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Endocrinology Vol. 138, No. 6 2380-2390
Copyright © 1997 by The Endocrine Society


ARTICLES

Two Protochordate Genes Encode Pituitary Adenylate Cyclase-Activating Polypeptide and Related Family Members1

John McRory and Nancy M. Sherwood

Department of Biology, University of Victoria, Victoria, British Columbia, Canada, V8W 2Y2

Address all correspondence and requests for reprints to: Dr. Nancy Sherwood, University of Victoria, Department of Biology, P.O. Box 1700, Victoria, British Columbia, Canada V8W 2Y2. E-mail: Nsherwoo{at}uvic.ca


    Abstract
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
To address the origin of the glucagon superfamily, we isolated and sequenced the complementary DNA and partial gene that encode pituitary adenylate cyclase-activating polypeptide (PACAP) from a protochordate (tunicate), a sister group of the amphioxus and vertebrates, but one that evolved before the amphioxus. This is the first report of any superfamily member sequenced from an invertebrate. Transcription of the tunicate pacap1 gene results in a messenger RNA that is 507 bp. The gene contains 3 exons that encode a signal peptide, GRF-like peptide1–27, and PACAP1–27. The tunicate GRF-like peptide has 59% identity with human GRF, whereas the deduced amino acids of tunicate PACAP1–27 have 96% identity with the ovine, human, and salmon PACAP1–27 forms. Another complementary DNA clone pacap2 was isolated and shown to contain 4 exons that encode a signal peptide, a cryptic peptide, and two peptides that are clearly members of the glucagon superfamily. One of the peptides has 89% sequence identity to the tunicate PACAP encoded in pacap1. A comparison of the two structurally related PACAP clones, each encoding two peptides on separate exons, shows high inter- and intraexon nucleotide sequence identity. Sequence analysis suggests that an exon duplication followed by a gene duplication was responsible for the origin of the two genes. It is argued that the PACAP gene is derived from the protochordate ancestral genes that led to the vertebrate forms of GRF and PACAP.


    Introduction
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
DURING THE past century, studies on protochordates (tunicates/sea squirts) have increased our understanding of chordate phylogeny (1, 2). Protochordate maturation consists of a two-step process involving a motile juvenile stage followed by morphogenesis to a settled stage when the organism matures. The Garstang theory postulates that vertebrates arose when an ancestral relative did not settle but became reproductive during the larval stage (3). Thereafter, this neotenous motile organism, like the present-day group of tunicates known as larvaceans, reproduced without settling and may have given rise to the ancestral cephalochordates (amphioxus) and vertebrates. This theory helps us to understand physiological features of vertebrate development and evolution. However, the evolution of the nervous system, in the transition from invertebrates to vertebrates, is not clearly understood. Even the origin of the pituitary in vertebrates remains unknown, because organisms that contain the primordial structure are lacking.

To understand the evolution of the nervous system, one approach is to compare the structure and location of neuropeptides in protochordates and mammals. However, limited structural data exists in protochordates for genes, complementary DNAs (cDNAs), and proteins with homology to their vertebrate counterparts. Studies have shown that protochordates produce neuropeptides that cross-react with antisera raised against mammalian peptides (4), including LHRH, SS (5), and neurotensin-like peptides (5). Also, glucagon (6) and {alpha}MSH (7) immunoreactivity have been detected within the protochordate Ciona intestinalis. In the same tunicate, cross-reactivity is detected in the nervous system and alimentary tract with antisera raised against mammalian insulin (8, 9, 10), neuropeptide Y (5, 11), peptide histidine isoleucine (12), vasoactive intestinal peptide (VIP), secretin, and pancreatic polypeptide (5). Evidence relating to immunocytochemical localization, tissue expression, and nucleotide and amino acid sequences of protochordate genes and peptides should clarify aspects of the evolution of the vertebrate nervous system. To date, the sequences for three protochordate neuropeptides with identity to their mammalian counterparts have been determined. The first tunicate neuropeptide to be identified was cionin (13), which is a unique hybrid of cholecystokinin and gastrin. The other two tunicate neuropeptides were GnRH-like peptides associated with tunicate neural structures (14, 15). Mackie (16) showed that immunoreactive GnRH cells form a neural plexus surrounding the dorsal strand. Determination of the peptide sequence of two forms of tunicate GnRH made it possible to prepare synthetic forms of GnRH (17). Injections of these two tunicate GnRH forms resulted in an increase in the content of estradiol in the gonads (Sherwood, Rivier, and Mackie; unpublished observation). Hence, a separation of approximately 600 million yr (18) did not obscure the origin of GnRH, in that the tunicate GnRH peptides each has a sequence identity (60%) and a conserved function to that found for mammalian GnRH.

The primary structure of members of the glucagon superfamily, however, has not been identified in protochordates. In humans, the glucagon superfamily is composed of GRF (19, 20), glucagon (21), glucagon-like peptides (GLP-1 and GLP-2) (22), secretin (23), VIP (24), glucose-dependent insulin-releasing polypeptide (GIP) (25), and pituitary adenylate cyclase-activating polypeptide (PACAP) (26, 27). PACAP, the newest family member, is of particular interest because: 1) the nucleotide and amino acid sequence is highly conserved among mammals (26, 27), birds (28), and fish (29); and 2) in addition to its role as a releaser of pituitary hormones, it seems to have a role as a growth factor in the developing nervous system (30, 31) and primordial germ cells (32). It is assumed that the glucagon superfamily members share a common ancestor, based on similar amino acid sequences and intron/exon structure (33, 34). However, the hypothesis that extant superfamily members originated from a common ancestor is speculative, because structural evidence is not available. To investigate the origin of the glucagon superfamily, we used molecular techniques to determine the nucleotide sequence and tissue expression of PACAP within the protochordate Chelyosoma productum. This paper reports the structure of two protochordate cDNAs and two partial genes in which the first gene, pacap1, encodes both a GRF1–27-like peptide and PACAP1–27, whereas the second gene, pacap2, encodes two structurally-related peptides of the glucagon superfamily.


    Materials and Methods
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Construction of cDNA library
Tunicates (Chelyosoma productum) were dissected from their tunic. The dorsal internal organs (mainly the neural ganglion, neural gland, and dorsal strand) were separated from the gonads, gut, and branchial basket. These dorsal organs were placed immediately in liquid nitrogen and stored at -80 C. Total RNA was extracted with an acidic guanidinium thiocyanate method (35), and poly A+-rich messenger RNA (mRNA) was purified with the Poly Attract System (Invitrogen, San Diego, CA). The cDNA library was constructed with the UNI-Zap-cDNA synthesis kit (Stratagene, La Jolla, CA) and Gigapack packaging mix.

Amplification of tunicate pacap1 cDNA by PCR
DNA was amplified using a cDNA library lysate and the degenerate primers Tun 1 (5'-cattcggatgggatcttcacggatag) and Tun 2 (5'-catgtttggacagaacacaacgtgagcg). First round amplification was done in a 50-µl vol reaction that contained 0.2 µg cDNA, 5U Taq, 1 x Taq buffer (Pharmacia, Baie d’urfé, Québec, Canada), 200 mM dNTPs (2'-deoxynucleoside-5'-triphosphates), 2 mM MgCl2, 20 pmol of primers Tun 1 and Tun-2 with 40 cycles at 94 C for 1.5 min, 45 C for 2 min, and 72 C for 2.5 min. PCR reactions were electrophoresed on a 2% agarose gel. The cDNA in the bands from the gel was cloned into pBluescript KS+ (Stratagene), electroporated into XL-1 Blue (MRF’) cells and prepared for sequencing with an alkaline hydrolysis method (36). Both strands of the plasmid were sequenced with [{alpha}-35S] dATP (2'-deoxyadenosine-5'-triphosphate) using the chain termination method (37) with Sequenase 2.0 (US Biochemical Corp., Cleveland, OH) and Vent (exo-) (New England Biolabs, Beverly, MA). All sequencing gels were 6% polyacrylamide/7 M urea wedge gels, dried under vacuum at 80 C and exposed to Kodak XAR-5 film for 12–24 h.

Tissue assay by RT/PCR
mRNA was isolated from the following tissues: neural gland, dorsal strand/neural ganglion, gonad, gonad/digestive gland, intestine, heart, tunic, and branchial basket. Single-stranded cDNA was synthesized from 0.5 µg mRNA for each tissue, using 200 U avian RT (H- Superscript RT, Gibco-BRL, Burlington, Ontario, Canada), 10 mM dithiothreitol, 1 mM each dNTP, 160 U RNA guard, 2 mM oligo dT20, and 1 x H- RT buffer, to a total reaction vol of 20 µl. The reaction proceeded for 90 min at 41 C, followed by 5 min at 90 C. DNA amplifications were done in a 50-µl vol that contained 0.5 µg cDNA, 1 x Taq buffer (Pharmacia), 200 µM dNTPs, 1.5 mM MgCl2, and 20 pmol of each primer. The pacap-specific primers were Tun 3, (5'-tacactggattgtcttggccgcc) and Tun 4 (5'-cgctcagcatgagttctgtc). The vip-specific primers were Tun 5 (5'-gacggtaacgattcttatgc) and Tun 6 (5'-gcctaacagatagcctagtc). All reagents, except the Taq enzyme, were mixed, layered with mineral oil, and heated to 95 C for 5 min. The mixture was frozen rapidly in a dry ice/ethanol bath and Taq DNA polymerase (5U, Promega) was added. The tubes were replaced in the preheated 95 C thermal cycler where 40 cycles at 95 C for 1 min, 55 C for 2 min, and 74 C for 1.5 min were completed. Tubulin PCR amplifications were in a 50-µl reaction that contained 0.5 µl cDNA from each tissue, 5U Taq DNA polymerase, 1 x Taq buffer (Pharmacia), 200 µM each dNTP, 3 mM MgCl2, and 20 pmol of each tubulin primer. The reactions were carried out for 35 cycles of 94 C for 1 min, 55 C for 1.5 min, and 72 C for 1.5 min.

Screening of cDNA library
A total of 5 x 104 pfu from the tunicate library was screened. Duplicate nylon membrane (Bio-Rad, Mississauga, Ontario, Canada) lifts were prehybridized at 50 C in 6 x SSC, 5 x Denhardt’s solution, and 0.5% SDS for 4 h. The hybridization solution consisted of 6 x SSC and 0.5% SDS, to which the probe was added. The probe was a 163-bp product amplified by PCR with primers Tun-1 and Tun-2. The probe was labeled with [{alpha}-32P]dCTP (7.8 x 106 cpm/ml), and the membranes and the probe were incubated at 50 C overnight. The membranes were washed under high stringency (0.1 x SSC/0.1% SDS) for 50 min at 65 C, then exposed to Kodak XAR-5 film for 5 days at -80 C. Isolated single positive clones were cored and inserts rescued with in vitro excision.

Genomic DNA amplification
Tunicate genomic DNA of high molecular weight was digested with proteinase K (Sigma), followed by repeated phenol:chloroform:isoamyl alcohol (24:24:1) washes. The extract was dialyzed against 0.01 M Tris-HCl/EDTA. Primers (Tun 3 and 4) to the 5' untranslated region (5'UTR) and 3'UTR of the tunicate pacap cDNA or primers Tun 5 and 6 to the vip cDNA were used in the amplification of the tunicate genes. Amplifications were done in a 50-µl vol (1.0 µg DNA, 5U Taq, 1 x Taq buffer, 200 µM dNTPs, 2 mM MgCl2, 20 pmol of each primer) with 40 cycles at 94 C for 1.5 min, 45 C for 2 min, and 72 C for 2.5 min. The reaction was electrophoresed through a 1.5% agarose gel. A band was cloned into pBluescript KS+ (Stratagene); the plasmid and insert were electroporated into XL-1 (MRF’) competent cells; and the extracted DNA was prepared for sequencing with an alkaline hydrolysis method (35).

Zoo blot and Southern analysis
For the zoo blot, DNA (10 µg) was prepared from rat (Rattus norviegus), starling (Sturnus vulgarus), chicken (Gallus domesticus), alligator (Alligator mississippiensis), Pacific salmon (Oncorhynchus nerka), catfish (Clarias macrocephalus), reedfish (Calamoichthys calabaricus), tunicate (Chelyosoma productum), urchin (Strongylocentrotus purpuratus), Drosophila (Drosophila melanogaster), yeast (Saccharomyces cerevisiae), and bacteria [Escherichia coli (E. coli)]. DNA for the zoo blot and Southern blot (tunicate DNA only) were digested to completion with EcoRI and electrophoresed in a 0.8% agarose gel. The DNA was transferred, as suggested by the manufacturer (Bio-Rad), for the alkaline Zeta-Probe GT membrane. Prehybridization was in 7% SDS, 0.5 M NaH2PO4, and 1 M EDTA at 65 C for 15 min. Hybridization was overnight (14 h) at 65 C in fresh prehybridization solution plus the 163-bp probe labeled with [{alpha}-32P]dCTP. The hybridized membranes were rinsed with 5% SDS, 40 mM NaHPO4, and 1 mM EDTA and then washed for 45 min at 45 C with fresh solution. The wash solution was then changed to 1% SDS, 40 mM NaHPO4, and 1 mM EDTA and washed twice for 45 min at 65 C with fresh solution. After washing, the membrane was sealed in plastic and exposed at -80 C for 8 days to Kodak BIOMAX (Rochester, NY) film.

In situ hybridization of tunicate pacap1 and pacap2 mRNA
Localization of the tunicate pacap1 or pacap2 mRNA in sections from the neural ganglion of Cheylosoma productum was done by in situ hybridization using a digoxigenin (DIG)-labeled tunicate pacap1 or pacap2 cRNA probe. All RNA probes were synthesized, purified, and tested in accordance with the manufacturer’s (Boehringer Mannheim, Laval, Québec, Canada) instructions. The changes in protocol for fixation, prehybridization, and hybridization are listed below. The tunicate neural gland and ganglia were dissected and pinned on Sylgard-coated dishes and fixed for 3 h in 4% paraformaldehyde in PBS (pH 7.4). The fixed tissues were washed in PBS and soaked overnight in 30% sucrose. Tissue was embedded in Tissue-Tek O.C.T. compound (Miles Inc., Elkhart, IN), then sectioned (10 µm), and allowed to dry on poly-L-lysine-coated slides. Sections were fixed again in 4% paraformaldehyde for 5 min, washed three times in PBS (5 min each), and placed for 10 min in 2 x SSC. Prehybridization was in 2 x SSC for 2 h at room temperature. This solution was exchanged for the hybridization solution that consisted of 2 x SSC with a DIG-labeled RNA probe diluted 1:200. The hybridization solution was incubated overnight at 42 C. The sections were washed with SSC (0.5 x SSC) followed with 2% normal goat serum in TBS buffer for 30 min at room temperature. The remaining steps, involving the anti-DIG antibody and the substrate detection, were performed in accordance with the manufacturer’s (Boehringer Mannheim) instructions.


    Results
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Isolation of the tunicate pacap1 and pacap2 mRNAs
We have isolated a cDNA that encodes PACAP1–27 (96% identity to human PACAP1–27) from a tunicate cDNA library (Fig. 1AGo). Encoded within the pacap cDNA is another peptide that could be a GRF-like peptide (59% identity to human GRF) or tunicate glucagon (67% identity to human glucagon). However, with GRF as the 5' adjacent peptide in preproPACAP in birds and fish, the peptide in the same position in tunicates is most likely a GRF-like peptide and not glucagon. Another clone, distinct from the pacap clone, was isolated from the tunicate cDNA library (Fig. 1BGo). This clone, pacap2, also encodes a PACAP-like peptide but is not the same as the pacap1 cDNA clone, because of nucleotide changes within the exons and differences in the exon/intron borders of the two isolated genes.



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Figure 1. Nucleotide and deduced amino acid sequences of the tunicate pacap1 and pacap2 cDNA clones. A, The 507-bp tunicate pacap1 cDNA; B, the tunicate 883-bp pacap2 cDNA. The primers used for the expression study are underlined or overlined in the sequences and shown on the box diagrams. Coding regions are indicated by boxes and 5' and 3' untranslated regions by thin lines. The box with horizontal lines encodes the signal peptide and the white box encodes a cryptic peptide. In box diagram A, the diagonally striped box encodes GRF-like peptide and the vertical lined box encodes PACAP. In box diagram B, the diagonally striped box encodes a distinct GRF-like peptide and the box with vertical lines encodes a distinct PACAP-like peptide.

 
For isolation of the tunicate pacap cDNA clone, 2 primers (Tun 1 and Tun 2) were used with the PCR to amplify a 163-bp fragment that encoded only tunicate PACAP and 57 bp of the 3'untranslated region. This fragment was used to screen a tunicate cDNA library. After screening 5 x 104 pfu from the library, 15 plaques were found that hybridized to the radioactive probe. Of the 15 clones that hybridized to the probe, 10 were purified. These clones were removed from the phage with in vitro excision, purified, and sequenced. It was determined that all clones were identical and all encoded tunicate GRF1–27/PACAP1–27 (Fig. 1AGo). The remaining 5 phage DNA clones that hybridized to the probe were purified, and 1 encoded a different cDNA. The latter clone is referred to as tunicate pacap2 cDNA, because it has 1 exon with 85% sequence identity to human PACAP1–27; another exon has 59% identity with human GRF1–27 and 63% identity with human glucagon (Fig. 1BGo). Therefore, tunicates contain 2 different mRNAs; both encode tunicate PACAP1–27, named because of the high identity to the mammalian PACAP1–27 protein. In addition, the 2 exons in each clone have identity with other family members: the PACAP exons have 67% identity with VIP, and the adjacent exons have 63–67% identity with glucagon.

The tunicate pacap1 cDNA clone was 507 bp long and encodes a signal peptide, a GRF-like peptide1–27 and PACAP1–27; no other proteins are encoded (Fig. 1AGo). The tunicate cDNA does not encode the longer version of PACAP1–38 or the GRF-like peptides of 43–46 amino acids that are found in vertebrates.

The tunicate pacap2 mRNA was 883 bp and encoded a signal peptide, possibly a cryptic peptide, and 2 peptides with identity to members of the glucagon superfamily (Fig. 1BGo). Encoded within the tunicate pacap2 cDNA sequence, but not found in the tunicate pacap1 cDNA, are 159 nucleotides that encode a 53-amino-acid cryptic peptide, if the first ATG codon is assumed to be the correct start site. However, if the 3rd ATG start site is correct, then a cryptic peptide does not exist, but the 5'UTR is longer. The tunicate peptide encoded immediately after the cryptic peptide has amino acid identity (33–63%) to all superfamily members in humans.

The two cDNAs are similar in sequence. The nucleotides in the coding regions for the tunicate PACAP1–27 and the corresponding region of the pacap2 gene are 93% identical, that is, only six bases are different. Identity of the tunicate PACAP amino acids to other members of the glucagon superfamily ranges from 96% with human PACAP to only 19% with human glucose-dependent insulin-releasing polypeptide (GIP).

Isolation of the tunicate pacap1 and pacap2 genes
The partial tunicate pacap1 gene isolated was 1590 bp long and encoded three exons, as deduced from the cDNA (Fig. 2Go). Located on the 1st exon is the 5'UTR and the signal peptide. The 2nd exon encodes GRF-like peptide, and the 3rd exon encodes PACAP1–27. No exon encoding a cryptic peptide was found between the signal and the bioactive peptides in the 14 cDNA clones isolated. In addition, a partial tunicate pacap2 gene of 1435 bp was isolated and, as deduced from its cDNA clone, contains 4 exons (Fig. 3AGo). Within the 1st intron of the pacap1 gene, nucleotides exist (position 313–442) that have a high identity (93%) with the encoded pacap2 cryptic segment (Fig. 3BGo). The 4 exons contain nucleotides encoding a signal peptide, possibly a cryptic peptide, 2 peptides that are similar to tunicate GRF1–27 and PACAP1–27, and a 3'UTR. Whether the tunicate pacap2 gene encodes a cryptic peptide, depends on the translation start site. The nucleotides encoding the cryptic peptide have high sequence identity to nucleotides within intron 1 of the pacap1 gene. However, corresponding exon/intron splice sites (exon/gt–intron–ag/exon) are not found in the pacap1 gene.



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Figure 2. Nucleotide sequence of the partial (1590-bp) tunicate pacap1 gene. PCR using primers directed to the 5' and 3' untranslated regions were used to amplify the gene. The exons are in bold print and have the encoded amino acid listed below. The region of intron 1 of the pacap1 gene that has high sequence identity to exon 2 of the pacap2 cDNA clone is underlined.

 


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Figure 3. Nucleotide sequence of the partial (1105-bp) tunicate pacap2 gene. A, The nucleotides for introns are shown in lower case and for exons in upper case. The translated amino acids are shown below their respective nucleotides. Both the amino acids and nucleotides are numbered on the right. The three possible start site ATG codons are boxed. The GRF-like peptide includes amino acids 75–101 and PACAP is amino acids 104–130. The cleavage sites (KR) between GRF and PACAP and at the end of PACAP are shown. B, A comparison of the nucleotides in intron 1 of pacap1 with those of exon 2 in pacap2 shows the high identity between the two regions.

 
Three putative start sites for the pacap2 prepropeptide
There are three ATG codons that are potential translation start sites for the pacap2 prepropeptide (Fig. 3AGo). If the first ATG is the correct start site, the prepropeptide is as described above, and a cryptic peptide is encoded. The second ATG site would mean that the 5'UTR is longer and the cryptic peptide is shorter than in the first prepropeptide. The third ATG site would result in the longest 5'UTR of the three cDNAs and loss of a cryptic peptide, compared with the other possible preprohormones. In contrast, there is only one possible ATG codon as a start site for the pacap1 prepropeptide (Fig. 2Go).

Tissue expression of tunicate pacap1 and pacap2 mRNA by a PCR method
A sensitive PCR detection method for the presence of tunicate pacap1 and pacap2 in various tissues was developed. For each cDNA clone, primers Tun 3 and 4 and Tun 5 and 6 (Fig. 1Go, A and B) were designed for the 5' and 3' untranslated regions. These regions were distinct and allowed the specific detection of either pacap1 or pacap2 mRNA/cDNA. Reverse transcribed cDNA of various tunicate tissues was amplified with clone-specific primers, and the results are shown in Fig. 4Go, A and B. Tunicate pacap1 mRNA was detected specifically in the neural ganglion but not in the reaction containing the tunicate neural gland, gonad, gonad/digestive gland, intestine, heart, branchial basket, negative control, or the reaction containing the tunicate pacap2 clone. Tunicate pacap2 mRNA was detected (Fig. 4BGo) in the neural ganglion, dorsal strand, intestine, and the reaction containing the tunicate pacap2 cDNA (positive control). Bands were not detected in the lanes containing the mRNA/cDNA from the neural gland, gonad, gonad/digestive gland, heart, branchial basket, negative control, or the lane containing the tunicate pacap1 clone.



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Figure 4. Tissue expression of tunicate pacap1 and pacap2 mRNA. A, Tunicate pacap1 mRNA detected by a RT/PCR assay. PCR reactions contained tissue cDNA as follows: neural ganglion (lane A), neural gland (lane B), gonad (lane C), gonad/digestive gland (lane D), intestine (lane E), heart (lane F), tunic (lane G), branchial basket (lane H), tunicate pacap2 cDNA clone (lane I), negative control (lane J), and pacap1 cDNA clone (positive control; lane K). B, Tunicate pacap2 mRNA detected by a RT/PCR assay. PCR reactions contained tissue cDNA as follows: neural ganglion (lane A), neural gland (lane B), gonad (lane C), gonad/digestive gland (lane D), intestine (lane E), heart (lane F), tunic (lane G), branchial basket (lane H), tunicate pacap1 cDNA clone (lane I), negative control (lane J), and pacap2 cDNA clone (positive control; lane K).

 
Localization of tunicate pacap1 and pacap2 mRNA with in situ techniques
To investigate the presence of pacap1 and pacap2 mRNA expression within the tunicate neural ganglion, we synthesized cRNA probes that are specific for either the pacap1 or pacap2 mRNA. The in situ hybridization sections were compared with sections stained with hematoxylin and eosin, which stains all cells in the neural ganglion (Fig. 5Go, A and B). Both mRNAs were localized in cortical cells of the neural ganglion (Fig. 5Go, C and E). Hybridization was not seen, using the sense RNA probe (Fig. 5DGo and F). The in situ hybridization evidence confirms the presence of both tunicate mRNAs in the cells of the neural ganglion.



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Figure 5. Sections (11 µm) of tunicate (Chelyosoma productum) neural gland and ganglion stained with (A and B) hematoxylin and eosin stain and (C–F) DIG-labeled probes. A, In a vertical section, the neural ganglion can be seen in the bottom half. The ring of large cells around the periphery of the ganglion is overlaid with the blood sinus, which contains a few blood cells. The neural gland (top) is the strip of tissue at the top of the section (magnification is x 40). B, In a horizontal section, the cells of the neural ganglion can be seen again at the periphery, whereas the neural gland is at the top of the section. C, Localization of tunicate pacap1 mRNA by in situ hybridization of the neural ganglion of Chelyosoma productum is shown using a DIG-labeled probe of pacap1 antisense mRNA (magnification x40). Also shown are (D) control reaction with a pacap1 sense (negative control) mRNA probe (magnification x16), (E) localization with a pacap2 antisense mRNA (magnification x40), and (F) control reaction with a pacap2 sense (negative control) mRNA (magnification x16).

 
Conservation of the pacap1 gene
A zoo blot containing genomic DNA from rat, starling, chicken, alligator, salmon, catfish, reedfish, tunicate, urchin, Drosophila, yeast, and E. coli was probed with the PCR-generated, 163-bp tunicate PACAP cDNA (Fig. 6Go). This 163-bp probe corresponds to the nucleotides encoding for tunicate PACAP. This probe not only has high sequence identity to all known pacap cDNAs, but may hybridize to other family members such as VIP. The tunicate 163-bp probe detected two bands in all lanes except the Drosophila, yeast, and E. coli, where bands were not detected. The two bands produced in the zoo blot may be caused by the conservation of the pacap and vip nucleotides; both pacap and vip are single-copy genes, at least in mammals, or the probe may have hybridized to the pacap1 and pacap2 genes in tunicates. In Fig. 7Go, tunicate DNA was digested to completion with EcoRI, and each lane was probed with one of four different cDNA probes. Lane A was probed with the 163-bp pacap PCR cDNA fragment and, because of a high identity between the two clones, is thought to have hybridized to both the pacap2 and pacap1 genomic sequences. Lane B was probed with a tunicate pacap1-specific probe (bases 387–531) that hybridized only to pacap1 genomic sequences. Specific hybridization to the tunicate pacap2 gene was obtained with a pacap2-specific probe (bases 713–907). In lane D, a clone-encoding tunicate pacap2 cDNA was used, and as expected, hybridization to both tunicate pacap1 and pacap2 occurred. Therefore, the two bands can be identified as pacap1 (5-kb band) and pacap2 (7.5-kb band) when digested with EcoRI.



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Figure 6. Zoo blot of DNA from various organisms probed with the 163-bp pacap1 PCR fragment. Zoo blot using rat (lane A), alligator (lane B), starling (lane C), chicken (lane D), salmon (lane E), catfish (lane F), tunicate (lane G), reedfish (lane H), tunicate (lane I), urchin (lane J), Drosophila (lane K), yeast (lane L), and E. coli (lane M) DNA that was hybridized with the 163-bp pacap1 PCR fragment. The two bands may be caused by the hybridization of the probe to both pacap and vip in vertebrates and to pacap1 and pacap2 in invertebrates.

 


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Figure 7. Southern blot analysis of tunicate DNA. The probes were the 163-bp pacap1 cDNA PCR probe (lane A), pacap1-specific probe (lane B), pacap2-specific probe (lane C), and a pacap2 probe (lane D). The tunicate DNA digested with EcoRI results in two bands that can be identified as pacap1 (5-kb band) or pacap2 (7.5-kb band). No EcoRI sites are present in the exons and introns within the areas probed.

 

    Discussion
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Tunicate PACAP is 96% identical to human PACAP
We have isolated from the protochordate Chelyosoma productum, a cDNA (Fig. 1AGo) and partial gene (Fig. 2Go) that encodes PACAP1–27. This finding is striking, in that the deduced amino acids from the tunicate pacap1 have 96% (26/27) identity, in comparison with the human and five other PACAP1–27 peptide sequences. The amino acids and nucleotides that encode PACAP have been maintained for over 600 million years (Fig. 8Go), a degree of identity unknown for any hormone of comparable size. PACAP was initially isolated and purified by Miyata (38) as a 38-amino-acid peptide. In the following year, another shorter form was found to be identical, in comparison with the first 27 amino acids of PACAP1–38 (39). A cDNA-encoding PACAP has been isolated from human (26, 27), sheep (26), rat (40), chicken (28), salmon (41), and catfish (29) brains, and interestingly, all PACAP peptides isolated have an amino acid sequence that is highly conserved. The isolation of tunicate pacap1 cDNA and partial gene is the first report of any superfamily member to be isolated from an invertebrate, and the deduced amino acids encode a peptide that is virtually identical to the vertebrate PACAP peptides.



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Figure 8. A comparison of the nucleotides that encode tunicate PACAP1–27 and human PACAP1–27. Identical nucleotides are shown by a connecting line ( ).

 
In mammals, the location and effects of PACAP suggest that one function is to stimulate the release of pituitary hormones. For example, in vitro studies showed that PACAP caused an increase in the release of not only GH, but also of several other pituitary hormones (42). PACAP stimulated GH and PRL release from GH3 tumor cells (43) and enhanced the effect of GnRH on LH release (44). In addition to PACAP’s role as a releaser of pituitary hormones, evidence suggests that PACAP acts as a growth factor during early stages of development. PACAP has been shown to promote neuroblast growth in the cerebral cortex, cerebellar granule cells, and sympathetic ganglia of fetal mice (30). Further evidence suggesting that PACAP is a potential growth factor is that PACAP promotes proliferation of mouse primordial germ cells (32). However, tunicates provide an interesting model for PACAP studies, because they seem to lack a pituitary gland. Pituitary-like hormones have not been reported for tunicates, and consequently, the ancestral role of PACAP must be distinct from that of a releasing hormone. Our findings, using in situ hybridization (Fig. 5CGo) and RT/PCR (Fig. 4Go) methods, show that tunicate pacap1 cDNA is expressed specifically in the neural ganglion. Therefore, the role of PACAP in protochordates is more likely to be that of a factor for cellular proliferation or growth than a releaser of pituitary hormones.

Tunicate pacap1 and pacap2 genes are related to other family members
A feature of the tunicate pacap1 and pacap2 genes is the high sequence identity found between the encoded peptides. The tunicate pacap2 mRNA encodes amino acids that have high sequence identity to the tunicate PACAP peptide (89%) and, in addition, to the human PACAP peptide (85%) (Fig. 9Go, A and B). This similarity is indicative of a gene duplication of the parent pacap gene, resulting in two tunicate genes. We argue that a duplication allowed one of the two genes, presumably pacap2, to evolve into a distinct gene, encoding related, but different peptides.



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Figure 9. A, Percent identity of the four tunicate peptides in comparison with the human members of the glucagon superfamily; B, schematic showing the percent identity of the deduced peptides in comparison with each peptide within the precursor and between each precursor.

 
Meanwhile, the ancestral pacap1 gene may have encoded the progenitors for mammalian pacap and grf genes. GRF is encoded on the same gene as PACAP, at least in tunicates, fish, and chickens. Based on sequence data from chickens (28) and fish (29, 41), distinct grf and pacap genes probably originated from a pacap gene duplication after the avian/reptilian lineage split from the lineage that gave rise to the present day mammals. A list of the identified glucagon family members for different vertebrate species has been published (33), but it is difficult to deduce whether specific members evolved from ancestral tunicate PACAP genes. It is interesting that the sequence identity is sometimes greater between tunicate and human peptides than with those of species closer in evolutionary origin to tunicates.

Exon and gene duplication produced two tunicate genes
The identity shared between exons on the same gene suggests exon duplication occurred before the gene duplication (Fig. 9BGo). Within the pacap2 gene, the similarity of amino acids between exons 3 and 4 suggest an exon duplication: the nucleotides encoding exons 3 and 4 are similar in length, the nucleotides are 57% identical, and the encoded amino acids have 48% identity. This data from the pacap2 gene is the best proof to date to confirm the speculation that the two exons originated by an exon duplication. Based on amino acid identity, we argue that exon duplication preceded the gene duplication (Fig. 9BGo).

pacap1 gene organization provides insight in glucagon superfamily evolution
Examination of the pacap2 gene shows how the next stage of gene organization may have evolved. The second exon of pacap2 seems to have resulted from the addition of splice sites within intron 1 of pacap1 gene ( Figs. 1–3GoGoGo). This would explain the origin of the cryptic peptide in the tunicate gene, in that the nucleotide coding is present in the intron and requires only a few base changes to create an intron/exon splice site on each side, resulting in a new exon (Fig. 3BGo). With the exception of the human grf gene, where a recent report shows that the cryptic peptide has a role in stimulating sertoli cell activity (45), the true function of the cryptic peptides is not known for any member of the superfamily. An additional exon seems to have occurred after the divergence of the pacap2 and pacap1 genes. Alternatively, the exon encoding the cryptic peptide may have been present before the protochordates evolved, but changed from an exon to an intron in the tunicate pacap1 gene because the splice-site nucleotides were altered. Within both tunicate genes reported here, consensus intron/exon splice sites are present at all intron/exon boundaries for proper intron removal.

This lack of an exon within the pacap1 gene is interesting because it demonstrates the evolution of an exon in relation to an intronic sequence. The ancestral gene is assumed to have contained a nucleotide sequence that is either being incorporated or lost as an exon. Depending on the translation start site, the exon encodes a cryptic peptide or 5'UTR. It was speculated by Campbell and Scanes (33) that the ancestral gene giving rise to the present day family contained only three exons. One possibility is that the tunicate pacap1 gene is derived from such an ancestral gene, because it contains only three exons.

Conservation of PACAP may extend to taxons predating tunicates
A feature of the many pacap genes is the conservation not only of the amino acids, but also the nucleotides encoding PACAP. The nucleotides that encode tunicate PACAP are highly conserved, 90% (73/81), in comparison with human PACAP1–27 (Fig. 8Go). Further evidence of pacap’s nucleotide conservation is shown by hybridization of the tunicate pacap probe within the zoo-blot. Using the tunicate pacap1 PCR fragment as a probe, we were able to detect a pacap gene in rat, starling, chicken, alligator, salmon, catfish, tunicate, reedfish, and sea urchin. Also, conservation of the chordate pacap gene sequence is suggested by the conservation of the restriction enzyme sites (EcoRI) used for the zoo-blot (Fig. 6Go) and the migration of the PACAP fragments at approximately the same position. Among the species represented in the zoo blot, conservation for the pacap cDNA sequences among the untranslated regions, both 3'UTR (41) and 5'UTR (46), has been reported. However, the extent of PACAP’s sequence conservation between species that are separated by 700 million years of evolution was unexpected. No other known hormone of comparable size has such high sequence conservation, which is even more intriguing because the basic function of PACAP is still speculative.

The other band that hybridized to the probe in the lanes containing the vertebrate DNA may be the vip gene, because the tunicate pacap probe has a high degree of identity to vertebrate VIP. However, because the lane containing the sea urchin DNA (lane I) also had two bands, it would be expected that sea urchins would have pacap1 and pacap2 genes similar to the tunicate genes. Echinoderms branched from a stem line that led to vertebrate evolution about 100 million years before tunicates. It is possible that sea urchin pacap1 and pacap2 genes have a higher degree of sequence identity than found in tunicates, provided there has not been a high number of substitutions in these genes between the present-day and ancestral sea urchins. One can speculate that some organisms, evolving before the sea urchins, contain a single parent pacap gene (Fig. 9Go).


    Acknowledgments
 
We thank Dr. G.O. Mackie and Lijuan Sun for their help with tissue sectioning and in situ staining.


    Footnotes
 
1 This work was supported by the Medical Research Council of Canada. Back

Received October 30, 1996.


    References
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 

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