Global analysis of phosphoproteome dynamics in embryonic development of zebrafish (Danio rerio)

Abstract

The zebrafish (Danio rerio) is a popular animal model used for studies on vertebrate development and organogenesis. Recent research has shown a similarity of approximately 70% between the human and zebrafish genomes and about 84% of human disease-causing genes have common ancestry with that of the zebrafish genes. Zebrafish embryos have a number of desirable features, including transparency, a large size, and rapid embryogenesis. Protein phosphorylation is a well-known PTM, which can carry out various biological functions. Recent MS developments have enabled the study of global phosphorylation patterns by using MS-based proteomics coupled with titanium dioxide phosphopeptide enrichment. In the present study, we identified 3500 nonredundant phosphorylation sites on 2166 phosphoproteins and quantified 1564 phosphoproteins in developing embryos of zebrafish. The distribution of Ser/Thr/Tyr phosphorylation sites in zebrafish embryos was found to be 88.9, 10.2, and 0.9%, respectively. A potential kinase motif was predicted using Motif-X analysis, for 80% of the identified phosphorylation sites, with the proline-directed motif appearing most frequently, and 35 phosphorylation sites having the pSF motif. In addition, we created six phosphoprotein clusters based on their dynamic pattern during the development of zebrafish embryos. Here, we report the largest dataset of phosphoproteins in zebrafish embryos and our results can be used for further studies on phosphorylation sites or phosphoprotein dynamics in zebrafish embryos.

First profiling of lysine crotonylation of myofilament proteins and ribosomal proteins in zebrafish embryos

“…A total of 97.7% of Kcr proteins and 76.8% of Kcr sites in zebrafish significantly overlapped with humans. Our previous study showed that 69% of zebrafish phosphoproteins were conserved in humans 9 . In addition, 51.7% of zebrafish Kac sites overlapped with humans and 34.5% of Kac sites were identified as human Kac sites 26 .…”

“…Among known PTMs, the phosphoproteome in zebrafish embryos has been well-studied; 1067 endogenous phosphorylation sites from 60 embryos were identified in 2008 8 . Moreover, we previously identified 3500 non-redundant phosphorylation sites on 2166 phosphoproteins and quantified 1564 phosphoproteins in developing zebrafish embryos 9 .…”

The Current Landscape of 3D In Vitro Tumor Models: What Cancer Hallmarks Are Accessible for Drug Discovery?

“…The transparency of zebrafish embryos allows rapid optical assessment of phenotypic changes associated with target modulation. Interestingly, sequencing showed that over 70% of human genes have a functional zebrafish homolog, including at least 84% of proteins implicated in human disease . For comparison, protein‐coding regions of human and mouse genomes are 85% similar .…”

A detailed proteomic profiling of plasma membrane from zebrafish brain

“…Development of high‐throughput techniques enabled obtaining the complex expression profiles in living systems. The annotated genome sequence for zebrafish is currently available and many proteomic studies on zebrafish were performed to analyze embryogenic stages , organ systems , or pathological effects of genetic mutations and toxins . A proteome profiling of adult zebrafish organs previously performed by Abramsson et al.…”

“…The annotated genome sequence for zebrafish is currently available [7] and many proteomic studies on zebrafish were performed to analyze embryogenic stages [8,9], organ systems [10,11], or pathological effects of genetic mutations [12] and toxins [13][14][15]. A proteome profiling of adult zebrafish organs previously performed by Abramsson et al [10] showed high percentage (40%) of brain-specific proteins.…”