Biology subjects

Kirsch, R.

Publications and source records attributed to Kirsch, R..

3 recordsLinked to original sources

bioRxiv2022

A quantitative and site-specific atlas of the in vivo citrullinome reveals widespread existence of citrullination

Citrullination is the conversion of peptidyl-arginine into the non-coded amino acid citrulline. Despite its importance in physiology and disease, global identification of citrullinated proteins and precise modification sites has remained challenging. Here, we employed quantitative mass spectrometry-based proteomics to generate a comprehensive atlas of citrullination sites in a physiologically relevant cell type. Collectively, we identified 14.056 citrullination sites within 4.008 proteins and quantified their regulation upon inhibition of the citrullinating enzyme PADI4. Using this rich dataset, we uncover general mechanistic and cell biological principles of citrullination function, while providing site-specific and quantitative information on thousands of PAD4 substrates within cells. Our findings include signature histone marks and numerous modifications on transcriptional regulators and chromatin-related signaling effectors. Additionally, we identify precise citrullination sites on an extensive list of known autoantigens. Collectively, we describe systems attributes of the human citrullinome and provide a resource framework for understanding citrullinaiton at the mechanistic level.

molecular biology↗

bioRxiv2019

Visualization of the Dynamics of Histone Modifications and Their Crosstalk Using PTM-CrossTalkMapper

Visualization of large-scale, multi-dimensional omics data is a major challenge. Experimental study designs in proteomics research produce multiple data layers, e.g. relationships between hundreds of proteins, their interactions and abundances as a function of time or perturbation, as well as dynamics of post-translational modifications (PTMs) and allelic variants (proteoforms). These different levels and types of information of proteins and proteoforms complicate data analysis and generation of insightful and comprehensible graphic visualizations. Middle-down mass spectrometry of histone proteins now allows quantifying hundreds of histone proteoforms including co-existing methylation, acetylation and phosphorylation events at distinct amino acid residues within histone molecules. The histone PTM landscape plays a dominant role in the regulation of chromatin activity and transcriptional and epigenetic control. The dynamics of these reversible modifications are governed by reader, writer and eraser enzymes that cooperate to regulate molecular mechanism that rely on multiple interdependent PTM marks in histones and nucleosomes in chromatin. This PTM crosstalk can be quantified and provides a detailed picture of the underlying rules for setting the histone PTM landscape and chromatin activity, and is available to the community via our CrosstalkDB platform. Here, we developed a new computational method, PTM-CrossTalkMapper, to visualize the dynamics of histone PTMs for different experimental conditions, replicates and proteoforms onto a landscape, thereby describing the crosstalk and interplay between PTMs in a more comprehensible manner. We show the power of combining different levels of information on such crosstalk maps for histone PTM dynamics in mouse organs during the aging process. The PTM-CrossTalkMapper toolkit provides flexible functions to create these maps in various scenarios of multi-dimensional experimental designs, including histone PTM patterns and PTM crosstalk.\n\nThe source code is available at https://github.com/veitveit/CrossTalkMapper.

bioinformatics↗

bioRxiv2018

Pectin digestion in herbivorous beetles: Impact of pseudoenzymes exceeds that of their active counterparts

Many protein families harbor pseudoenzymes that have lost the catalytic function of their enzymatically active counterparts. Assigning alternative function and importance to these proteins is challenging [1]. Because the evolution towards pseudoenzymes is driven by gene duplication, they often accumulate in multigene families. Plant cell wall-degrading enzymes (PCWDEs) are prominent examples of expanded gene families. The pectolytic glycoside hydrolase family 28 (GH28) allows herbivorous insects to break down the PCW polysaccharide pectin. GH28 in the Phytophaga clade of beetles contains many active enzymes but also many inactive counterparts. Using functional characterization, gene silencing, global transcriptome analyses and recordings of life history traits, we found that not only catalytically active but also inactive GH28 proteins are part of the same pectin-digesting pathway. The robustness and plasticity of this pathway and thus its importance for the beetle is supported by extremely high steady-state expression levels and counter-regulatory mechanisms. Unexpectedly, the impact of pseudoenzymes on the pectin-digesting pathway in Phytophaga beetles exceeds even the influence of their active counterparts, such as a lowered efficiency of food-to-energy conversion and a prolongation of the developmental period.

physiology↗