Dataset Information

Reversible Lysine Derivatization Enables High Specificity of Arg-C Digestion Using Trypsin

ABSTRACT: Bottom-up proteomics approach has become an important strategy in diverse areas of biological research, and the enzymatic digestion is essential for this technology. Endopeptidase Arg-C catalyzing the hydrolytic cleavage of peptide bonds C-terminal to arginine could be an important protease in bottom-up proteomics. However, it has been seldom applied due to its low specificity and high cost. Reversible chemical derivatization of amine allows a real Arg-C digestion using trypsin. In this paper, a reversible amine derivatization method, citraconylation and decitraconylation were optimized and evaluated for large-scale proteomics studies. Combination of the reversible derivatization and trypsin digestion (termed Arg-C* digestion to distinguish from the conventional Arg-C digestion) resulted in 64.2% more peptide identification (11,925 ± 199 vs 7,262 ± 59) and significantly higher cleavage specificity (95.6% vs 73.6%) than the conventional Arg-C digestion. Comparison of Arg-C* digestion with the widely used trypsin and Lys-C digestion revealed that Arg-C* performed equally or slightly better than Lys-C although not comparable to trypsin. Therefore, the well-established Arg-C* digestion method is a promising approach for proteomics studies and could be used as the prior alternative digestion method to trypsin digestion in order to achieve higher proteome coverage.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (human) Escherichia Coli

TISSUE(S): Whole Body

SUBMITTER: Zhen Wu

LAB HEAD: Xumin Zhang

PROVIDER: PXD007994 | Pride | 2018-01-04

REPOSITORIES: Pride

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Reversible Lysine Derivatization Enabling Improved Arg-C Digestion, a Highly Specific Arg-C Digestion Using Trypsin.

Wu Zhen Z Huang Jichang J Lu Jianan J Zhang Xumin X

Analytical chemistry 20180108 3

The bottom-up proteomics approach has become an important strategy in diverse areas of biological research, and the enzymatic digestion is essential for this technology. Endopeptidase Arg-C catalyzing the hydrolytic cleavage of peptide bonds C-terminal to arginine could be an important protease in bottom-up proteomics. However, it has been seldom applied due to its low specificity and high cost. In this report, the reversible amine derivatization method (citraconylation and decitraconylation) wa ...[more]

PMID: 29260870

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Project description:Reactive nitrogen species (RNS) derived from dietary and salivary inorganic nitrates (NO3-) foment innate host defenses associated with the acidity of the stomach. The mechanisms by which these reactive species exert antibiotic activity in the gastric lumen are, however, poorly understood. To identify targets of RNS, the genetically tractable acid tolerance response (ATR) that enables enteropathogens to survive the harsh acidity of the stomach was screened for signaling pathways responsive to RNS. The nitric oxide (NO) donor spermine NONOate derepressed the Fur regulon that controls secondary lines of resistance against organic acids. Despite inducing a Fur-mediated adaptive response, acidified RNS largely boosted gastric host defenses as demonstrated by the fact that Salmonella bacteria exposed to spermine NONOate during mildly acidic conditions were not only shed in low amounts in feces, but also exhibited ameliorated oral virulence. NO prevented Salmonella from mounting a de novo ATR, but was unable to suppress an already functional protective response, indicating that RNS target regulatory cascades but not the effectors that defend against the rigors of gastric acidity. Transcriptional and translational analyses revealed that the PhoPQ signaling cascade is a critical ATR target of NO in rapidly growing Salmonella. Inhibition of PhoPQ signaling appears to contribute to most of the NO-mediated abrogation of the ATR in log phase bacteria, because the augmented acid sensitivity of phoQ-deficient Salmonella was not further enhanced after RNS treatment. Since PhoPQ-regulated acid resistance is widespread in enteric pathogens, the RNS-mediated inhibition of the Salmonella ATR described herein may represent a common component of the innate host defenses of the gastric lumen. Keywords: acid tolerance response, nitric oxide Microarray analyses were conducted comparing transcript levels of log-phase Salmonella cultured in minimal E salts + 0.4% glucose, pH 4.4 in the presence or absence of 250 ÂµM spermine NONOate for 1 hour. Microarrays were performed in triplicate under identical conditions (3 biological replicates).

Dataset Information

Reversible Lysine Derivatization Enables High Specificity of Arg-C Digestion Using Trypsin

Publications

Reversible Lysine Derivatization Enabling Improved Arg-C Digestion, a Highly Specific Arg-C Digestion Using Trypsin.

Similar Datasets

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