Methionine residues around phosphorylation sites are preferentially oxidized in vivo under stress conditions

Abstract

Protein phosphorylation is one of the most prevalent and well-understood protein modifications. Oxidation of protein-bound methionine, which has been traditionally perceived as an inevitable damage derived from oxidative stress, is now emerging as another modification capable of regulating protein activity during stress conditions. However, the mechanism coupling oxidative signals to changes in protein function remains unknown. An appealing hypothesis is that methionine oxidation might serve as a rheostat to control phosphorylation. To investigate this potential crosstalk between phosphorylation and methionine oxidation, we have addressed the co-occurrence of these two types of modifications within the human proteome. Here, we show that nearly all (98%) proteins containing oxidized methionine were also phosphoproteins. Furthermore, phosphorylation sites were much closer to oxidized methionines when compared to non-oxidized methionines. This proximity between modification sites cannot be accounted for by their co-localization within unstructured clusters because it was faithfully reproduced in a smaller sample of structured proteins. We also provide evidence that the oxidation of methionine located within phosphorylation motifs is a highly selective process among stress-related proteins, which supports the hypothesis of crosstalk between methionine oxidation and phosphorylation as part of the cellular defence against oxidative stress.

Methionine in proteins: The Cinderella of the proteinogenic amino acids

“…This isolated observation prompted us to test the hypothesis that reversible methionine oxidation might be used in a generalized way as a rheostat to control the phosphorylation of proximal phospho acceptors. To this end, we analyzed the co‐occurrence of these two types of PTMs (sulfoxidation and phosphorylation) within the human proteome . In that study we showed that as many as 98% of the proteins containing oxidized methionine after an oxidative insult were also phosphoproteins.…”

“…Furthermore, phosphoserine (pSer) and MetO sites cluster together in a statistically significant way when compared to Ser and Met. This proximity between modification sites could not be accounted for by their colocalization within unstructured regions because it was faithfully reproduced in a smaller sample of structured proteins . Overall, the results of that study strongly suggest that methionine sulfoxidation in the phosphorylation motifs it is not a random process directed by mass action, but on the contrary, it is a highly specific and selective process.…”

“…A relevant constituent of the stress granules is ataxin‐2, an intrinsically disordered protein with an increasingly larger number of known molecular functions. In a previous work, ataxin‐2 was identified as a putative candidate to be regulated via cross talk between methionine sulfoxidation and serine phosphorylation in response to oxidative stress . More recently, the group led by Benjamin Tu has unraveled a prominent role for methionyl residues from Pbp1 (the yeast orthologous of ataxin‐2) in the formation of intracellular drop‐like condensates required for the inhibition of TORC1 signaling during respiratory growth …”

Regulated methionine oxidation by monooxygenases

“…The only established pattern known to affect methionine reactivity is the interaction of its sulfur atom with the aromatic ring of tyrosine and other aromatic amino acids 37,38 , reducing its propensity to oxidation 39 . Additionally, a recent report provided a bioinformatics evidence that methionine oxidation is enriched in the proximity of phosphorylation sites 40 . Identification of methionines oxidized in vivo lags behind the research on cysteine oxidation.…”

Prediction of methionine oxidation risk in monoclonal antibodies using a machine learning method

“…38–40 For example, a previous study showed that oxidized Met residues were located in closer proximity to phosphorylation sites than non-oxidized ones. 41 In addition, Met residues are often located in spatial proximity to aromatic rings, contributing to protein stability through the hydrophobic effect. 42 The oxidation of such Met residues can lead to conformational changes that result in the exposure of previously unexposed hydrophobic residues.…”