Comparative Phospho- and Acetyl Proteomics Analysis of Posttranslational Modifications Regulating Intestine Regeneration in Sea Cucumbers

Abstract

Sea cucumbers exposed to stressful circumstances eviscerate most internal organs, and then regenerate them rapidly under favorable environments. Reversible protein phosphorylation and acetylation are major modifications regulating protein function. Herein, for the first time, we perform quantitative phospho- and acetyl proteomics analyses of intestine regeneration in a sea cucumber species Apostichopus japonicus. We identified 1,862 phosphorylation sites in 1,169 proteins, and 712 acetylation sites in 470 proteins. Of the 147 and 251 proteins differentially modified by phosphorylation and acetylation, respectively, most were related to cytoskeleton biogenesis, protein synthesis and modification, signal recognition and transduction, energy production and conversion, or substance transport and metabolism. Phosphorylation appears to play a more important role in signal recognition and transduction than acetylation, while acetylation is of greater importance in posttranslational modification, protein turnover, chaperones; energy production and conversion; amino acid and lipid transport and metabolism. These results expanded our understanding of the regulatory mechanisms of posttranslational modifications in intestine regeneration of sea cucumbers after evisceration.

Molecular Aspects of Regeneration Mechanisms in Holothurians

“…After 3 dpe, these processes are also detected in the esophagus remnant [ 74 , 75 , 135 , 136 , 137 ]. An analysis of metabolites and phosphorylation and acetylation processes has shown that a significant rearrangement of cellular metabolism occurs in the holothurian esophagus after 3 dpe [ 135 , 136 ]. As in the activation of the mesenterial coelomic epithelium, it influences the key processes: Transcription, translation, and processing of proteins.…”

“…Almost half of the proteins involved in the amino acid transport and metabolism were upregulated [ 137 ]. It is worth noting here that almost all proteins associated with the “energy production and conversion” term underwent deacetylation [ 136 ]. Thus, the accumulation of energy reserves and their further utilization during regeneration in holothurians is regulated by deacetylation [ 136 ].…”

Genomic and Metagenomic Insights Into the Microbial Community in the Regenerating Intestine of the Sea Cucumber Apostichopus japonicus

“…Regeneration is a fascinating biological event that has aroused interest in many researchers. For the past two decades, studies have investigated many mechanisms of regenerative processes in sea cucumbers, including morphological features, cell division, dedifferentiation, cell proliferation and migration, nerve regrowth, and molecular regulatory mechanisms (García-Arrarás et al, 1998; Dolmatov and Ginanova, 2009; Sun et al, 2011, 2017a, 2018; Sun L.N. et al, 2013; Li et al, 2017b; Zhang et al, 2017).…”

Lysine Acetylation is an Important Post-Translational Modification that Modulates Heat Shock Response in the Sea Cucumber Apostichopus japonicus

“…Trypsin/P was specified as the cleavage enzyme, allowing up to two missed cleavages, five modifications per peptide, and five charges. Carbamidomethylation on Cys was specified as a fixed modification, and oxidation on Met, phosphorylation on Ser, Thr, Tyr, and acetylation on the protein N-terminus were specified as variable modifications [49]. False discovery rate thresholds for peptide, protein, and modification site were specified at 5%.…”

“…A quantification value was the intensity, and the area was detected for a given quantification channel depending on the setting in the precursor ions quantifier in the consensus method. A t-test with a p -value < 0.05 was applied to distinguish the differential quantitation of acetylated sites [26,49,50]. Fold changes (FCs) >1.2 or <0.83 were also regarded as the criteria of differentially acetylated sites [51].…”