Abstract
BackgroundAmphibians have the remarkable ability to regenerate missing body parts. After complete removal of the eye lens, the dorsal but not the ventral iris will transdifferentiate to regenerate an exact replica of the lost lens. We used reverse-phase nano-liquid chromatography followed by mass spectrometry to detect protein concentrations in dorsal and ventral iris 0, 4, and 8 days post-lentectomy. We performed gene expression comparisons between regeneration and intact timepoints as well as between dorsal and ventral iris.ResultsOur analysis revealed gene expression patterns associated with the ability of the dorsal iris for transdifferentiation and lens regeneration. Proteins regulating gene expression and various metabolic processes were enriched in regeneration timepoints. Proteins involved in extracellular matrix, gene expression, and DNA-associated functions like DNA repair formed a regeneration-related protein network and were all up-regulated in the dorsal iris. In addition, we investigated protein concentrations in cultured dorsal (transdifferentiation-competent) and ventral (transdifferentiation-incompetent) iris pigmented epithelial (IPE) cells. Our comparative analysis revealed that the ability of dorsal IPE cells to keep memory of their tissue of origin and transdifferentiation is associated with the expression of proteins that specify the dorso-ventral axis of the eye as well as with proteins found highly expressed in regeneration timepoints, especially 8 days post-lentectomy.ConclusionsThe study deepens our understanding in the mechanism of regeneration by providing protein networks and pathways that participate in the process.Electronic supplementary materialThe online version of this article (doi:10.1186/s40246-014-0022-y) contains supplementary material, which is available to authorized users.
Highlights
Amphibians have the remarkable ability to regenerate missing body parts
Direct comparisons with proteins found in previous proteomic studies in newts revealed that 701 of these annotated proteins have not been detected in newts before [7]
In this study, we employed LC-mass spectrometry (MS)/MS to identify proteins that are highly expressed during newt lens regeneration
Summary
Amphibians have the remarkable ability to regenerate missing body parts. After complete removal of the eye lens, the dorsal but not the ventral iris will transdifferentiate to regenerate an exact replica of the lost lens. After surgical removal of the lens, the whole organ regenerates by transdifferentiation of Recently, the first newt transcriptome was assembled, and RNA sequencing of newt iris has been used to study differences in gene expression between the dorsal and ventral iris. Custom newt microarrays were used to detect 467 genes that were differentially expressed during lens regeneration [8] These studies provided essential information about the expression of genes during newt lens regeneration, protein data were missing so far. We computed the newt proteome from the assembled transcriptome and performed liquid chromatography followed by tandem mass spectrometry (LC-MS/MS) to identify proteins differentially expressed between dorsal and ventral iris as well as between regenerating and intact iris. We compared available high-throughput mRNA and protein expression data obtained from amphibian organ model systems undergoing regeneration, identifying a common regeneration program
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