Summary of the experimental workflow.

<p><b>A</b>. Emission spectrum of the UVB lamps used to irradiate the cultured cells of <i>P. angustum </i><b>B</b>. Bacterial cells were collected at the beginning of log phase (OD = 0.1) and cultured either under UVB radiation or in the dark <b>C</b>. After 1.75 h of incubation, quantitative proteomics was performed by using either gel-free (Post-digest ICPL labeling) or gel-based (2D-DIGE) approaches. Quantitative data for ICPL were obtained from the MS spectrum (L: Light label: H: Heavy label).</p

Detection of the RecA protein (≈40 kDa) by quantitative fluorescent western blot analysis of both UVB-treated cells and dark control cultures.

<p>Four different biological replicates are shown for each condition.</p

UVB protein biomarkers of <i>P. angustum</i> quantified by both ICPL and 2D-DIGE.

*<p>: 2 values are indicated for VAS14_06783 with 2D-DIGE because it was identified under 2 spots (1U, 2U).</p

A representative standard 2D gel showing protein spots that were down-regulated (A) and up-regulated (B).

<p>Proteins of interest are circled in green, and excised spots are circled in blue or red according their relative spot volumes (D = down-regulated by UVB; U = up-regulated by UVB). Green circles correspond to the up- or down-regulated proteins not excised for MS analysis.</p

Venn diagram showing the non-redundant proteins quantified in four biological replicates.

<p>Venn diagram showing the non-redundant proteins quantified in four biological replicates.</p

List of the quantified proteins in four biological replicates using the post-digest ICPL labeling methodology.

<p>Proteins significantly different from the control within a given biological replicate are indicated with bold characters. <b>Ratio</b>: UVB/Dark, <b>SD</b>: standard deviation, <b>#Pept</b>: number of peptides used for protein quantification.</p

Identification of the two-dimensionally separated protein spots of interest with the average fold change and associated p-values obtained from seven replicates.

<p>The ratio was determined by comparing the peak intensities in LC-MS runs of UVB <i>versus</i> dark conditions (UVB/Dark). The number of peptides assigned a Mascot score above 35, as well as the protein mass, score and empAI value, are also listed for each identified protein. (D: down-regulated; U: up-regulated).</p

Quantification of carbonylated proteins and peptides and location of the modification.

<p>Protein ratio refers to the differential abundance of the protein between UVB and dark treatments. Peptide ratio refers to the differential abundance of the carbonylated peptides. Peptides were scored as either carbonylated or not irrespective of whether multiple residues in the peptide were carbonylated. Data is for the combination of all replicates.</p>*<p>Stars show proteins with similar trends for peptide and protein ratios (UVB/dark ratio <1 or >1). Bold residues in the sequence of peptides indicate sites of carbonylation.</p

SDS-PAGE of proteins purified by avidin affinity chromatography.

<p>Replicates (A and B) of proteins extracted from cells exposed to UV or darkness, electrophoresed on 4–12% acrylamide gradient gels and visualized by silver staining. MW: molecular weight marker (kDa).</p

Relative proportion of R, T, P and K residues that were carbonylated.

<p>Proportion of each residue as a fraction of the total R+T+P+K content in the 62 carbonylated proteins <i>P. angustum</i> (blue), and relative proportion of those residues that were carbonylated (orange). Comparing the percentage that each residue represents versus the percentage that was experimentally determined to be carbonylated highlights the disproportionately high level of carbonylation of P residues.</p