@phdthesis{14280,
  abstract     = {Cell division in Escherichia coli is performed by the divisome, a multi-protein complex composed of more than 30 proteins. The divisome spans from the cytoplasm through the inner membrane to the cell wall and the outer membrane. Divisome assembly is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes at the center of the E. coli cell and determines the position of the future cell septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue FtsZ, which forms treadmilling filaments. These filaments are recruited to the inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic components of the divisome. 
A previous model postulated that FtsA regulates maturation of the divisome by switching from an oligomeric, inactive state to a monomeric and active state. This model was based mostly on in vivo studies, as a biochemical characterization of FtsA has been hampered by difficulties in purifying the protein. Here, we studied FtsA using an in vitro reconstitution approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic, treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space and (ii) How does FtsA regulate the maturation of the divisome?
We found that the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments. When we investigated the underlying mechanism by imaging single molecules of FtsNcyto, we found the peptide to interact transiently with FtsA. An in depth analysis of the single molecule trajectories helped to postulate a model where PG synthases follow the dynamics of FtsZ by a diffusion and capture mechanism. 
Following up on these findings we were interested in how the self-interaction of FtsA changes when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer switch. For this, we compared the behavior of the previously identified, hyperactive mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly however, we found that this was not due to a difference in the self-interaction strength of the two variants, but a difference in their membrane residence time. Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured self-interaction of FtsA actually increased. 
We propose that FtsNcyto induces a rearrangement of the oligomeric architecture of FtsA. In further consequence this change leads to more persistent FtsZ filaments which results in a defined signalling zone, allowing formation of the mature divisome. The observed difference between FtsA WT and R286W is due to the vastly different membrane turnover of the proteins. R286W cycles 5-10x faster compared to WT which allows to sample FtsZ filaments at faster frequencies. These findings can explain the observed differences in toxicity for overexpression of FtsA WT and R286W and help to understand how FtsA regulates divisome maturation.},
  author       = {Radler, Philipp},
  isbn         = {978-3-99078-033-6},
  issn         = {2663-337X},
  keywords     = {Cell Division, Reconstitution, FtsZ, FtsA, Divisome, E.coli},
  pages        = {156},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Spatiotemporal signaling during assembly of the bacterial divisome}},
  doi          = {10.15479/at:ista:14280},
  year         = {2023},
}

@misc{5587,
  abstract     = {Supporting material to the article 
STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH

boundscoli.dat
Flux Bounds of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium. 

polcoli.dat
Matrix enconding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium, 
obtained from the soichiometric matrix by standard linear algebra  (reduced row echelon form).

ellis.dat
Approximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium
obtained with the Lovasz method.

point0.dat
Center of the approximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium
obtained with the Lovasz method.

lovasz.cpp  
This c++ code file receives in input the polytope of the feasible steady states of a metabolic network, 
(matrix and bounds), and it gives in output an approximate Lowner-John ellipsoid rounding the polytope
with the Lovasz method 
NB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. 
For further details we refer to  PLoS ONE 10.4 e0122670 (2015).

sampleHRnew.cpp  
This c++ code file receives in input the polytope of the feasible steady states of a metabolic network, 
(matrix and bounds), the ellipsoid rounding the polytope, a point inside and  
it gives in output a max entropy sampling at fixed average growth rate 
of the steady states by performing an Hit-and-Run Monte Carlo Markov chain.
NB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. 
For further details we refer to  PLoS ONE 10.4 e0122670 (2015).},
  author       = {De Martino, Daniele and Tkacik, Gasper},
  keywords     = {metabolic networks, e.coli core, maximum entropy, monte carlo markov chain sampling, ellipsoidal rounding},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Supporting materials "STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH"}},
  doi          = {10.15479/AT:ISTA:62},
  year         = {2018},
}