Label-free quantitative proteomic analysis of nitrogen starvation in Arabidopsis root reveals new aspects of H2S signaling by protein persulfidation

Hydrogen sulfide (H2S)-mediated signaling pathways regulate many physiological and pathophysiological processes in mammalian and plant systems. The molecular mechanism by which hydrogen sulfide exerts its action involves the post-translational modification of cysteine residues to form a persulfidated thiol motif, and it is named protein Persulfidation. We have developed a comparative and label-free quantitative proteomic analysis approach for the detection of endogenous persulfidated proteins in Arabidopsis thaliana nitrogen-starved roots and carbon-starved leaves by using the tag-switch method. In this work, we have identified 5214 and 4691 unique proteins from root and leaf tissue, respectively, that represent almost a 13% of the entire annotate proteome in Arabidopsis. Bioinformatic analysis revealed that persulfidated cysteines are part of a wide range of biological functions, regulating important processes such as carbon metabolism, plant responses to abiotic and biotic stresses, plant growth and development, RNA translation and protein degradation. Quantitative analysis in both tissues showed important H2S-regulated metabolic processes through changes in the persulfidation level of key protein targets involved in ubiquitin-dependent protein degradation and autophagy, among others.