Research Group „Physiological Proteomics & Bioinformatics“ (Prof. K. Riedel, Dr. J. Pané-Farré)

The Riedel group focus on the following research topics:

  • elucidation of the molecular basis of infections by opportunistic pathogens such as Pseudomonas aeruginosa, Burkholderia sp., Clostridium difficile, Staphylococcus aureus by in vitro and in vivo proteome analyses
  • metaproteomics and microscopic analyses to unravel structure and functions of pathogenic mono- and mixed-species biofilms
  • environmental proteomics to study microbial communities in terrestric and aquatic habitats, i.e. leaf litter, soil, lichens, fresh water & marine microbial aggregates
  • development of innovative tools for the analysis, integration and visualization of comprehensive „omics“ datasets

Further Reading & Key Publications:

  • Müller et al. Deletion of membrane-associated Asp23 leads to up-regulation of cell wall stress genes in Staphylococcus aureus. Mol Microbiol. Jul 29. doi: 10.1111/mmi.12733. [Epub ahead of print] PMID:25074408
  • Fuchs et al. Aureolib – a proteome signature library: Towards an understanding of Staphylococcus aureus pathophysiology. PLoS One. 8(8):e70669. PMID:23967085
  • Mehlan et al. Data visualization in environmental proteomics. Proteomics. 2013 Oct;13(18-19):2805-21. PMID: 23913834.
  • Becher et al. Metaproteomics to unravel major microbial players in leaf litter and soil environments: challenges and perspectives. Proteomics. 2013 Oct;13(18-19):2895-909. PMID: 23894095.
  • Schneider et al. Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions. ISME J. 2012 Sep;6(9):1749-62. PMID: 22402400.
  • Eberl & Riedel. Mining quorum sensing regulated proteins – Role of bacterial cell-to-cell communication in global gene regulation as assessed by proteomics. Proteomics. 2011 Aug;11(15):3070-85. PMID: 21548094.

Subgroup „Pathogenomics“ (Dr. Jan Pané-Farré)

In our group we use global as well as gene specific approaches to investigate the pathophysiology of Staphylococcus aureus. Furthermore, we are also interested in the evolution and function of signaling pathways controlled by the stressosome, a large 1.8 MDa cytosolic protein complex that was first described in the soil bacterium Bacillus subtilis. To achieve these goals, we enjoy collaborations with many other groups from the University of Greifswald and across Europe.

  • Pathophysiology of Staphylococci

The primary goal of these studies is the use of proteomics to map and characterize the response of S. aureus to infection-related growth and stress conditions. In particular, we wish to learn how S. aureus allocates its metabolic resources in order to generate the energy and building blocks required for growth and proliferation. Furthermore, a special emphasis is put on the metabolic control of virulence gene expression in S. aureus. Since different parts of the human body are characterized by specific carbon sources available to S. aureus, it is conceivable that they may also act as host niche identification signal, helping S. aureus to fine tune virulence factors production to adapt and survive inside its human host. In addition, to providing a global and quantitative view of the S. aureus physiology, these studies always identify a large number of proteins of unknown function that based on their induction pattern are likely to play important roles during the adaptation to hunger and stress. Therefore, in addition to the bird´s eye view provide by proteomics, we are particularly interested in the characterization of these proteins to uncover the molecular basis for their function in stress adaptation. During the last years it became very clear that localization matters even in the seemingly simple world of bacterial cells. Therefore, a focus is put on the analysis of the spatial distribution of these proteins and how localization relates to protein function.

Current collaborators: Thomas Dandekar (Würzburg), Susanne Engelmann (Braunschweig), Stephan Fuchs (RKI Wernigerode), Michael Lalk, (Greifswald), Department of functional genomics (Greifswald)

  • Stressosome function

The genes encoding the stressosome proteins can be identified in Gram-positive as well as Gram-negative bacteria where they control the activity of transcription factors or the turnover of second messengers such as c-di-GMP. One focus of our studies is the investigation of how a conserved signal sensing input system, the stressosome, transmits is signal to various output systems to generate the appropriate change in gene expression or second messenger production.  Using proteomics and phenotypic assays we also map the biological processes controlled by the stressosome in Gram-negative bacteria including animal and plant pathogens to unravel the functional diversity of the stressosome pathway.

Current collaborators: Christine Ziegler (Regensburg), Rick Lewis (Newcastle UK), Jon Marles-Wright (Edinburgh)

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Subgroup „Data analysis and Data integration“ (Prof. Katharina Riedel, Dr. Jörg Bernhardt)

Very large dataset are generated particularly by omics technologies and meta studies. We are working on global analysis strategies and how to integrate data from different omics technologies such as Transcriptomics, Proteomics, and Metabolomics. By this new insights can be provided into the adaptive physiology and pathogenicity of bacteria (e.g. Staphylococcus aureus). Furthermore, we are interested in complex microbial communities (microbiomes) and are working on appropiate meta analysis workflows. Prophane (http://www.prophane.de) and Aureolib (http://aureolib.de) are examples of successful data analysis and, respectively, integration ressources initiated by our group.

Senior Research Group „Stress Physiology" (Dr. Ulf Gerth)

  • The Bacillus subtilis σB-dependent general stress response: More than 200 genes belong to the σB-dependent general stress regulon. These proteins equip the non-growing cells with a multiple, non-specific and preventive stress resistance in anticipation of “future stress”. The “fine-tuned” gene regulation and function of single stress proteins in the establishment of a global resistance against heat, ethanol, oxidative and osmotic stress are currently analyzed. Furthermore, the integration of the general stress regulon into a highly sophisticated adaptational network is being investigated.
  • “The Bacillus subtilis Clp machinery”: Regulation of the stress-inducible clp genes depends predominantly on the transcriptional CtsR repressor. CtsR is targeted by the ClpEP and ClpCP proteases during heat stress. Moreover, ATP-dependent proteolysis mediated by Clp proteases can also be observed during general stationary-phase phenomena, such as glucose starvation, competence development and sporulation. Mechanisms that finally result in the inactivation and degradation of transcriptional regulators and proteins, which lost their “duty” are currently investigated. Moreover, the role of the McsB arginine kinase, an adaptor protein of the ClpCP protease, is in the focus of our research.

 

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Further Reading & Key Publications:

  • Reder et al. Cross-talk between the general stress response and sporulation initiation in Bacillus subtilis – the σB promoter of spo0E represents an AND-gate. Environ Microbiol (2012) 14(10), 2741–2756. PMID: 22524514.
  • Reder et al. The modulator of the general stress response, MgsR, of Bacillus subtilis is subject to multiple and complex control mechanisms. Environ Microbiol (2012) 14(10), 2838–2850.PMID: 22812682.
  • Elsholz et al. CtsR, the Gram-positive master regulator of protein quality control, feels the heat. EMBO J. 2010 Nov 3;29(21):3621-9.
  • Elsholz et al. Global impact of protein arginine phosphorylation on the physiology of Bacillus subtilis. PNAS 2012 May 8;109(19):7451-6 PMID: 22517742.