Insights into Octopus maya cathepsins from metatranscriptome and genome: structure evolutionary relationships and functional role prediction in digestive processes

Abstract

Physiological response to feeding is crucial for various production factors such as feed catabolism and growth. Despite growing significance in red Octopus maya aquaculture, large-scale commercial production is limited by not sufficiently knowing their nutritional needs, especially their digestive physiology. Since this species is carnivorous, one of the main feeding aspects is directed to protein digestion, but its enzymatic digestive repertoire has not been studied yet at genomic and transcriptomic levels. This study searched for protease enzymes encoded in O. maya genome and expressed in the transcriptome, allowing an initial annotation of genes involved in protein catabolism; 117 amino acid sequences related to 'octopus digestive enzymes' were retrieved from 66 available-species' genomes in the NCBI database, coding for cathepsins, papilins, and metalloproteases. Homology analysis identified 36 homologous sequences from O. maya transcriptome and three from its genome. Phylogenetic analysis grouped 37 of 39 sequences into 11 of 14 main clades, offering new insights into the evolutionary relationships and functional roles of these proteases. Phylogenetic and motif analyses resulted in selecting 19 amino acid O. maya sequences using multiple sequence alignment that were used to generate three-dimensional protein models. The obtained models revealed a diverse structural architecture among 16 modelled cathepsins; however, their catalytic potential to fully clarify their role in protein hydrolysis and cellular processes remains to be determined. Foundational data provides insights into biochemistry and physiology behind O. maya protein digestion. Further complementation of these results with enzymatic characterization of the identified proteases should allow for improved diet formulation in order to foster this species aquaculture.

Keywords: Octopus maya; Cathepsin; Digestive physiology; Genome; Metatranscriptome.

Fig. 1.

Phylogenetic analysis (using maximum likelihood) of the gene coding for proteinases retrieved from databases and O. maya metatranscriptomics. Each sequence selected from the NCBI GenBank appears with its accession number. At each node, bootstrap (1000 iterations) values >90 are depicted with a purple circle. Each main clade has a different color. Red typeface indicates O. maya enzymes. The number on each tree branch indicates the evolutionary distance in millions of years according to WAG+R6 evolutionary model obtained for the sequences in this analysis.

Fig. 2.

Analysis of (A) JAOPJW010129046, (B) JAOPJW010002573 protein sequence using InterProScan. Each colored bar represents a specific domain identified in the protein sequence. The positions of the domains along the protein sequence are indicated by the length scale at the top. The results highlight the presence of catalytic and binding domains, providing a detailed prediction on the possible biological functions of protein XYZ.

Fig. 3.

Three-dimensional AlphaFold2 models of O. maya proteins. Clade numbers as in Fig. 1.

Fig. 4.

Multiple sequence alignments of the isoforms of cathepsin B, DN64673, and of cathepsin L, DN78812 and DN61172. Red areas: differences between sequences within the alignment. Only the regions with differences are displayed; the full alignment is not shown.

Fig. 5.

Schematic representation of the role and regulation of various cathepsins in O. maya under different environmental stressors. (A) Distribution of different cathepsin types (B, L1, F, S, and Z) within the cell, highlighting their involvement in intracellular and extracellular protein degradation. (B) Effects of environmental factors on cathepsin expression.