Portfolio Prof. Dr. Boris Macek

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Academic title:
Prof. Dr.
Name:
Boris Macek
Organizational units:
Faculty of Science
University of Tübingen
Department of Biology
Faculty of Science
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Contact data

Curriculum vitae

Research focus

Proteomics in experimental systems biology

Systems biology relies on global analytical methodologies such as genomics, transcriptomics and proteomics to provide a quantitative description of the living cell. It is widely appreciated that system complexity grows in the direction genome-transcriptome-proteome, and that studying proteins, as well as their modifications and interactions provides the best measure of the gene function. Modern, gel-free and mass spectrometry (MS)-based quantitative proteomics is making a decisive impact across all life sciences;  Relatively simple experimental set-ups based on high accuracy MS and powerful bioinformatics tools are capable of reliably identifying and quantifying expression levels of several thousand proteins in a single experiment, approaching the depth of message-based assays and reaching the analytical capacity to completely map the smaller proteomes, such as that of bacteria and yeasts. Likewise, recent progress in biochemical separation and enrichment protocols made it possible to detect dynamics of posttranslational modification sites upon a treatment, providing a wealth of specific and general clues about eukaryotic and prokaryotic signal transduction mechanisms that cannot be otherwise studied by genomics or transcriptomics. We are currently developing and applying methods that are capable of comprehensive and accurate identification and quantitation of proteomes in various model systems.

 

Phosphoproteomics - identification of kinase substrates

Increasing number of publications demonstrate that the proteomics has “matured” enough to comprehensively detect and quantify phosphoproteomes of eukaryotic and prokaryotic organisms. The challenge and the emphasis in the fields of proteomics and cell biology have now shifted to the next stage - detection of kinase and phosphatase substrates and their integration into regulatory networks in the cell. We are using a phosphoproteomics workflow based on SILAC labeling and phosphopeptide enrichment to identify kinase substrates in several eukatyotic and prokaryotic systems.

 

Microbial S/T/Y phosphoproteomics

Phosphorylation on serine, threonine, and tyrosine (Ser/Thr/Tyr) has long been considered  exclusive to eukaryotes, especially metazoans, and either not present or not functionally significant in bacteria. Instead, the two-component signaling system involving histidine and aspartate phosphorylation is the paradigm of bacterial signal transduction. We  recently applied the qualitative global peptide-based phosphoproteomics workflow to study Ser/Thr/Tyr protein phosphorylation in the model bacteria Bacillus subtilis, Escherichia coli,  Lactococcus lactis and in archaeon Halobacterium salinarum. This approach allowed us to analyze the bacterial phosphoproteome at the phosphorylation site level and to detect approximately 100 phosphorylation events in each analyzed bacterium. The number of phosphoproteins and phosphorylation sites detected in bacteria is much lower than in eukaryotes, where there is evidence for more than 10,000 phosphosites. However, essential proteins and enzymes involved in carbon metabolism and sugar transport were found to be significantly over-represented among detected phosphoproteins, supporting the emerging concept of Ser/Thr/Tyr phosphorylation as an important regulatory mechanism in the bacterial cell. Almost all glycolytic and tricarboxylic acid (TCA) cycle enzymes were found to be phosphorylated, and regulation of some of these enzymes by phosphorylation is already known. Interestingly, bacterial phosphoproteins and phosphorylated residues are significantly more conserved than their non-phosphorylated counterparts. A number of potential phosphorylation sites are conserved from Archaea to humans, pointing to the likely presence of this regulatory modification since the earliest stages of cellular life. Given the rapid increase of antibiotic resistance among pathogenic species, there is an urgent need for identification of alternative regulatory pathways in microorganisms and Ser/Thr/Tyr phosphorylation should be considered as a potential avenue to disrupt bacterial growth.

 

Proteogenomics (refinement of genomics data using shot-gun proteomics)

The ongoing efforts in genome sequencing have to date resulted in numerous completed genomes with little or no gene annotation. Available annotations usually rely on computational predictions of protein coding genes. Peptides from proteome lysates identified by mass spectrometry can be mapped directly onto the raw genome sequence, thus enabling the verification, re-annotation as well as the identification of unpredicted genes in a straightforward manner. We are developing proteogenomics strategies based on high accuracy mass spectometry and use them to refine the genome annotation of several model organisms.

 

Quantitative analysis of posttranslational modifications 

Mass spectrometry provides a unique opportunity to study posttranslational modifications on proteins, especially those that are low abundant, sub-stoichiometric and therefore not accessible to other methods. We are developing and applying methods for enrichment, structural analysis and quantitation of key regulatory modifications such as ubiquitylation and acetylation. 

Projects

2019 - 2021
Boris Macek
Deutsche Forschungsgemeinschaft e.V. (DFG)
2019 - 2021
Boris Macek
German-Israeli Foundation for Scientific Research and Development (GIF)
2019 - 2023
Heike Brötz-Oesterhelt
Deutsche Forschungsgemeinschaft e.V. (DFG)
2018 - 2019
Boris Macek
Deutscher Akademischer Austauschdienst e.V. (DAAD)
2018
Boris Macek
Deutsche Forschungsgemeinschaft e.V. (DFG)
2018 - 2022
Doron Rapaport
Deutsche Forschungsgemeinschaft e.V. (DFG)
2015 - 2019
Wolfgang Wohlleben
Deutsche Forschungsgemeinschaft e.V. (DFG)
2015 - 2018
Boris Macek
Deutsches Zentrum für Luft- und Raumfahrt e. V. (DLR)

Cooperations

Ruđer Bošković Institute (RBI)
Zagreb, Croatia (Hrvatska)
Indiana University
Bloomington, Indiana, United States of America
Katholieke Universiteit Leuven
Leuven, Belgium
Chalmers University of Technology
Göteborg, Sweden
Ohio State University
Columbus, Ohio, United States of America
University of Manchester
Manchester, United Kingdom
Ruđer Bošković Institute (RBI)
Zagreb, Croatia (Hrvatska)
Sveučilište u Zagrebu
Zagreb, Croatia (Hrvatska)

Publications

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