Isotopically Labeled Desthiobiotin Azide (isoDTB) Tags Enable Global Profiling of the Bacterial Cysteinome

Abstract

Rapid development of bacterial resistance has led to an urgent need to find new druggable targets for antibiotics.In this context, residue-specific chemoproteomic approaches enable proteome-wide identification of binding sites for covalent inhibitors.D escribed here are easily synthesized isotopically labeled desthiobiotin azide (isoDTB) tags that shortened the chemoproteomic workflowa nd allowed an increased coverage of cysteines in bacterial systems.They were used to quantify 59 %o fa ll cysteines in essential proteins in Staphylococcus aureus and enabled the discovery of 88 cysteines that showed high reactivity,w hichc orrelates with functional importance.F urthermore,2 68 cysteines that are engaged by covalent ligands were identified. Inhibition of HMG-CoA synthase was verified and will allow addressing the bacterial mevalonate pathway through an ew target. Overall, ab road map of the bacterial cysteinome was obtained, which will facilitate the development of antibiotics with novel modesof-action.

Degrasyn exhibits antibiotic activity against multi-resistantStaphylococcus aureusby modifying several essential cysteines

“…We therefore performed competitive residue-specific proteomics using the recently developed isoDTB-ABPP method 19 that is based on the isoTOP-ABPP (isotopic tandem orthogonal proteolysis-ABPP) platform 12,20 as an alternative strategy. In this approach, S. aureus cells are lysed and the lysate is split into two samples.…”

“…Competitive cysteine binders such as DGS block this labeling at their specific binding sites in the proteome. In order to read out these differences in alkynylation, isotopically labeled desthiobiotin azide (isoDTB) tags 19 are appended using CuAAC. 17 The samples are combined, enriched on streptavidin, and digested.…”

“…Interestingly, 96 of these cysteines were not liganded by any of 19 covalent a-chloro-acetamides that were previously used to profile cysteines in S. aureus. 19 This indicates that the reversibly covalent a-cyano-acrylamide is able to interact with a unique set of cysteines. Many cysteines respond to DGS treatment in a clearly concentration-dependent manner (Fig.…”

A Tailored Phosphoaspartate Probe Unravels CprR as a Response Regulator in Pseudomonas Aeruginosa Interkingdom Signaling

“…The tailored conditions of these model studies were integrated into an advanced chemical proteomic platform featuring a minimal clickable 17 hydroxylamine alkyne probe (HA-yne) with access to sterically demanding protein pockets (Fig. 1c) as well as the application of isotopically labeled desthiobiotin azide (isoDTB) tags 18 for the detection and quantification of pAsp sites. This methodology revealed 123 HA-yne modified aspartate sites with high fidelity, whose sequence motif closely resembles the known RR recognition sequence.…”

Light-Activatable, 2,5-Disubstituted Tetrazoles for the Proteome-Wide Profiling of Aspartates and Glutamates in Living Bacteria

“…10 Recently, isotopically labeled desthiobiotin azide (isoDTB) tags (figure 1B) have been introduced that obliviate the need to use a cleavable linker (isoDTB-ABPP). 11 After combination of the samples, enrichment and proteolytic digestion, the probe-modified peptides are identified and quantified by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). Because the peptides modified with the probe are directly detected, not only the target protein of the covalent inhibitor but also its exact interaction site are identified.…”