Molecular evolution of hatching enzymes and their paralogous genes in vertebrates

Abstract

Background Hatching is identified as one of the most important events in the reproduction of oviparous vertebrates. The genes for hatching enzymes, which are vital in the hatching process, are conserved among vertebrates. However, especially in teleost, it is difficult to trace their molecular evolution in detail due to the presence of other C6astacins, which are the subfamily to which the genes for hatching enzymes belong and are highly diverged. In particular, the hatching enzyme genes are diversified with frequent genome translocations due to retrocopy. Results In this study, we took advantage of the rapid expansion of whole-genome data in recent years to examine the molecular evolutionary process of these genes in vertebrates. The phylogenetic analysis and the genomic synteny analysis revealed C6astacin genes other than the hatching enzyme genes, which was previously considered to be retained only in teleosts, was also retained in the genomes of basal ray-finned fishes, coelacanths, and cartilaginous fishes. These results suggest that the common ancestor of these genes can be traced back to at least the common ancestor of the Gnathostomata. Moreover, we also found that many of the C6astacin genes underwent multiple gene duplications during vertebrate evolution, and the results of gene expression analysis in frogs implied that genes derived from hatching enzyme genes underwent neo-functionalization. Conclusions In this study, we describe in detail the molecular evolution of the C6astacin gene in vertebrates, which has not been summarized previously. The results revealed the presence of the previously unknown C6astacin gene in the basal-lineage of jawed vertebrates and large-scale gene duplication of hatching enzyme genes in amphibians. The comprehensive investigation reported in this study will be an important basis for studying the molecular evolution of the vertebrate C6astacin genes, hatching enzyme, and its paralogous genes and for identifying these genes without the need for gene expression and functional analysis.

Structural and evolutionary insights into astacin metallopeptidases

“…In egg-laying vertebrates like fishes, amphibians, reptiles and birds, a specialized group of astacin MPs termed hatching enzymes has evolved ( Nagasawa et al, 2022 ). They are absent from mammals and involved in the cleavage of the eggshell.…”

Molecular evolution of patristacin genes in teleosts based on the genome survey

“…According to our previous study, patristacin genes can be found between the c1qtnf4 and atp6v0d1 genes, in a region that received the name Pastn‐synteny‐set (Nagasawa et al, 2022). On the same chromosome, but far from the Pastn‐synteny‐set region, other c6ast genes (nephrosin and pactacin) can be found in a region located between the fadd and mtch2 genes, termed Npsn&Pac‐synteny‐set (Nagasawa et al, 2022). In this study, we first searched c6ast genes of 33 species in 18 different orders among Euteleostei using both syntenic regions as an index (Tables S1 and S2).…”

“…The assembled whole-genome sequence data were obtained from NCBI (all species and accession numbers used in this study are listed in Table S1). To find the coding region of the c6ast gene, we performed TBLASTN search using the amino acid sequences of the c6ast genes, identified in our previous study (Nagasawa et al, 2022), as a query, and selected the genes showing more than 65% similarity. To exclude intronic sequences of c6ast genes, we performed the genewise2 using the c6ast sequences of closely related species as references.…”

“…Previously, we analyzed the evolution of c6ast genes, and divided the c6ast gene family into five clades: hatching enzymes, pactacins, nephrosins, patristacins, and c6ast4/5. This division is based on phylogenetic analysis (Table 1) (Kawaguchi et al, 2021; Nagasawa et al, 2022). Among them, the functions of pactacins (digestive enzyme), nephrosins (immune defense), and hatching enzymes are known, while those of patristacins and c6ast4/5 are not.…”

“…Among them, the functions of pactacins (digestive enzyme), nephrosins (immune defense), and hatching enzymes are known, while those of patristacins and c6ast4/5 are not. In this study, we focused on patristacin genes together with pactacin and nephrosin genes, as they are located on the same chromosome (Kawaguchi et al, 2021; Nagasawa et al, 2022).…”