Global proteomic analysis of lysine acetylation in zebrafish (Danio rerio) embryos

Abstract

Lysine acetylation is an important post-translational modification (PTM). Since the development of MS-based proteomics technology, important roles of lysine acetylation beyond histones have focused on chromatin remodeling during the cell cycle and regulation of nuclear transport, metabolism, and translation. Zebrafish (Danio rerio) is a widely used vertebrate model in genetics and biologic studies. Although studies in several mammalian species have been performed, the mechanism of lysine acetylation in D. rerio embryos is incompletely understood. Here, we investigated the global acetylome in D. rerio embryos by using an MS-based proteomics approach. We identified 351 acetylated peptides and 377 nonredundant acetylation sites on 189 lysine-acetylated proteins in 5-day postfertilization (hpf) embryos of D. rerio. Among lysine-acetylated peptides, 40.2% indicated three motifs: (ac)KxxxK, (ac)KxxxxK, and Lx(ac)K. Of 190 acetylated proteins, 81 (42.6%) were mainly distributed in the cytoplasm. Gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that lysine acetylation in D. rerio was enriched in metabolic pathways. Additionally, 17 of 30 acetylated ribosomal proteins were evolutionarily conserved between zebrafish and humans. Our results indicate that acetyllysine might have regulatory effects on ribosomal proteins involved in protein biosynthesis.

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

“…S1c ). To compare crotonylation and acetylation in zebrafish, we used a previously acquired Kac dataset in zebrafish 26 (Fig. S1d ).…”

“…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 . Particularly, our dataset revealed that crotonylation of ribosomal proteins and myofilament proteins was highly enriched and evolutionarily conserved.…”

Comprehensive Profiling of Lysine Acetylome in Baculovirus Infected Silkworm (Bombyx mori) Cells

“…In fact, it has been reported that the metabolic process is a major biological process involving acetylation in many species, such as Danio rerio , mouse, and E . coli , indicating that Kac synthetically regulates metabolism during BmNPV infection.…”

“…The acetylomes of many species, including Bombyx mori, Streptomyces roseosporus , Synechocystis sp , Danio rerio , Escherichia coli , mouse, Drosophila melanogaster , Saccharomyces cerevisiae , Oryza sativa , Arabidopsis thaliana , and Toxoplasma gondii , have been identified . In the current study, we comprehensively examined the proteome for changes of acetylated proteins in BmNPV infected BmN cells.…”

Comparative Proteomic Analysis of Lysine Acetylation in Fish CIK Cells Infected with Aquareovirus

“…In contrast to these studies focused on human disease induced by viruses or bacteria, little is known about protein acetylation in aquatic species. Recently, the lysine acetylome has been investigated in zebrafish embryos [ 26 ], Daphnia [ 27 ], and also in the pathogenic bacterium Spiroplasma eriocheiris [ 28 ]. To date, there is no report on the cellular responses of the lysine acetylome in response to viral infection in aquatic species.…”