Hydrophilic Shell Matrix Proteins ofNautilus pompiliusand The Identification of a Core Set of Conchiferan Domains

Abstract

Despite being a member of the shelled mollusks (Conchiferans), most members of extant cephalopods have lost their external biomineralized shells, except for the Nautiloids. Here, we report the result of our study to identify major Shell Matrix Proteins and their domains in the Nautiloid Nautilus pompilius, in order to gain a general insight into the evolution of Conchiferan Shell Matrix Proteins. In order to do so, we conducted transcriptomics of the mantle, and proteomics of the shell of N. pompilius simultaneously. Analyses of obtained data identified 61 distinct shell-specific sequences. Of the successfully annotated 27 sequences, protein domains were predicted in 19. Comparative analysis of Nautilus sequences with four Conchiferans for which Shell Matrix Protein data were available (the pacific oyster, the pearl oyster, the limpet, and the Euhadra snail) revealed that three proteins and six domains of the shell proteins are conserved in all Conchiferans. Interestingly, when the terrestrial Euhadra snail was excluded, another five proteins and six domains were found to be shared among the four marine Conchiferans. Phylogenetic analyses indicated that most of these proteins and domains were present in the ancestral Conchiferan, but employed in shell formation later and independently in most clades. Although further studies utilizing deeper sequencing techniques to obtain genome and full-length sequences, and functional analyses, must be done in the future, our results here provide important pieces of information for the elucidation of the evolution of Conchiferan shells at the molecular level.

Independent adoptions of a set of proteins found in the matrix of the mineralized shell-like eggcase of Argonaut octopuses

“…(2) a database of Conchiferan shell matrix proteins we assembled from data published until March, 2020 (Setiamarga et al, 2020), and (3) Octopus bimaculatus genome data. Protein domains were predicted using the SMART domain search online tool (http://smart.emblheidelberg.de/; Letunic et al 2021) under the "Genomic" mode.…”

“…A combination of transcriptome and proteome analysis has been used to identify these proteins (e.g., Miyamoto et al 2013;Arivalagan et al 2017;Zhao et al 2018;Setiamarga et al 2020), with some data validated at the genomic level because of the availability of draft genomes (Mann et al 2012;Zhang et al 2012;Takeuchi et al 2016;Kenny et al 2020). Many of these proteins are present in trace amounts inside the shell and are therefore referred to as SMPs.…”

“…In this case, the SMPs detected in the Argonauts are expected to be very different from the standard gene set of the Conchiferans (Setiamarga et al 2020). On the other hand, there is a known case in which degeneration of the shell results in small changes at the genetic level.…”

“…800 species of extant cephalopods had evolutionarily internalized, reduced, or completely lost their shells (Kröger et al 2011). Only the single surviving family of the Nautiloidea, the Nautiliids, still retain their true calcified external shell (e.g., Setiamarga et al 2020). 300 of the extant cephalopod species are members of the order Octopodiformes, which include octopuses and vampire squids (Sanchez et al 2016).…”

“…Recent development in genome, transcriptome, and proteome sequencings, however, has allowed for large-scale molecular dissection (e.g., Zhang et al 2012; Mann et al 2012; Marie et al 2012; Miyamoto et al 2013; Arivalagan et al 2017; Zhao et al 2018; Setiamarga et al 2020) and identification (e.g., Miyamoto et al 1996; Sudo et al 1997; Tsukamoto et al 2004) of major proteins in the shell of the Conchiferans (e.g., Miyamoto et al 1996; Sudo et al 1997; Tsukamoto et al 2004). Many of these proteins are present in trace amounts inside the shell and are therefore referred to as shell matrix proteins (SMPs), which are also a part of the organic component of the shell.…”