Figure 1.
Experimental system for SILAC labelling of Arabidopsis seedlings.
Seedlings were grown from seeds germinated in liquid medium with reciprocal labelling of salt-treated and control plants (A); seedlings prior to harvest formed an island of material which floated on the medium with roots immersed (B); experimental plan showing days after germination, media changes, salt treatment duration and time of harvest (C).
Figure 2.
Efficient SILAC labelling of Arabidopsis seedlings and assessment of arginine-proline conversion.
Mass spectra of unlabelled (“light”) and labelled (“heavy”) peptides of L37-2 ribosomal protein showing efficient labelling (SILAC ratio = 1.0023) (A). Mass spectra of “light” and “heavy” (heavy proline) peptides of an RNA helicase protein (B).
Figure 3.
Changes in the proteome of salt-treated Arabidopsis seedlings.
Quantification of protein changes in response to 80 mM NaCl - the relative fold increase or decrease of all of the proteins analysed is indicated on the y axis expressed as the log2 of the average SILAC ratio across the five bioreps plotted against –log10 of the t-test p-value. For further analysis, up- and down-regulated proteins were taken as those outside the cut-off of 0.2 to −0.4.
Figure 4.
Distribution of up- and down-regulated proteins by biological process.
Gene ontology (GO) term enrichment distribution of up-regulated proteins (A) and down-regulated proteins (B) using DAVID. Frequency distribution (%) of proteins in significantly enriched (p<0.05) GO:Biological Process function terms are given (see also Table S4 and Table S5).