Research Projects

 

Context matters:

Engineering orthogonality in synthetic circuits

The success of implementing novel functionalities into living cells is challenged by the inherent complexity of even the simplest biological systems, such as microbial cells. This gives rise to context-dependence, which originates in the high level of interconnectivity of virtually any compound within a living cell. For synthetic biology this is a major challenge, since even small changes in cellular physiology can have major impact on the desired characteristics of synthetic circuits. A primary goal in this project is to understand how genetic context, i.e., the “chassis”, can affect the function of regulatory circuits and, vice versa, how genetic circuits can be designed to function robustly in various contexts. Ultimately, we aim at establishing a suite of orthogonal genetic building blocks for the construction of context-independent synthetic circuits.

Collaborators

Anke Becker (SYNMIKRO)Calin Guet (IST Vienna, Austria)

Relevant publications

  • Radeck J, Kraft K, Bartels J, Cikovic T, Dürr F, Emenegger J, Kelterborn S, Sauer C, Fritz G, Gebhard S, Mascher T (2013). The Bacillus BioBrick box: Generation and evaluation of essential genetic building blocks for standardized work with Bacillus subtilisJ. Biol. Eng. 7, 29.

 

Memory in microbes:

Design schemes of sequential transcription logic

Epigenetic memory plays a vital role in the development of multicellular organisms and in the social organization of microbial communities. In analogy to digital electronics, genetic networks with memory are often referred to as sequential logic circuits. While the schemes of pure combinatorial cis-regulatory logic have been studied to great detail before, little is known about the schemes of sequential logic in gene regulation. In this project we develop on such a general perspective by scrutinizing how the molecular repertoire of bacterial gene regulation can be leveraged to find compact and robust genetic implementations of latches and flip-flops known from digital electronics. In synthetic biology these new devices might foster exciting applications, as they greatly expand the functional spectrum of available building blocks. But also existing gene networks seem to make active use of sequential logic, as is illustrated by well-known examples of eukaryotic development and bacterial differentiation. 

Collaborators

Ulrich Gerland (TU Munich, Germany)

Relevant publications

  • Hillenbrand P, Fritz G, Gerland U (2013). Biological signal processing with a genetic toggle switch. PLoS ONE 8, e68345.
  • Fritz G, Buchler NE, Hwa T, Gerland U (2007). Designing sequential transcription logic: a simple genetic circuit for conditional memory. Syst. Synth. Biol. 1, 89-98.

 

On the anatomy of antibiotic resistance modules:

Modeling bacitracin resistance in B. subtilis

In their natural habitats many bacterial species compete for a limited amount of nutrients despite high total cell densities. Here, many microorganisms produce a variety of antimicrobial agents, leading to a “chemical warfare” in these densely populated habitats. Amongst those compounds, peptide antibiotics play a crucial role and mostly target important steps in cell wall biosynthesis. Bacitracin, for instance, binds undecaprenyl pyrophosphate and inhibits its dephosphorylation, thereby blocking its recycling and, ultimately, inhibiting cell wall biosynthesis. Hence, for bacteria to successfully thrive in such environments it is of pivotal importance to mount specific stress responses, which allow them to cope with endo- and exogenously produced peptide antibiotics.

The BceRS-BceAB system of B. subtilis is one of such peptide sensing and detoxification modules, conferring resistance both to bacitracin as well as to a broader spectrum of compounds. As illustrated in Fig. 1, it consists of the ABC transporter BceAB, which facilitates the removal of the antibiotic from its active site, and the two-component system BceRS. Upon sensing the signal, that is, the presence of the antibiotic, the histidine kinase BceS phosphorylates its cognate response regulator BceR, which in turn induces the expression of BceAB. In addition, the ABC transporter is directly required for stimulus perception – both in B. subtilis as well as in the homologous BceABRS system of S. mutans. In this project we develop alternative mathematical models for the regulatory dynamics of the BceRS-BceAB system and discriminate between them by measuring the in vivo expression dynamics of this system. In doing so, our combined theoretical and experimental approach sheds new light on this unusual mode of stimulus perception.

Collaborators

Susanne Gebhard (University of Bath, UK)Thorsten Mascher (TU Dresden, Germany)Ulrich Gerland (TU Munich, Germany)

Relevant publications

  • Fritz G, Dintner S, Treichel N, Radeck J, Gerland U, Mascher T, Gebhard S (2015). A new way of sensing: Need-based activation of antibiotic resistance by a flux-sensing mechanism. mBio 6, e00975-15

 

From modules to networks:

Cell envelope stress response in B. subtilis

The cell envelope is of vital importance for any bacterial cell and serves as a prime target for antimicrobial compounds. Consequently, in B. subtilis the response towards cell envelope stress involves several lines of defense: On the one hand, the expression of specific transport- and detoxification modules, such as the Bce module above, directly remove or neutralize antimicrobials from their site of action. On the other hand, more unspecific mechanisms stabilize and protect the cell envelope as soon as damage is detected. In this project we study the interdependence between the various lines of defense and try to reveal how these systems contribute to resistance. Do they act redundantly, independently, or even cooperatively? How is the expression of the different resistance modules coordinated within the cell? To study these questions we monitor gene expression with bulk level and single cell techniques and develop mathematical models for the regulatory dynamics of the entire stress response network.

Collaborators

Susanne Gebhard (University of Bath, UK)Thorsten Mascher (TU Dresden, Germany)

Relevant publications

  • Radeck J, Fritz G , and Mascher T (2016). The cell envelope stress response of Bacillus subtilis: from static signaling devices to dynamic regulatory network. Curr. Genet., early view
  • Radeck J, Orchard PS, Kirchner M, Höfler C, Gebhard S, Mascher T, and Fritz G (2016). Anatomy of the bacitracin resistance network in Bacillus subtilis. Mol. Microbiol. 
  • Höfler C, Heckmann J, Fritsch A, Popp P, Gebhard S, Fritz G, Mascher T (2015). Cannibalism stress response in Bacillus subtilis. Microbiology (ahead of print)
  • Fritz G, Mascher T (2014). A balancing act times two: Sensing and regulating cell envelope homeostasis in Bacillus subtilisMol. Microbiol. 6, 1201-1207
  • Domínguez-Escobar J, Wolf D, Fritz G, Höfler C, Wedlich-Söldner R, Mascher T (2014). Protein localization, interactions and cellular dynamics of the phage-shock protein-like Lia response in Bacillus subtilisMol. Microbiol. 92, 716–732.

 

SYNMIKRO Young Researchers Groups

Almost all scientific members of SYNMIKRO are actively involved in DFG’s Collaborative Research Centers (Sonderforschungsbereiche), Research Training Groups (Graduiertenkollegs), or other Cooperative Research projects. Alongside performing adventurous experiments, and reporting excellent science, SYNMIKRO substantially promotes potential Young Research Group Leaders by constantly keeping its doors open to welcome and support Young Researchers planning to set up an Independent Research Group.
Our Young Research Groups