ABSTRACT
Background Protein expression patterns underlie physiological processes and phenotypic differences including those occurring during early development. The Pacific oyster (Crassostrea gigas) undergoes a major phenotypic change in early development from free-swimming larval form to sessile benthic dweller while proliferating in environments with broad temperature ranges. Despite the economic and ecological importance of the species, physiological processes occurring throughout metamorphosis and the impact of temperature on these processes have not yet been mapped out.
Results Towards this, we comprehensively characterized protein abundance patterns for 7978 proteins throughout metamorphosis in the Pacific oyster at different temperature regimes. We used a multi-statistical approach including principal component analysis, ANOVA-simultaneous component analysis, and hierarchical clustering coupled with functional enrichment analysis to characterize these data. We identified distinct sets of proteins with time-dependent abundances generally not affected by temperature. Over 12 days, adhesion and calcification related proteins acutely decreased, organogenesis and extracellular matrix related proteins gradually decreased, proteins related to signaling showed sinusoidal abundance patterns, and proteins related to metabolic and growth processes gradually increased. Contrastingly, different sets of proteins showed temperature-dependent abundance patterns with proteins related to immune response showing lower abundance and catabolic pro-growth processes showing higher abundance in animals reared at 29°C relative to 23°C.
Conclusion Although time was a stronger driver than temperature of metamorphic proteome changes, temperature-induced proteome differences led to pro-growth physiology corresponding to larger oyster size at 29°C, and to altered specific metamorphic processes and possible pathogen presence at 23°C. These findings offer high resolution insight into why oysters may experience high mortality rates during this life transition in both field and culture settings. The proteome resource generated by this study provides data-driven guidance for future work on developmental changes in molluscs. Furthermore, the analytical approach taken here provides a foundation for effective shotgun proteomic analyses across a variety of taxa.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Abstract, Figures, Manuscript text, and Supplemental material to address Reviewers' comments
ABBREVIATIONS
- ADAM-TS
- A disintegrin and metalloproteinase with thrombospondin motifs
- ANOVA
- Analysis of variance
- ASCA
- ANOVA-simultaneous component analysis
- BCA
- Bicinchoninic acid assay
- COMMD9
- Copper metabolism MURR1 domain-containing protein 9
- DEAD box
- family of proteins containing a motif with the amino acid sequence asp-glu-ala-asp
- dpf
- day post-fertilization
- dsRNA
- double stranded ribonucleic acid
- FABP
- Fatty acid-binding protein
- GABA
- Gamma aminobutyric acid
- GO
- Gene ontology
- GRIM-19
- Gene associated with retinoid-IFN-induced mortality
- Hcs70
- Heat shock cognate protein 70
- LC-MS/MS
- liquid chromatography coupled tandem mass spectrometry
- lincRNA
- Long intergenic noncoding RNA
- MAPK
- Mitogen-activated protein kinase
- NSAF
- Normalized spectral abundance factor
- PAK1
- p21-activating kinase 1
- PCA
- Principal component analysis
- PVC
- polyvinyl chloride
- RNA
- ribonucleic acid
- RRP40
- Ribosomal RNA-processing protein 40
- TPR repeat
- tetratricopeptide repeat
- tRNA
- transfer ribonucleic acid