Bacterial viability and oxidative stress
Carbonyl derivatives are mainly formed by direct metal-catalysed oxidation (MCO) attacks on the amino-acid side chains of proline, arginine, lysine and threonine residues. For reasons unknown, only some proteins are prone to carbonylation. We used mass spectrometry analysis to identify carbonylated sites in : BSA that had undergone in vitro MCO, and 23 carbonylated proteins in E. coli. The presence of a carbonylated site rendered the neighbouring carbonylatable site more prone to carbonylation. Most carbonylated sites were present within hot spots of carbonylation. These observations led us to suggest rules for identifying sites more prone to carbonylation. We used these rules to design an in silico model (available at http://www.lcb.cnrs-mrs.fr/CSPD/), allowing an effective and accurate prediction of sites and of proteins more prone to carbonylation in the E. coli proteome. We observed that proteins evolve to either selectively maintain or lose predicted hot spots of carbonylation depending on their biological function. As our predictive model also allows efficient detection of carbonylated proteins in Bacillus subtilis, we believe that our model may be extended to direct MCO attacks in all organisms (Maisonneuve et al., 2009).
The details of the principle of detection are described in Materials and Methods section (Maisonneuve et al., 2009). A predicted HSC (grey box) is defined by two regions. A) An RKPT-enriched region (3 carbonylatable residues within a sequence of 4 amino acids (R, K, P, T ; 3 ; 4) containing at least one proline (P ; 1 ; 0). B) A specific environment around an RKPT-enriched region, enriched in various residues : (i) iron binding sites (D, E, Y, H, C, namely 1 residue within a window of 2 residues (D, E, Y, H, C ; 1 ; 2) and 8 residues within a window of 29 residues (D, E, Y, H, C ; 8 ; 29) ; (ii) hydrophobic amino acids (A, V, G, I, namely 1 residue within a window of 2 (A, V, G, I ; 1 ; 2)) ; (G namely 2 residues within a window of 14 (G ; 2 ; 14)) ; and (iii) (P, T) with 2 residues occurring within a window of 21 residues (P, T ; 2 ; 21). E, environment ; r, right ; l, left and w, window.