Proteome and phosphoproteome dynamic change during cell dedifferentiation in Arabidopsis thaliana
Chitteti, Brahmananda Reddy
Boyle, A. John
Cell dedifferentiation is a cell fate switching process in which a differentiated cell reverts to a status with competence for cell division and organ regeneration like an embryonic stem cell. Although the phenomenon of cell dedifferentiation has been known for over two and a half centuries in plants, little is known of the underlying mechanisms. Here, the proteome map of Arabidopsis cotyledons has been established and investigated the dynamic change of the cotyledon proteome in the time course of cell dedifferentiation. Among the 353 distinct genes, corresponding to 500 2-DE gel protein spots identified with high confidence, 12% have over twofold differential regulations within the first 48 h of induction of cell dedifferentiation. The distributions of these genes among different Gene Ontology categories and gene differential regulations within each of the categories have been examined. In addition, the cotyledon phosphoproteome has been investigated using Pro-Q Diamond Phosphoprotein in Gel Stain followed by mass spectrometry analyses. Among the 53 identified putative phosphoproteins, nine are differentially regulated during cell dedifferentiation. Arabidopsis cotyledon proteome at four different time points after the induction of cell dedifferentiation with MudPIT approach has been investigated and analyzed the protein quantity change using two label-free methods, the Spectral Count (SC) and SEQUEST Cross Correlation Coefficient (ÓXcorr) methods. Among the 662 MudPIT identified proteins, one hundred forty eight displayed differential regulation. The up-regulated proteins include transcription factors, calmodulins, translational regulators, and stress response proteins. The Spectral Count and the cross correlation coefficient quantification results are highly consistent in over 81% of the differentially regulated proteins. These studies have provided significant new insight into cell dedifferentiation process in Arabidopsis thaliana and also enhanced the Arabidopsis cotyledon proteome database established using gel based and non gel based methods. The results show that cell dedifferentiation involves extensive protein quantitative and qualitative changes in almost every cellular compartment and cellular process. Proteins like 14-3-3 proteins, Translational controlled tumor protein (TCTP) and its possible interaction protein-Translational elongation factor eEF1 alpha chain, GTP binding nuclear protein RAN2, GTP binding protein SAR1B and several other hypothetical and expressed proteins and nine other phosphoproteins showed significant differential expression during early dedifferentiation. Deciphering the molecular mechanisms regulating the cellular dedifferentiation certainly enhances the understandings and mechanisms of reprogramming all types of differentiated cells including animal cells.