Neofunctionalization of a duplicate hatching enzyme gene during the evolution of teleost fishes
BMC Evolutionary Biology volume 14, Article number: 221 (2014)
Duplication and subsequent neofunctionalization of the teleostean hatching enzyme gene occurred in the common ancestor of Euteleostei and Otocephala, producing two genes belonging to different phylogenetic clades (clade I and II). In euteleosts, the clade I enzyme inherited the activity of the ancestral enzyme of swelling the egg envelope by cleavage of the N-terminal region of egg envelope proteins. The clade II enzyme gained two specific cleavage sites, N-ZPd and mid-ZPd but lost the ancestral activity. Thus, euteleostean clade II enzymes assumed a new function; solubilization of the egg envelope by the cooperative action with clade I enzyme. However, in Otocephala, the clade II gene was lost during evolution. Consequently, in a late group of Otocephala, only the clade I enzyme is present to swell the egg envelope. We evaluated the egg envelope digestion properties of clade I and II enzymes in Gonorynchiformes, an early diverging group of Otocephala, using milkfish, and compared their digestion with those of other fishes. Finally, we propose a hypothesis of the neofunctionalization process.
The milkfish clade II enzyme cleaved N-ZPd but not mid-ZPd, and did not cause solubilization of the egg envelope. We conclude that neofunctionalization is incomplete in the otocephalan clade II enzymes. Comparison of clade I and clade II enzyme characteristics implies that the specificity of the clade II enzymes gradually changed during evolution after the duplication event, and that a change in substrate was required for the addition of the mid-ZPd site and loss of activity at the N-terminal region.
We infer the process of neofunctionalization of the clade II enzyme after duplication of the gene. The ancestral clade II gene gained N-ZPd cleavage activity in the common ancestral lineage of the Euteleostei and Otocephala. Subsequently, acquisition of cleavage activity at the mid-ZPd site and loss of cleavage activity in the N-terminal region occurred during the evolution of Euteleostei, but not of Otocephala. The clade II enzyme provides an example of the development of a neofunctional gene for which the substrate, the egg envelope protein, has adapted to a gradual change in the specificity of the corresponding enzyme.
Gene duplication is one of the driving forces of evolution. In the most cases, one of the duplicated genes is subsequently lost, but in some cases, both genes are retained and diverged, leading to shared original function (subfunctionalization). Alternatively, one of the genes acquires a new function (neofunctionalization) ,. To understand this process, there is a need to study the evolution of the protein and its function. However, progress in this field has been slow because of the complexity of protein structures and their interactions. In this study, we propose a model for understanding neofunctionalization of duplicated genes using hatching enzymes and egg envelopes.
Teleostean egg envelopes, the substrate for hatching enzymes, are constructed of two types of glycoproteins, the ZP proteins ZPB and ZPC related to mammalian zona pellucida subunits ZP1 and ZP3, respectively. ZP proteins commonly possess an N-terminal region and Zona Pellucida (ZP) domain, which consists of two folds (ZP-N and ZP-C) connected by a linker sequence . In addition, ZPB proteins have a trefoil domain between the N-terminal region and the ZP domain (Figure 1A). The macromolecular architecture of the vertebrate egg envelope develops as follows (Figure 1A). The ZP domains are polymerized to each other to form long filaments by inter-molecular non-covalent interactions between the subdomains -. The N-terminal regions loop out from the filaments , and tie or bunch the filamentous structures . In fish, the ε-(γ-glutamyl) lysine isopeptide cross-links (Glu-Lys cross-links) are formed between the filamentous structures at fertilization. This makes the inter-filament interactions tight, and turns the egg envelope into a hard and tough structure. At the time of hatching, the fertilized egg envelopes are digested by a hatching enzyme that is secreted by the embryo.
Hatching enzyme, which belongs to the astacin metalloproteinase family ,, is found in fish, amphibians, birds, reptiles, and mammals ,-. In teleosts, we have cloned 67 hatching enzyme genes from 27 species, and elucidated their evolutionary pathway ,. The majority of fishes have several hatching enzyme genes in their genomes, suggesting that there were several duplication events of hatching enzyme genes during evolution of the fish lineage .
Teleostean fishes are classified into three subdivisions, Elopomorpha, Otocephala, and Euteleostei . Phylogenetic analysis of hatching enzyme genes suggests the elopomorph genes form a monophyletic clade. Seven hatching enzyme cDNAs with 85–95% amino acid identity were cloned from the Japanese eel Anguilla japonica (Elopomorpha) . However, these isozymes were functionally the same in terms of their role in egg envelope digestion . Gene diversification has occurred in the common ancestor of Otocephala and Euteleostei, such that members of these subdivisions possess two types of genes, belonging to two clades, clade I and clade II. Moreover, during the evolution of Otocephala, the clade II gene of Otophysi has been lost .
Analysis of the egg envelope digestion mechanism by hatching enzymes has been studied in a number of fish species. The primitive mechanism of teleostean hatching was predicted using Japanese eel. A single type of hatching enzyme digests the N-terminal region of ZPB and ZPC into short peptide fragments. Its cleavage leads to cancelation of the inter-molecular Glu-Lys cross-links of ZP proteins and renders the egg envelope swollen and softened .
In contrast, medaka Oryzias latipes (Euteleostei) hatch by the cooperative action of two hatching enzymes, clade I and II enzymes (Figure 1B). The clade I enzyme named MHCE (medaka high choriolytic enzyme) cleaves the N-terminal regions of ZPB, where many of the Glu-Lys cross-links are located , into short peptide fragments, thereby swelling the egg envelope in a manner similar to the Japanese eel single enzyme . The clade II enzyme named MLCE (medaka low choriolytic enzyme) cleaves two specific sites on the swollen egg envelope, termed the mid-ZPd and N-ZPd sites. The mid-ZPd site is located at the intervening sequence between two subdomains, ZP-N and ZP-C, in the ZP domain of ZPB ,,,, whereas the N-ZPd site is located at the N-terminus of the ZP domain of ZPC (Figure 1A). The cleavage of the two sites causes disruption of ZP domain filamentous structures, thereby solubilizing the swollen egg envelope. The position of respective cleavage sites of the clade I and clade II enzymes on ZP proteins is highly conserved in euteleostean fishes .
Based on the egg envelope digestion manner, it is thought that the ancestral function of the fish hatching enzyme was to induce swelling of the egg envelope by cleaving the N-terminal region and breaking the intermolecular Glu-Lys cross-links. The Japanese eel hatching enzyme gene and the clade I genes of Euteleostei have inherited this ancestral function. In contrast, euteleostean clade II genes are thought to have developed a new function, the solubilization of the swollen egg envelope by cleavage at two specific sites. As described above, the clade II gene was lost during evolution of the otocephalan lineage. Zebrafish Danio rerio belong to the Otophysi, a late group of Otocephala, and possess only the clade I enzyme (ZHE1), the activity of which is analogous to that of Japanese eel hatching enzyme and MHCE . From an evolutionary perspective, the egg envelope digestion mechanism of otophysans appears to have reverted to the ancestral form.
We evaluated the mechanisms of egg envelope digestion in Gonorynchiformes, an early diverging group of Otocephala, using milkfish Chanos chanos. This species possesses both clade I and II genes. We compared their digestion properties with those of other fishes and inferred the neofunctionalization process of the clade II hatching enzyme as follows. After diversification of the gene, the ancestral clade II gene has gained N-ZPd cleavage activity in the lineage of common ancestors of Euteleostei and Otocephala. Subsequently, acquisition of cleavage activity at the mid-ZPd site and loss of cleavage activity in the N-terminal region has occurred during the evolution of Euteleostei, but not Otocephala. Therefore, the addition of the two cleavage sites is presumed to be the result of independent evolutionary events (Figure 1C). Finally, by comparing their egg envelope cleavage specificities, we propose a hypothesis to explain why the clade II gene was lost in the otocephalan lineage and how the euteleostean clade II gene acquired a new function.
Results and discussion
Characterization of recombinant hatching enzymes
Two clade I enzymes (MfHE1 and MfHE2) and a clade II enzyme (MfHE3) have been cloned from milkfish . The active recombinant enzymes were successfully refolded from the inclusion bodies, although the refolding efficiency of recombinant MfHE2 (rMfHE2) was much lower than that of rMfHE1 and rMfHE3. SDS-PAGE of the rMfHE1 and rMfHE3 yielded bands at 23 and 24.5 kDa, respectively, which is consistent with values calculated from mature enzyme sequences of cDNAs and His-tag (24076.69 for rMfHE1 and 24129.73 for rMfHE3, Figure 2A). The results of zymography revealed that the mobility of bands having caseinolytic activity corresponded to that of the CBB stained bands (Figure 2B). The specific caseinolytic activities of the nickel column-purified rMfHE1 and rMfHE3 were 26.8 and 14.2 Δ280 • min–1 • mg protein–1, respectively. These values are similar to those of other fish hatching enzymes (30.7 Δ280 • min–1 • mg protein–1 for ZHE1, 27.3 Δ280 • min–1 • mg protein–1 for MHCE, and 18.4 Δ280 • min–1 • mg protein–1 for MLCE) . Thus, we concluded that recombinant enzymes were of sufficient quality to use in the egg envelope digestion experiments.
Structural changes in the egg envelope induced by MfHE1 and MfHE3
First, we observed the morphological changes in the milkfish fertilized egg envelope digested by recombinant hatching enzymes (rMfHE1 and rMfHE3) using an optical microscope. The MfHE1-treated envelope was softened and became slightly thicker than the intact envelope (Figure 3A, B). In contrast, treatment with MfHE3 caused dramatic swelling in the egg envelope (Figure 3C), and became quite fragile and easily broken into gelatinous pieces by crushing with forceps (Figure 3D). The morphology of the egg envelopes treated by a mixture of MfHE1 and MfHE3 was similar to that of the MfHE3-treated envelope (data not shown), suggesting the two enzymes do not have a synergistic effect.
Determination of the MfHE1 and MfHE3 cleavage sites in unfertilized egg envelopes
The egg envelope becomes hardened after fertilization by formation of ε-(γ-glutamyl) lysine isopeptide cross-links ,. Because these cross-links make it difficult to clearly determine the cleavage sites of the egg envelope, unfertilized egg envelopes were used as substrates. The cleavage sites of egg envelope proteins by rMfHEs were determined by sequencing the N-terminal of the digests and matching the sequences with those of milkfish ZP proteins deduced from cDNAs cloned previously (MfZPB, AB759543; MfZPCa, AB759544; MfZPCb, AB759545). Because MfZPCa and MfZPCb share similar amino acid sequences, only the MfZPCa sequence is shown.
SDS-PAGE of the unfertilized egg envelope yielded a major 44 kDa band and several minor bands (Figure 4 lane 1). SDS-PAGE of the MfHE1 digest after a 15 min incubation yielded two major bands at 44 and 41 kDa (Figure 4, lane 2). The sequencing of the 44-kDa band revealed that it was a mixture of two peptides. The major sequence, VPWWSGA, corresponded to the N-terminal of undigested MfZPB (Figure 5A). Another minor sequence, EPVDF, was found from E67 in MfZPCa, and the cleavage sites were Q66/E67 (site-C1, Figure 5A). The sequence of the 41-kDa product was also a mixture of two sequences, APQRYE and GPVKELA. The former sequence was found in MfZPB from A54, and the cleavage site was S53/A54 (site-B1, Figure 5A). The latter sequence was found in MfZPCa from G79, and the cleavage sites were Q78/G79 (site-C2, Figure 5A). After incubation for 30 min, the 44-kDa band weakened, and a 36-kDa band developed (Figure 4, lane 3). The N-terminal sequences obtained from the 41-kDa band were the same as after the 15 min incubation. The N-terminal sequence of the 36-kDa band corresponded to the sequence of MfZPB from A69 and the cleavage site was K68/A69 (site-B2, Figure 5A). A longer incubation period (60 min) did not alter the SDS pattern and the cleavage sites are the same as those of 30 min-incubation (Figure 4, lane 4), suggesting that the digests obtained from the 30 min incubation were the final products and there was no further cleavage by MfHE1.
In summary, two MfHE1 cleavage sites in MfZPB (site-B1 and site-B2) and two sites in MfZPCa (site-C1 and site-C2) were located in the N-terminal region of MfZPB and MfZPCa (Figure 5A, B). The cleavage sites of MfHE2 and MfHE1 were identical (data not shown), suggesting that these two clade I enzymes act on the egg envelope in the same manner.
The SDS-PAGE patterns of the MfHE3 digests were similar, but not identical to those of MfHE1. SDS-PAGE of MfHE3 digests yielded four bands at 41, 36, 33, and 31 kDa following a 30 min incubation (Figure 4, lane 5). The cleavage sites determined from the first two products were identical to those for MfHE1, i.e., 41 kDa for site-C2 and site-B1, and 36 kDa for site-B2 (Figure 5A). Therefore, sites-B1, –B2, and -C2 were in common between MfHE1 and MfHE3. Conversely, latter two bands (33 and 31 kDa) represented MfHE3 specific cleavage sites. Sequencing of these bands yielded the same sequence (TPLPAN) found in MfZPCa from T106, and the cleavage sites (site-C3) were at K105/T106 (Figure 5A). The difference in molecular mass between the two digests is thought to be caused by differences in their sugar moieties. Interestingly, the position of site-C3 corresponds to the N-ZPd site in euteleosts, medaka, and killifish Fundulus heteroclitus (Figure 5C). Thus, MfHE3 cleaved three sites located in the N-terminal region in common with MfHE1, and one unique site, site-C3, named N-ZPd, in MfZPCa (Figure 5A, B). There was no difference between the SDS-PAGE patterns from the 60 (Figure 4, lane 6) and 30 min incubations, suggesting that the digests obtained following a 30 min incubation represented the final digestion products of MfHE3.
Determination of the MfHE1 and MfHE3 cleavage sites in fertilized egg envelopes
The fertilized egg envelope provides a substrate for hatching enzymes at the time of hatching. The fertilized egg envelope was digested by rMfHE1 and rMfHE3 to determine the location of the cleavage sites. The fertilized eggs were not soluble in SDS (Figure 6A, lane 1), but became soluble following digestion by MfHE1 or MfHE3. SDS-PAGE of the MfHE1 digests yielded a broad band at 39 kDa and a band at ~100 kDa (Figure 6A, lane 2). The two cleavage sites determined from the N-terminal amino acid sequences of the 39-kDa band were site-B2 and site-C1. The molecular weights from the cleavage sites to the C-terminus of ZP proteins estimated from the respective cDNAs were 36,281.33 and 36,347.47, respectively (Figure 5A). Our results suggest that the 39-kDa band was a mixture of two peptides spanning the region from site-B2 to the end of the ZP domain of MfZPB (B2-MfZPB) and from site-C1 to the C-terminal processing site of MfZPCa (C1-MfZPCa) (Figure 6B). The cleavage sites determined from the 100 kDa band included sites-B2, -C1, and -C2 (Figures 5A and 6B). Two of the three cleavage sites obtained from the 100 kDa band were identical to those of the 39 kDa band. Thus, we concluded that the 100 kDa band was a dimer or trimer of the digests of the 39 kDa band (Figure 6B). Together, our observations suggest that the 100 kDa band is a complex formed by B2-MfZPB, C1-MfZPCa, and C2-MfZPCa, and presumably linked by ε-(γ-glutamyl) lysine bonds.
SDS-PAGE of fertilized egg envelopes digested by MfHE3 yielded three bands at 39, 33, and 31 kDa (Figure 6A, lane 3). The cleavage sites determined from the 39 kDa band included sites-B2, -C1, and -C2, which are identical to those of the 100 kDa band from MfHE1 (Figure 5A). The sequences determined for the 33 and 31 kDa bands were identical, and the cleavage site was located at site-C3 (also known as the N-ZPd site) which corresponds to the unique site for MfHE3 determined by the digestion of unfertilized egg envelopes (Figure 5A, B, Figure 6C). The 100 kDa band observed in the MfHE1 digest was not observed in the MfHE3 digest. Four of the five cleavage sites of MfHE3 were shared with MfHE1. Therefore, cleavage of the N-ZPd site (site-C3) by MfHE3 resulted in further digestion of the 100 kDa band into a 39 and 31/33 kDa band, leading to the removal of the cross-link between the 39 kDa peptides (Figure 6C). It is reasonable to conclude that one of the two amino acid residues responsible for ε-(γ-glutamyl) lysine cross-link formation was present in the region between site-C2 and site-C3 in MfZPCa. Indeed, two lysine residues that are candidates for the acceptor site of the cross-links are present in this region (Figure 5A, C). Consequently, cleavage of the N-ZPd site by MfHE3 cleaved a small section of the peptides, including the cross-links (Figure 6C). As a result, the tight bindings between the ZP proteins are eliminated.
The same SDS-PAGE pattern was obtained from the mixture of MfHE1 and MfHE3, and from the egg envelopes after natural hatching (Figure 6A, lane 4 and 5). Their cleavage sites were consistent with those obtained from the MfHE3 digests. Our results are also consistent with morphological observations. MfHE1 slightly swelled and softened the egg envelope by cleaving the N-terminal region into fine fragments, while MfHE3 caused markedly swelling of the egg envelope by cleaving both the N-terminal region and the N-ZPd site leading to complete elimination of the cross-links (Figure 3). In the following section, we compare the egg envelope digestion process and the substrate specificity of milkfish hatching enzymes with those of other fish hatching enzymes to trace the neofunctionarization process. The characters of fish hatching enzymes discussed in the following sections are listed in Table 1.
Why was the otocephalan clade II gene lost during evolution to Otophysi?
We compared the egg envelope digestion manner between milkfish and medaka hatching enzymes (Figure 7A, B). Both clade I enzymes are thought to have conserved the ancestral function of cleaving the N-terminal region, resulting in swelling of the egg envelope. However, the clade II enzymes differ between the two groups. The otocephalan clade II enzyme does not exhibit cleavage activity at the mid-ZPd site, where a euteleostean clade II enzyme specifically cleaves. Furthermore, it does cleave the N-terminal region. Thus, the process of neofunctionalization does not appear to be complete for the otocephalan clade II gene, MfHE3. However, the otocephalan clade II enzyme rendered the egg envelope more swollen and softened than the clade I enzymes because it had cleavage activity at the N-ZPd site (Figure 7A). Thus, the otocephalan clade II enzyme is more effective than the clade I enzyme, and was therefore conserved in the early diverging group of Otocephala, Clupeiformes and Gonorynchiformes. However, the possession of two enzymes for egg envelope digestion would be dispensable for hatching, so otophysans were able to persist despite the loss of one of the enzymes. Embryos are able to rupture the softened egg envelope by moving, and thereby hatch. The egg envelope digestion of fish in the more recently diverged groups (Otophysi) have reverted to the ancestral manner, namely the swelling of the egg envelope by a single enzyme, cf. zebrafish hatching enzyme, ZHE1 .
Another factor to consider is the evolution of egg envelope genes. We focused our evaluation on the tissue of synthesis of egg envelope proteins, ZP proteins. The teleostean ZP proteins were originally synthesized by oocytes in the ovary. The zp genes expressed in both the liver and the ovary of the common ancestor of Otocephala and Euteleostei were produced by gene duplication ,. A number of euteleosts synthesize the major components of the egg envelope in the liver, whereas the otocephalan liver expressing genes have disappeared in the evolutionary lineage to Ostariophysi, which synthesize ZP proteins in the ovary. Therefore, the evolution of the egg envelope digestion system, from a single enzyme to a two-enzymes system, has nearly overlapped with a change in the expression sites of zp genes. The liver is the largest organ in the body, and has the capacity to synthesize a large amount of protein, including yolk proteins (vitellogenins) in fish and frogs ,. In fact, when the thicknesses of the egg envelopes were compared, the egg envelopes of euteleosts tended to be thicker than those of otophysans ,. It is conceivable that hatching from a thicker envelope requires a more efficient digestion system involving two enzymes. Conversely, swelling and softening of the egg envelope by a single enzyme may be sufficient for hatching of otocephalan embryos because of the thin egg envelope. It is possible that the duplication of the zp genes followed by a switch of the expression site is closely related to the evolutional event of loss of the clade II gene in otocephalan lineage.
In the following section, we develop a hypothesis to explain the conditions under which a gene acquires a new function by comparing MLCE and MfHE3, representatives of the euteleostean and otocephalan clade II enzymes, respectively.
Exchange of hatching enzyme-egg envelope combination
Conservation of activity of the clade I enzyme
To infer the mechanism by which egg envelope digestion by hatching enzymes was conserved during evolution, the egg envelope-enzyme combinations were altered between milkfish and medaka. First, we focused on the clade I enzymes, MfHE1 and MHCE. MHCE slightly swelled and softened milkfish egg envelope, as did MfHE1 (Figures 7C and 3B). The SDS-PAGE patterns of the digests were similar (Figure 7E lane 2, 4), and N-terminal sequences of the digests from MHCE were the same as those from MfHE1. Similarly, digestion of medaka egg envelope by MfHE1 resulted in morphological changes that were similar to those caused by MHCE (Figure 7D). Additionally, the N-terminal sequences of the digests corresponded to the sequences obtained from MHCE digests (Figure 7F lane 7, 9). Therefore, the xenogeneic combination of MHCE and MfHE1 cleaved the same sites as the allogeneic combination, suggesting conservation of substrate specificity in clade I enzymes during evolution.
Acquisition of a new function by the clade II enzyme
The pattern of digestion by the xenogeneic combination of clade II enzymes, MfHE3 and MLCE, differed from that of the allogeneic combination. MLCE did not digest the intact medaka egg envelope to any significant extent, but did dissolve the swollen egg envelope following digestion by MHCE (Figure 7D). The dissolved egg envelope yielded a 37 kDa band caused by cleavage of the N-ZPd site in ZPC and two low molecular bands at 17 and 16 kDa produced by cleavage mid-ZPd in ZPB (Figure 7B, F lane 8) . Interestingly, MLCE caused significant swelling of the milkfish egg envelope, as did MfHE3 (Figures 3C and 7C). Sequence analysis of the digests revealed that MLCE cleavage sites in the milkfish egg envelope were the same as those of MfHE3. These observations suggest that MLCE cleaves the N-terminal region and the N-ZPd site but not the mid-ZPd site of the milkfish egg envelope.
The single action of MfHE3 had little effect on the intact medaka egg envelope. However, swelling was observed in the inner surface of the egg envelope (Figure 7D). These observations suggest that MfHE3 is inefficient at digesting the N-terminal region. When MfHE3 acts on the MHCE-swollen egg envelope, the egg envelope undergoes further swelling (Figure 7D). This structural change was similar to that caused by MfHE3 in the milkfish egg envelope (Figure 3C). Cleavage of the N-ZPd site was confirmed by sequencing of the broad 36 kDa band of MHCE-MfHE3 digests (Figure 7F lane 10). The low molecular digests produced by the cleavage of the mid-ZPd site were not observed in the MHCE-MfHE3 digest, suggesting that MfHE3 did not have the activity to cleave the mid-ZPd site in the medaka egg envelope.
Inferring changes in the substrate specificity of clade I and II enzymes during evolution
The cleavage activity of N-terminal region; ancestral function
We further investigated the efficiency of cleavage at sites in the N-terminal regions using synthetic peptide substrates that were designed based on the cleavage sites of two euteleosts, medaka , and killifish , and two otocephalans, zebrafish , and milkfish (present study, site-C1 and -C2) (Table 2). In addition to milkfish and medaka hatching enzymes, we used zebrafish hatching enzyme, ZHE1 , as an additional representative of the otocephalan clade I enzyme.
When the specific activities toward the substrates of otocephalan N-terminal region were compared, all of the enzymes tended to cleave their peptides with sufficient specific activity, although MLCE only partially cleaved the peptides (three of the six, Figure 8). However, the specificity toward peptides designed from the euteleostean N-terminal region differed between clade I and II enzymes. The clade I enzymes MfHE1, MHCE, and ZHE1 cleaved most of the substrates designed from euteleostean N-terminal region, whereas the clade II enzymes MfHE3 and MLCE were inefficient at cleaving these peptides (Figure 8). Thus, the substrate specificity was similar within the clade I and within II enzyme groups, suggesting that the substrate specificities of these two clades have been conserved during evolution. The difference between clade I and II enzymes in terms of their specificity for the euteleostean N-terminal regions, was consistent with the results in the cross-species digestion experiments in which MfHE3 and MLCE caused swelling of the intact milkfish egg envelope, but not the intact medaka egg envelope.
The ZPB N-terminal regions in many euteleosts, but not otocepharans, contain a characteristic three amino acid repeat motif, known as the Pro-Gln-X repeat . This implies that the N-terminal region sequence of the ZP protein has changed significantly along the evolutionary pathway to Euteleostei. Given that both euteleostean and otocephalan clade I enzymes cleave at the Glu-X bonds in the repeat sequence, we hypothesize that the euteleostean N-terminal region has changed within the range of cleavage specificity of clade I enzyme to maintain the ancestral function, swelling egg envelope. However, this change has led to loss of cleavage activity by clade II enzymes. Our results suggest that a change in the substrate sequences in evolutionary pathway to the Euteleostei would be important for the loss of ancestral function of the clade II gene.
Two cleavage sites, N-ZPd and mid-ZPd, acquire a new function
The cleavage activity of N-ZPd sites
Both Euteleostei and Otocephala shared a specific cleavage site (N-ZPd) for the clade II enzyme in their respective ZP proteins. We compared the cleavage activities toward the N-ZPd site using peptide substrates designed from milkfish and medaka, and the corresponding position in zebrafish (Table 3). The clade II enzymes MfHE3 and MLCE cleaved not only their own N-ZPd site but also the peptides designed from other fish N-ZPd sites (Figure 9). Conversely, clade I enzymes were inefficient at cleaving the N-ZPd sites. These results were consistent with observations in the egg envelope digestion experiment.
The cleavage activity of mid-ZPd sites
The cross-species egg envelope digestion experiments revealed that cleavage of the N-ZPd site by MfHE3 did not solubilize the medaka egg envelope (Figure 7D, F). Therefore, acquisition of the mid-ZPd site during evolution was likely critical for the establishment of the euteleostean two-enzymes system. We compared the amino acid sequences around the mid-ZPd site among the ZPBs of various fish species (Figure 10). Euteleostean egg envelopes are constructed by two ZPBs corresponding to the precursor proteins, choriogenin H (ChgH) and choriogenin Hm (ChgHm) . The euteleostean clade II enzymes cleave the mid-ZPd site of ChgH, but not ChgHm . The alignment of amino acid sequences, including the mid-ZPd site, is shown in Figure 10. In elopomorph and otocephalan sequences, the proline cluster (located between –1 to +4 of the cleavage site) was well conserved. Additionally, the sequences of ChgHm of Euteleostei contained a cluster of three prolines spanning the sites corresponding to the mid-ZPd (located between –1 to +2 of the cleavage site). Conversely, the euteleostean ChgH did not have a proline cluster spanning the cleavage site, and the proline residues at the +1 and –1 sites were frequently substituted by other amino acid residues (Figure 10). There are no prior reports regarding proteases that cleave between Pro-Pro bonds (MEROPS, the peptidase database http://merops.sanger.ac.uk/). These findings suggest that the addition of the cleavage site in the mid-ZPd is accompanied with mutations of the amino acid sequences around the cleavage sites. However, the otocephalan clade II enzyme MfHE3 did not cleave the mid-ZPd site of the medaka egg envelope during cross-species digestion experiments (Figure 7D). Furthermore, MfHE3 was inefficient at cleaving the peptide designed from the medaka mid-ZPd site (0.002 μg peptide • mg enzyme–1 • 30 min–1). Our results suggest that both the substrate and the substrate specificity of the clade II enzyme was altered during the evolution of Euteleostei to gain the mid-ZPd site.
The driving force of neofunctionalization
The third round of whole genome duplication (3R-WGD) that occurred in the teleost ancestor produced a large number of duplicated genes ,. Subsequent to this, hatching enzyme genes were subject to several additional lineage-specific duplication events . This series of duplication events has resulted in a high level of hatching enzyme gene diversity, and is a driving force of neofunctionalization. Interestingly, we have reported that the hatching enzyme genes of teleosts frequently lost their introns during the evolution . Chromosomal synteny around clade II gene was conserved in euteleosts, such as medaka, three-spined stickleback, and Tetraodon. However, the synteny around clade I gene was not conserved in euteleosts. Furthermore, conserved synteny was not observed between euteleostean clade I genes and clade II genes, or between otocephalan clade I genes (zebrafish, ZHE1) and euteleostean clade I genes. The ZHE1 gene cluster is located at inton 17 of the aox2 gene, suggesting the genes were translocated by retrotransposable element (s) . Such evolutionary events accompanied with a large structural change in the hatching enzyme genes likely contributed to the diversification of the hatching enzyme genes.
We inferred the neofunctionalization process of the clade II hatching enzyme (Figure 1C). After duplication of the gene, the ancestral clade II gene has gained N-ZPd cleavage activity in the lineage of common ancestors of Euteleostei and Otocephala. Subsequently, acquisition of cleavage activity at the mid-ZPd site and loss of cleavage activity in the N-terminal region has occurred during the evolution of Euteleostei, but not Otocephala. Therefore, the addition of the two cleavage sites is presumed to be the result of independent evolutionary events. This hypothesis is supported by the egg envelope structure dependent cleavage of N-ZPd and mid-ZPd sites as follows. The euteleostean clade II enzyme is inefficient at digesting the intact egg envelope, but is able to cleave at two sites in the clade I enzyme-mediated swollen egg envelope. Therefore, MHCE-mediated cleavage renders the egg envelope structure loosened and provides MLCE access to the cleavage sites. Furthermore, the cleavage of the N-ZPd site is a prerequisite for cleavage of the mid-ZPd site. The nine-spined stickleback is unique in that the species possesses two types of clade II genes, LCEα and LCEβ, that share the original function, i.e., subfunctionalization. LCEα cleaves the N-ZPd site but not the mid-ZPd site, whereas LCEα cleaves only the mid-ZPd site. LCEβ cannot solubilize the HCE-mediated swollen egg envelope, but solubilizes the swollen egg envelope treated by HCE and LCEα, which digest the sites at the N-terminal region and N-ZPd site . These observations suggest that the stepwise cleavage of the egg envelope proteins, N-terminal region, N-ZPd site, and the mid-ZPd site, leads to complete solubilization. Therefore, the neofunctionalization of the euteleostean clade II gene occurred during two independent evolutionary events, the first resulted in the addition of the N-ZPd site and the second the addition of the mid-ZPd site.
Our enzymological experiments suggest that the change in substrate was one of the most important factors for both the addition of the mid-ZPd site and the loss of activity at the N-terminal region. The peptide digestion experiment revealed that the cleavage specificity of clade II and clade I enzymes were the same in some instances, but also differed for some sites. This implies that the specificity of the clade II enzyme was changed in a gradual process during evolution after the duplication. A drastic change in specificity during evolution would likely have resulted in loss of biological function of the gene, followed by loss of the gene itself. Astacin family proteases suggested to have broad substrate specificity , and fish hatching enzymes are no exception ,,. Therefore, after the duplication, the clade II enzymes have apparently shifted their substrate preference from that of the ancestral enzyme, while retaining some of the cleavage specificity of clade I enzymes. The creation of a new cleavage sites seems to have been achieved by a mutation in the ancestral sequence at the corresponding sites N-ZPd and mid-ZPd which resulted in a sequence match for the substrate preference of clade II enzymes. Following this change, the role sharing of clade I and II enzymes in egg envelope digestion have been established during the co-evolutional process of the enzymes and their respective cleavage sites. Thus, the two-enzymes system for solubilization of the egg envelope has been conserved in Euteleostei.
Our results suggest that neofunctionalization of genes occurs when a gene product creates a new interaction with another product, and the genes successfully co-evolve. Our results provide an example of the process of appearance of a neofunctional gene resulting from coordination of a mutation that occurred in two related genes.
The experiments were performed in accordance with Law for the Humane Treatment and Management of Animals in Japan . The law was enacted in 1973, amended in 1999, and coordinated with the Institutional Animal Care and Use Committee (IACUC) protocols .
Milkfish, C. chanos, ovary samples were provided by the Aquaculture Department of Southeast Asia Fisheries Development Center (SEAFDEC/AQD) in the Philippines. For sacrifice of the milkfish, mature female milkfish were spinalized under anesthetized using 2-phenoxy-ethanol. Ovary with unfertilized egg envelopes was homogenized in 20 mM Tris–HCl (pH 8.0) containing 0.13 M NaCl, 5 mM EDTA, and 5 mM iodoacetic acid. The envelopes were washed several times with the same buffer. The isolated unfertilized egg envelopes were stored at –20°C until analysis. To isolate the milkfish fertilized egg envelope, pre-hatch embryos (9–11 h after fertilization) were crushed in seawater. The crushed egg envelopes were washed several times with seawater to completely remove the yolk proteins and cell debris. The fertilized egg envelopes of medaka Oryzias latipes were isolated from eggs 5 d after fertilization, and washed with distilled water using the procedure described above. The isolated unfertilized and fertilized egg envelopes were used for digestion experiments.
Generation of recombinant hatching enzymes
The fragments containing the mature enzyme portion of each MfHE cDNA were individually transferred into the expression vector pET3c (Promega, Madison, WI). The recombinant proteins were harvested as the inclusion bodies . To facilitate refolding, the inclusion bodies were dissolved in 50 mM Tris–HCl (pH 8.0) containing 8 M urea and 0.1 M 2-mercaptoethanol. After incubation at 37°C for 30 min, the mixture was diluted 1000-fold with 50 mM Tris–HCl (pH 8.0) containing 0.8 M arginine, 1 mM GSH, 0.1 mM GSSG, 5 μM ZnSO4, and 0.01% Briji 35, and allowed to stand for 2 days at 4°C. The solution was then dialyzed against 50 mM Tris–HCl (pH 8.0) containing 0.5 M NaCl and 0.01% Briji 35. The recombinant MfHEs were purified by Ni-NTA Superflow chromatography (Qiagen, Valencia, CA, USA) or concentrated by an Amicon Ultra-15 (Millipore Co., Billerica, MA). Recombinant zebrafish hatching enzyme, rZHE1, was prepared according to a method described previously .
Estimation of caseinolytic activity
The caseinolytic activity of the hatching enzymes was measured in a 375 μL reaction mixture consisting of 83 mM Tris–HCl (pH 8.0) and 3.3 mg/mL of casein and the enzyme. The reaction mixture was incubated for 30 min at 30°C. After the reaction was stopped by adding 125 μL of 20% perchloric acid, the mixture was allowed to stand in an ice-cold water bath for 10 min, then centrifuged at 18,500 g for 5 min at 4°C. The absorbance of the supernatant was measured at 280 nm.
Zymography of rMfHE1 and rMfHE3
The bands for active rMfHE1 and rMfHE3 were observed by casein zymography. Briefly, the recombinant proteins were electrophoresed on a sodium dodecyl sulfate-polyacrylamide gel containing 0.1% casein. The refolded rMfHE1 or rMfHE3 samples were mixed with an equal volume of 2 × SDS-sample buffer without 2- mercaptoethanol, at 80°C for 30 min. After electrophoresis, the gel was washed in 20 mM Tris–HCl (pH 8.0) containing a 2% Triton-X 100 for 1 h at 30°C, then incubated in 20 mM Tris–HCl (pH 8.0) and 0.1 mM ZnSO4 at 30°C overnight with gentle agitation. The gel was stained with Coomassie Brilliant Blue R-250 (Sigma, St. Louis, MO) and then destained.
Egg envelope digestion experiments
Eight to ten unfertilized and fertilized egg envelopes were incubated in 20 μL of 25 mM Tris–HCl (pH 8.0), 0.5 M NaCl, and an appropriate amount of enzyme at 30°C. Because the refolding efficiencies of mutant recombinant proteins differed from sample to sample, the amount of active enzyme added to the reaction mixture was adjusted based on the caseinolytic activity. The same amount of caseinolytic activity was added to the reaction mixture (0.075 Δ280 • 30 min–1 for digestion of unfertilized egg envelopes and 0.3 Δ280 • 30 min–1 for digestion of fertilized egg envelopes). After incubation, the digested egg envelopes were photographed by Leica MZFLIII stereo microscope (Leica, Solms, Germany), and subjected to SDS-PAGE.
Determination of N-terminal sequences of the digests
Egg envelopes were analyzed by SDS-PAGE, and electrically blotted onto a PVDF membrane (Hybond-P, GE Healthcare UK Ltd., Buckinghamshire, England). After staining with CBB, the band was cut out and submitted for protein sequencing (Procise 491HT, Applied Biosystems, Foster City, CA, USA).
Synthetic peptide cleavage activity
The synthetic peptides spanning 10–11 amino acids were designed based on the sequence around the cleavage sites of several fish hatching enzymes. For ZHE1, MHCE, and MLCE, a 25 μL reaction mixture consisting of 50 mM Tris–HCl (pH 8.0), 2.5 nmol peptide, and an appropriate amount of enzyme was incubated at 30°C for 30 min. For MfHE1 and MfHE3, a 25 μL reaction mixture consisting of 50 mM Tris–HCl (pH 8.0), 0.5 M NaCl, 2.5 nmol peptide, and an appropriate amount of enzyme was incubated at 30°C for 30 min. After the reaction was stopped by the addition of 2.5 μL of 0.1 M EDTA, the reaction mixtures were applied to a C18 column (YMC Co. Ltd., Kyoto, Japan) on an HPLC system equilibrated with 0.1% TFA and eluted with a linear gradient of 0–60% acetonitrile in 0.1% TFA. The activity was calculated from the ratio of the peak areas of the digested and undigested peptides. The values were expressed as the specific activity of the purified enzymes (μg peptide • mg enzyme–1 • 30 min–1).
Purification of medaka hatching enzyme
KS, MK, and SY participated in the design of the experiments. SW prepared milkfish unfertilized and fertilized eggs. KS performed biochemical experiments. KS, MK and SY analyzed the data. KS and SY wrote the paper. All authors read and approved the final manuscript.
Milkfish hatching enzyme
Recombinant milkfish hatching enzyme
N-terminus of ZP domain
Middle of ZP domain
High choriolytic enzyme
Low choriolytic enzyme
Medaka high choriolytic enzyme
Medaka low choriolytic enzyme
Zebrafish hatching enzyme 1
Fundulus low choriolytic enzyme
Choriogenin H minor
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This work was supported by grants from JSPS; grant numbers: 21570240 and 70612092.
The authors declare that they have no competing interests.
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Sano, K., Kawaguchi, M., Watanabe, S. et al. Neofunctionalization of a duplicate hatching enzyme gene during the evolution of teleost fishes. BMC Evol Biol 14, 221 (2014). https://doi.org/10.1186/s12862-014-0221-0