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. 2016 Mar;22(3):193-9.
doi: 10.1093/molehr/gav052. Epub 2015 Sep 22.

Proteomics of Xenopus development

Liangliang Sun  1 , Matthew M Champion  1 , Paul W Huber  1 , Norman J Dovichi  2
Affiliations

Proteomics of Xenopus development

Liangliang Sun et al. Mol Hum Reprod. 2016 Mar.

Abstract

Modern mass spectrometry-based methods provide an exciting opportunity to characterize protein expression in the developing embryo. We have employed an isotopic labeling technology to quantify the expression dynamics of nearly 6000 proteins across six stages of development in Xenopus laevis from the single stage zygote through the mid-blastula transition and the onset of organogenesis. Approximately 40% of the proteins show significant changes in expression across the development stages. The expression changes for these proteins naturally falls into six clusters corresponding to major events that mark early Xenopus development. A subset of experiments in this study have quantified protein expression differences between single embryos at the same stage of development, showing that, within experimental error, embryos at the same developmental stage have identical protein expression levels.

Keywords: Xenopus laevis; early vertebrate development; expression clustering; iTRAQ chemistry; mass spectrometry; quantitative proteomics.

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Figures

Figure 1
Figure 1
Dimethyl labeling chemistry.
Figure 2
Figure 2
Example of a 4-plex iTRAQ reagent.
Figure 3
Figure 3
Fragmentation spectrum of 8-plex labeled peptide. (A) Full spectrum is used to identify the peptide; iTRAQ signal region is circled. (B) Close-up of the iTRAQ signal region to determine relative abundance of each sample.
Figure 4
Figure 4
Protocol for each experiment.
Figure 5
Figure 5
iTRAQ Labeling of single embryos in biological duplicate at stages 1, 5, 8 and 11 in Experiment 1. Similar labeling was performed for stage 1, 5, 13 and 21 embryos in Experiment 2.
Figure 6
Figure 6
Cumulative distribution of protein coverage for experiment E3.
Figure 7
Figure 7
Log2 ratio of protein expression ratio of two single embryos at stage 1 of development.
Figure 8
Figure 8
Clustergram for 1200 proteins with significant expression changes in Experiment 3. Data are plotted as the log2 values, normalized to the stage 1 expression.
Figure 9
Figure 9
Number of members of each cluster from experiment 3.
Figure 10
Figure 10
Expression profiles for the six clusters identified in Experiment 3. Data from Sun et al. (2014). Data were subjected to a clustering algorithm to generate the six clusters.
See this image and copyright information in PMC

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