Asymmetric distribution of biomolecules of maternal origin in the Xenopus laevis egg and their impact on the developmental plan

Abstract

Asymmetric cell division is a ubiquitous feature during the development of higher organisms. Asymmetry is achieved by differential localization or activities of biological molecules such as proteins, and coding and non-coding RNAs. Here, we present subcellular transcriptomic and proteomic analyses along the animal-vegetal axis of Xenopus laevis eggs. More than 98% of the maternal mRNAs could be categorized into four localization profile groups: animal, vegetal, extremely vegetal, and a newly described group of mRNAs that we call extremely animal, which are mRNAs enriched in the animal cortex region. 3′UTRs of localized mRNAs were analyzed for localization motifs. Several putative motifs were discovered for vegetal and extremely vegetal mRNAs, while no distinct conserved motifs for the extremely animal mRNAs were identified, suggesting different localization mechanisms. Asymmetric profiles were also found for proteins, with correlation to those of corresponding mRNAs. Based on unexpected observation of the profiles of the homoeologous genes exd2 we propose a possible mechanism of genetic evolution.

Novel functions of the ubiquitin-independent proteasome system in regulatingXenopusgermline development

“…By the 2-cell stage, these RNAs are restricted to the animal hemisphere and become separated from vegetally localized germ plasm. This observation is consistent with results from a recently published RNAseq analysis (Sindelka et al, 2018). We assessed the subcellular localization of 20S CP by immunofluorescence and observed similar dynamic changes, albeit with slower kinetics.…”

“…We have noticed that the graded distribution of the proteasome was not detected in a recently published proteomic study (Sindelka et al, 2018). This discrepancy is likely caused by the difference in sampling methods to harvest cytoplasmic proteins.…”

“…Second, we collected cytoplasm from animal and vegetal hemispheres of otherwise unperturbed fertilized eggs using a micropipette and cytoplasm was then analyzed directly by mass spectrometry. In contrast, Sindelka et al, extracted proteins from relatively large pieces of eggs using a bottom-up proteomic sample preparation approach coupling NP40 extraction with filtering (Sindelka et al, 2018). Although this method effectively reduces contamination from yolk proteins, other proteins, including proteasomal proteins, may also have been removed during sample preparation.…”

Spatio-temporal mRNA dynamics in the early zebrafish embryo

“…S5). The existence of animally localized genes was previously controversial, since either very few (0.2%, Owens et al 45 ) or a large majority of genes (94.4%, Sindelka et al 46 ) were found to be enriched at the animal pole. This highlights the advantages of our high-resolution analysis of subcellular RNA localization.…”

Single Cell Proteomics by Data-Independent Acquisition To Study Embryonic Asymmetry in Xenopus laevis

“…32 Furthermore, the protein DDX4/Vasa (also known as Xenopus vasa-like gene 1) was localized to the vegetal hemisphere of the embryo (indicated in yellow in Figure 4A), in line with previous findings by Sindelka et.al. 50 DDX4/Vasa belongs to the family of DEAD-box RNA helicases and is a marker for germ cell specification in diverse animal species. Vasa mRNA or protein is localized to germ plasm in oocytes and early embryos of Drosophila , C. elegans , sea urchins, and zebrafish.…”