoded by distinct genes (P. H.
Taghert, personal communication, 11). LPAM is unique in that it has
four strongly structurally divergent (Fig. 4)
yet functional (Fig. 5)
PHM domains. All four LPHM domains and the LPAL domain show typical
sequence characteristics, in which all residues essential for catalytic
activity and for copper and substrate binding have been conserved (Fig. 4)
. Apart from these residues, sequence conservation is low.
During evolution, proteins have evolved frequently by duplication of entire genes and further mutation, giving rise to families of structurally related proteins. A clear example is represented by the prohormone convertases [reviewed by Seidah and Chrétien (46) ], which form a family of structurally and functionally related serine proteases. In contrast, examples of intragenic duplication in genes encoding enzymes are rare. However, there is an example where intragenic duplication is thought to have given rise to two isoenzymes, i.e., endothelial angiotensin I-converting enzyme (47 , 48 ). The two enzymes that have evolved may, in some instances, convert different substrates (49 , 50 ). The LPAM precursor is a unique example of intragenic duplication and subsequent mutation that gave rise to the specific kinetic features of four (PHM) isoenzymes.
LPAM expression in the Lymnaea brain
Many neurons of the Lymnaea CNS use complex peptide
cocktails as messages for communication with follower cells [reviewed
by Nässel (51)
]. Therefore, diversity and ratio of
the peptides in a cocktail must be strictly controlled in order to
assign a message-specific informational content to the peptide
cocktail. The
-amidation of peptides is often essential for their
bioactivity and, as such, to the specificity of peptide messages in the
Lymnaea CNS. Clearly, in addition to the molecular
mechanisms underlying the generation of different LPHM enzymes, a
strictly regulated cellular expression of LPAM is an important
mechanism assuring complete amidation of peptide substrates. It has
been observed that in the rat CNS, PAM is expressed in regions where
many amidated peptides are produced, such as the hippocampus and
hypothalamus (52
, 53
). On the other hand, PAM
immunoreactivity is also observed in neurons and other tissues not
known to produce
-amidated peptides (52
,
54
). However, in the rat brain it is not possible to
examine cellular coexpression by applying single-cell analysis. Because
of the large size of Lymnaea neurons, this issue can be
examined by applying the very sensitive method of RT-PCR on individual
identifiable neurons. Indeed, using this approach demonstrated a
tightly regulated expression of LPAM exclusively in neurons
that coexpress amidated peptides (Fig. 3)
.
The LPAM gene, like the PAM gene in the rat,
generates two major transcripts, LPAM-1 and
LPAM-2, probably by alternative splicing of the exon A
domain in the pre-mRNA (Fig. 2)
. The exon A domain containing
LPAM-1 transcript is coexpressed with LPAM-2 in a
few neurons that express the peptide conopressin and APGWamide (Fig. 3)
, whereas the LPAM-2 transcript is found in all other
neurons that synthesize amidated peptides. Because the role of exon A
in the LPAM-1 precursor is not understood (see below), the functional
reason for the difference in cellular expression pattern of the
LPAM-1 and LPAM-2 transcripts is not clear.
Processing of the LPAM precursor into five distinct enzymes
The LPAM-1 and 2 zymogens are endoproteolytically processed to
five individual catalytic domains (Fig. 1)
. Endoproteolytic cleavage
has to occur at sites by a hitherto unknown protease. Furthermore,
based on LPAL activity in the soluble fraction, LPAL is generally
cleaved from the transmembrane domain (Fig. 1)
. Because dibasic or
multiple basic processing sites are absent carboxy-terminal to LPAL,
the endoproteolytic cleavage that generates soluble LPAL must occur at
a different site. Thus, the LPAM zymogens are cleaved at
nonconventional sites, illustrating that enzymes different from the
Kex2-related prohormone convertases (46)
are active in the
secretory pathway. That the region carboxy-terminally from PHM is
accessible for cleavage is suggested by the limited tryptic digestion
of rat PAM in vitro, which results in endoproteolysis at the
carboxyl terminus of rat PHM in a protease accessible region (exon 15:
rat PHM Met360 to Gln392; 23) that is not
required for catalytic activity. This cleavage increases the turnover
number and affinity of PHM for its substrates in rat (44
,
55
). The rat PHM protease accessible region has virtually
no sequence identity with its counterpart in any of the four LPHM
domains (Fig. 4A
).
In vivo, endoproteolytic processing of rat PAM-1 can occur
at a cleavage site consisting of paired basic amino residues present in
the noncatalytic linker (exon A or exon 16; 5), which separates the PHM
domain from the PAL domain. When this cleavage site is used,
monofunctional PHM is generated from integral membrane PAL
(16
, 56
). The region in LPAM-1 corresponding
to the exon A domain is present, but much longer (157 vs. 105 amino
acid residues) and without significant sequence identity (Fig. 2B
and Fig. 4C
). However, it contains the
residues
Arg1378-His1379-Lys1380-Arg1381,
which may serve both as a potential dibasic cleavage site and a
consensus sequence for furin catalyzed cleavage (57)
.
Conservation of cleavage sites without conservation of the overall
sequence would be consistent with a role for exon A in the generation
of soluble LPHM(1-4) domains. The functional relevance of a cleavage in
exon A remains obscure because all the LPHM enzyme domains are
solubilized anyway, very likely by endoproteolysis at the protease
sensitive regions.
Each LPHM displays a different combination of substrate affinity
and reaction velocity
The precursor of carboxypeptidase D (gp180; 58) encodes three
(different) carboxypeptidase domains. Because only two of these domains
show catalytic activity, the question rises whether, in analogy to
this, all four LPHM domains and the LPAL domain maintained their
activity. Clearly, single amino acid changes can obliterate all enzyme
activity (41)
. Individual LPHM domains expressed and
secreted by hEK293 cells are capable of converting synthetic
-N-Ac-Tyr-Xxx-Gly tripeptide substrates (Fig. 5
and Fig. 6
). This demonstrated that, although the LPHM domains have strongly
divergent sequences, they are all catalytically active. Next, the
maximal conversion rates and affinity values of each domain toward the
three substrates (i.e.,
-N-Ac-Tyr-Val-Gly,
-N-Ac-Tyr-Phe-Gly and
-N-Ac-Tyr-Gly-Gly)
were tested (Table 1)
. When the substrate affinities for the different
substrates were compared, each LPHM domain displayed a unique set of
affinity values. Whereas LPHM-1 and -2 showed high affinities (low
Km) toward the three substrates tested, LPHM-3
and -4 showed lower affinities. The affinity of rat PHM toward
-N-Ac-Tyr-Gly-Gly was very low, with a
Km of 680 ±230 µM (see also ref 7
). In
contrast, the LPHM domains displayed about 10-fold higher affinity for
this substrate. In short, the affinity of the LPHM domains toward the
three substrates were in most cases higher than the affinity of rat PHM
toward the same substrates. Subsequently, the relative
Vmax values of the LPHM domains for the three
different substrates were compared. Based on the relative
Vmax values for the
-N-Ac-Tyr-Gly-Gly substrate, LPHM-2 and LPHM-4 form a
class distinct from LPHM-1 and LPHM-3. Yet LPHM-2 and LPHM-3 show a
relative low Vmax for the
-N-Ac-Tyr-Phe-Gly substrate, which is in contrast to
LPHM-1 and LPHM-4.
Together, the results indicate that sequence divergence of the LPHM domains resulted in a unique combination of Km and relative Vmax values for each LPHM and for the three substrates studied. The physiological relevance of this finding could be the involvement of one or more LPHMs in brain fatty acid amide formation, as postulated for mammalian PHM (59 , 60 ). In addition, the four LPHM enzymes together may allow for maximal reaction velocities under conditions of various distinct substrate and varying substrate concentrations, a situation that occurs in secretory granules of different Lymnaea neurons.
| ACKNOWLEDGMENTS |
|---|
| FOOTNOTES |
|---|
1 Abbreviations: CNS, central nervous system;
DTßH, Drosophila TßH; LPAL, Lymnaea PAL
domain; LPAM, Lymnaea peptidyl glycine
-amidating
monooxygenase; PAL, peptidyl-
-hydroxyglycine
-amidating lyase;
PAM, peptidylglycine
-amidating monooxygenase; PHM, peptidylglycine
-hydroxylating monooxygenase; 5'-RACE, 5'-rapid amplification of
cDNA ends; RT-PCR, reverse transcriptase polymerase chain reaction;
TßH, Drosophila tyramine ß-hydroxylase; TGN,
trans-Golgi network; TMT, TM with 1% Triton X-100. ![]()
Received for publication September 15, 1998.
Revision received December 3, 1998.
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