TY  - JOUR
AU  - Jovanović, Goran
AU  - Sheng, Xia
AU  - Ale, Angelique
AU  - Feliu, Elisenda
AU  - Harrington, Heather A.
AU  - Kirk, Paul
AU  - Wiuf, Carsten
AU  - Buck, Martin
AU  - Stumpf, Michael P. H.
PY  - 2015
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/885
AB  - Two-component systems play a central part in bacterial signal transduction. Phosphorelay mechanisms have been linked to more robust and ultra-sensitive signalling dynamics. The molecular machinery that facilitates such a signalling is, however, only understood in outline. In particular the functional relevance of the dimerization of a non-orthodox or hybrid histidine kinase along which the phosphorelay takes place has been a subject of debate. We use a combination of molecular and genetic approaches, coupled to mathematical and statistical modelling, to demonstrate that the different possible intra- and inter-molecular mechanisms of phosphotransfer are formally non-identifiable in Escherichia coli expressing the ArcB non-orthodox histidine kinase used in anoxic redox control. In order to resolve this issue we further analyse the mathematical model in order to identify discriminatory experiments, which are then performed to address cis- and trans-phosphorelay mechanisms. The results suggest that exclusive cis- and trans-mechanisms will not be operating, instead the functional phosphorelay is likely to build around a sequence of allosteric interactions among the domain pairs in the histidine kinase. This is the first detailed mechanistic analysis of the molecular processes involved in non-orthodox two-component signalling and our results suggest strongly that dimerization facilitates more discriminatory proof-reading of external signals, via these allosteric reactions, prior to them being further processed.
PB  - Royal Soc Chemistry, Cambridge
T2  - Molecular Biosystems
T1  - Phosphorelay of non-orthodox two component systems functions through a bi-molecular mechanism in vivo: the case of ArcB
EP  - 1359
IS  - 5
SP  - 1348
VL  - 11
DO  - 10.1039/c4mb00720d
ER  - 

@article{
author = "Jovanović, Goran and Sheng, Xia and Ale, Angelique and Feliu, Elisenda and Harrington, Heather A. and Kirk, Paul and Wiuf, Carsten and Buck, Martin and Stumpf, Michael P. H.",
year = "2015",
abstract = "Two-component systems play a central part in bacterial signal transduction. Phosphorelay mechanisms have been linked to more robust and ultra-sensitive signalling dynamics. The molecular machinery that facilitates such a signalling is, however, only understood in outline. In particular the functional relevance of the dimerization of a non-orthodox or hybrid histidine kinase along which the phosphorelay takes place has been a subject of debate. We use a combination of molecular and genetic approaches, coupled to mathematical and statistical modelling, to demonstrate that the different possible intra- and inter-molecular mechanisms of phosphotransfer are formally non-identifiable in Escherichia coli expressing the ArcB non-orthodox histidine kinase used in anoxic redox control. In order to resolve this issue we further analyse the mathematical model in order to identify discriminatory experiments, which are then performed to address cis- and trans-phosphorelay mechanisms. The results suggest that exclusive cis- and trans-mechanisms will not be operating, instead the functional phosphorelay is likely to build around a sequence of allosteric interactions among the domain pairs in the histidine kinase. This is the first detailed mechanistic analysis of the molecular processes involved in non-orthodox two-component signalling and our results suggest strongly that dimerization facilitates more discriminatory proof-reading of external signals, via these allosteric reactions, prior to them being further processed.",
publisher = "Royal Soc Chemistry, Cambridge",
journal = "Molecular Biosystems",
title = "Phosphorelay of non-orthodox two component systems functions through a bi-molecular mechanism in vivo: the case of ArcB",
pages = "1359-1348",
number = "5",
volume = "11",
doi = "10.1039/c4mb00720d"
}

Jovanović, G., Sheng, X., Ale, A., Feliu, E., Harrington, H. A., Kirk, P., Wiuf, C., Buck, M.,& Stumpf, M. P. H.. (2015). Phosphorelay of non-orthodox two component systems functions through a bi-molecular mechanism in vivo: the case of ArcB. in Molecular Biosystems
Royal Soc Chemistry, Cambridge., 11(5), 1348-1359.
https://doi.org/10.1039/c4mb00720d

Jovanović G, Sheng X, Ale A, Feliu E, Harrington HA, Kirk P, Wiuf C, Buck M, Stumpf MPH. Phosphorelay of non-orthodox two component systems functions through a bi-molecular mechanism in vivo: the case of ArcB. in Molecular Biosystems. 2015;11(5):1348-1359.
doi:10.1039/c4mb00720d .

Jovanović, Goran, Sheng, Xia, Ale, Angelique, Feliu, Elisenda, Harrington, Heather A., Kirk, Paul, Wiuf, Carsten, Buck, Martin, Stumpf, Michael P. H., "Phosphorelay of non-orthodox two component systems functions through a bi-molecular mechanism in vivo: the case of ArcB" in Molecular Biosystems, 11, no. 5 (2015):1348-1359,
https://doi.org/10.1039/c4mb00720d . .

TY  - JOUR
AU  - Jovanović, Goran
AU  - Mehta, Parul
AU  - Ying, Liming
AU  - Buck, Martin
PY  - 2014
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/734
AB  - All cell types must maintain the integrity of their membranes. The conserved bacterial membrane-associated protein PspA is a major effector acting upon extracytoplasmic stress and is implicated in protection of the inner membrane of pathogens, formation of biofilms and multi-drug-resistant persister cells. PspA and its homologues in Gram-positive bacteria and archaea protect the cell envelope whilst also supporting thylakoid biogenesis in cyanobacteria and higher plants. In enterobacteria, PspA is a dual function protein negatively regulating the Psp system in the absence of stress and acting as an effector of membrane integrity upon stress. We show that in Escherichia coli the low-order oligomeric PspA regulatory complex associates with cardiolipinrich, curved polar inner membrane regions. There, cardiolipin and the flotillin 1 homologue YqiK support the PspBC sensors in transducing a membrane stress signal to the PspA-PspF inhibitory complex. After stress perception, PspA high-order oligomeric effector complexes initially assemble in polar membrane regions. Subsequently, the discrete spatial distribution and dynamics of PspA effector(s) in lateral membrane regions depend on the actin homologue MreB and the peptidoglycan machinery protein RodZ. The consequences of loss of cytoplasmic membrane anionic lipids, MreB, RodZ and/or YqiK suggest that the mode of action of the PspA effector is closely associated with cell envelope organization.
PB  - Microbiology Soc, London
T2  - Microbiology-Sgm
T1  - Anionic lipids and the cytoskeletal proteins MreB and RodZ define the spatio-temporal distribution and function of membrane stress controller PspA in Escherichia coli
EP  - 2386
SP  - 2374
VL  - 160
DO  - 10.1099/mic.0.078527-0
ER  - 

@article{
author = "Jovanović, Goran and Mehta, Parul and Ying, Liming and Buck, Martin",
year = "2014",
abstract = "All cell types must maintain the integrity of their membranes. The conserved bacterial membrane-associated protein PspA is a major effector acting upon extracytoplasmic stress and is implicated in protection of the inner membrane of pathogens, formation of biofilms and multi-drug-resistant persister cells. PspA and its homologues in Gram-positive bacteria and archaea protect the cell envelope whilst also supporting thylakoid biogenesis in cyanobacteria and higher plants. In enterobacteria, PspA is a dual function protein negatively regulating the Psp system in the absence of stress and acting as an effector of membrane integrity upon stress. We show that in Escherichia coli the low-order oligomeric PspA regulatory complex associates with cardiolipinrich, curved polar inner membrane regions. There, cardiolipin and the flotillin 1 homologue YqiK support the PspBC sensors in transducing a membrane stress signal to the PspA-PspF inhibitory complex. After stress perception, PspA high-order oligomeric effector complexes initially assemble in polar membrane regions. Subsequently, the discrete spatial distribution and dynamics of PspA effector(s) in lateral membrane regions depend on the actin homologue MreB and the peptidoglycan machinery protein RodZ. The consequences of loss of cytoplasmic membrane anionic lipids, MreB, RodZ and/or YqiK suggest that the mode of action of the PspA effector is closely associated with cell envelope organization.",
publisher = "Microbiology Soc, London",
journal = "Microbiology-Sgm",
title = "Anionic lipids and the cytoskeletal proteins MreB and RodZ define the spatio-temporal distribution and function of membrane stress controller PspA in Escherichia coli",
pages = "2386-2374",
volume = "160",
doi = "10.1099/mic.0.078527-0"
}

Jovanović, G., Mehta, P., Ying, L.,& Buck, M.. (2014). Anionic lipids and the cytoskeletal proteins MreB and RodZ define the spatio-temporal distribution and function of membrane stress controller PspA in Escherichia coli. in Microbiology-Sgm
Microbiology Soc, London., 160, 2374-2386.
https://doi.org/10.1099/mic.0.078527-0

Jovanović G, Mehta P, Ying L, Buck M. Anionic lipids and the cytoskeletal proteins MreB and RodZ define the spatio-temporal distribution and function of membrane stress controller PspA in Escherichia coli. in Microbiology-Sgm. 2014;160:2374-2386.
doi:10.1099/mic.0.078527-0 .

Jovanović, Goran, Mehta, Parul, Ying, Liming, Buck, Martin, "Anionic lipids and the cytoskeletal proteins MreB and RodZ define the spatio-temporal distribution and function of membrane stress controller PspA in Escherichia coli" in Microbiology-Sgm, 160 (2014):2374-2386,
https://doi.org/10.1099/mic.0.078527-0 . .

TY  - JOUR
AU  - Mehta, Parul
AU  - Jovanović, Goran
AU  - Lenn, Tchern
AU  - Bruckbauer, Andreas
AU  - Engl, Christoph
AU  - Ying, Liming
AU  - Buck, Martin
PY  - 2013
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/660
AB  - Bacterial enhancer-dependent transcription systems support major adaptive responses and offer a singular paradigm in gene control analogous to complex eukaryotic systems. Here we report new mechanistic insights into the control of one-membrane stress-responsive bacterial enhancer-dependent system. Using millisecond single-molecule fluorescence microscopy of live cells we determine the localizations, two-dimensional diffusion dynamics and stoichiometries of complexes of the bacterial enhancer-binding ATPase PspF during its action at promoters as regulated by inner membrane interacting negative controller PspA. We establish that a stable repressive PspF-PspA complex is located in the nucleoid, transiently communicating with the inner membrane via PspA. The PspF as a hexamer stably binds only one of the two psp promoters at a time, suggesting that psp promoters will fire asynchronously and cooperative interactions of PspF with the basal transcription complex influence dynamics of the PspF hexamer-DNA complex and regulation of the psp promoters.
PB  - Nature Publishing Group, London
T2  - Nature Communications
T1  - Dynamics and stoichiometry of a regulated enhancer-binding protein in live Escherichia coli cells
VL  - 4
DO  - 10.1038/ncomms2997
ER  - 

@article{
author = "Mehta, Parul and Jovanović, Goran and Lenn, Tchern and Bruckbauer, Andreas and Engl, Christoph and Ying, Liming and Buck, Martin",
year = "2013",
abstract = "Bacterial enhancer-dependent transcription systems support major adaptive responses and offer a singular paradigm in gene control analogous to complex eukaryotic systems. Here we report new mechanistic insights into the control of one-membrane stress-responsive bacterial enhancer-dependent system. Using millisecond single-molecule fluorescence microscopy of live cells we determine the localizations, two-dimensional diffusion dynamics and stoichiometries of complexes of the bacterial enhancer-binding ATPase PspF during its action at promoters as regulated by inner membrane interacting negative controller PspA. We establish that a stable repressive PspF-PspA complex is located in the nucleoid, transiently communicating with the inner membrane via PspA. The PspF as a hexamer stably binds only one of the two psp promoters at a time, suggesting that psp promoters will fire asynchronously and cooperative interactions of PspF with the basal transcription complex influence dynamics of the PspF hexamer-DNA complex and regulation of the psp promoters.",
publisher = "Nature Publishing Group, London",
journal = "Nature Communications",
title = "Dynamics and stoichiometry of a regulated enhancer-binding protein in live Escherichia coli cells",
volume = "4",
doi = "10.1038/ncomms2997"
}

Mehta, P., Jovanović, G., Lenn, T., Bruckbauer, A., Engl, C., Ying, L.,& Buck, M.. (2013). Dynamics and stoichiometry of a regulated enhancer-binding protein in live Escherichia coli cells. in Nature Communications
Nature Publishing Group, London., 4.
https://doi.org/10.1038/ncomms2997

Mehta P, Jovanović G, Lenn T, Bruckbauer A, Engl C, Ying L, Buck M. Dynamics and stoichiometry of a regulated enhancer-binding protein in live Escherichia coli cells. in Nature Communications. 2013;4.
doi:10.1038/ncomms2997 .

Mehta, Parul, Jovanović, Goran, Lenn, Tchern, Bruckbauer, Andreas, Engl, Christoph, Ying, Liming, Buck, Martin, "Dynamics and stoichiometry of a regulated enhancer-binding protein in live Escherichia coli cells" in Nature Communications, 4 (2013),
https://doi.org/10.1038/ncomms2997 . .

TY  - JOUR
AU  - Huvet, M.
AU  - Toni, T.
AU  - Sheng, X.
AU  - Thorne, T.
AU  - Jovanović, Goran
AU  - Engl, C.
AU  - Buck, M.
AU  - Pinney, J. W.
AU  - Stumpf, M. P. H.
PY  - 2011
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/483
AB  - Here, we use a systematic analysis of the genes that make up and regulate the Psp system in E. coli in order to elucidate the evolutionary history of the system. We compare gene sharing, sequence evolution, and conservation of protein-coding as well as noncoding DNA sequences and link these to comparative analyses of genome/operon organization across 698 bacterial genomes. Finally, we evaluate experimentally the biological advantage/disadvantage of a simplified version of the Psp system under different oxygen-related environments. Our results suggest that the Psp system evolved around a core response mechanism by gradually co-opting genes into the system to provide more nuanced sensory, signaling, and effector functionalities. We find that recruitment of new genes into the response machinery is closely linked to incorporation of these genes into a psp operon as is seen in E. coli, which contains the bulk of genes involved in the response. The organization of this operon allows for surprising levels of additional transcriptional control and flexibility. The results discussed here suggest that the components of such signaling systems will only be evolutionarily conserved if the overall functionality of the system can be maintained.
PB  - Oxford Univ Press, Oxford
T2  - Molecular Biology and Evolution
T1  - The Evolution of the Phage Shock Protein Response System: Interplay between Protein Function, Genomic Organization, and System Function
EP  - 1155
IS  - 3
SP  - 1141
VL  - 28
DO  - 10.1093/molbev/msq301
ER  - 

@article{
author = "Huvet, M. and Toni, T. and Sheng, X. and Thorne, T. and Jovanović, Goran and Engl, C. and Buck, M. and Pinney, J. W. and Stumpf, M. P. H.",
year = "2011",
abstract = "Here, we use a systematic analysis of the genes that make up and regulate the Psp system in E. coli in order to elucidate the evolutionary history of the system. We compare gene sharing, sequence evolution, and conservation of protein-coding as well as noncoding DNA sequences and link these to comparative analyses of genome/operon organization across 698 bacterial genomes. Finally, we evaluate experimentally the biological advantage/disadvantage of a simplified version of the Psp system under different oxygen-related environments. Our results suggest that the Psp system evolved around a core response mechanism by gradually co-opting genes into the system to provide more nuanced sensory, signaling, and effector functionalities. We find that recruitment of new genes into the response machinery is closely linked to incorporation of these genes into a psp operon as is seen in E. coli, which contains the bulk of genes involved in the response. The organization of this operon allows for surprising levels of additional transcriptional control and flexibility. The results discussed here suggest that the components of such signaling systems will only be evolutionarily conserved if the overall functionality of the system can be maintained.",
publisher = "Oxford Univ Press, Oxford",
journal = "Molecular Biology and Evolution",
title = "The Evolution of the Phage Shock Protein Response System: Interplay between Protein Function, Genomic Organization, and System Function",
pages = "1155-1141",
number = "3",
volume = "28",
doi = "10.1093/molbev/msq301"
}

Huvet, M., Toni, T., Sheng, X., Thorne, T., Jovanović, G., Engl, C., Buck, M., Pinney, J. W.,& Stumpf, M. P. H.. (2011). The Evolution of the Phage Shock Protein Response System: Interplay between Protein Function, Genomic Organization, and System Function. in Molecular Biology and Evolution
Oxford Univ Press, Oxford., 28(3), 1141-1155.
https://doi.org/10.1093/molbev/msq301

Huvet M, Toni T, Sheng X, Thorne T, Jovanović G, Engl C, Buck M, Pinney JW, Stumpf MPH. The Evolution of the Phage Shock Protein Response System: Interplay between Protein Function, Genomic Organization, and System Function. in Molecular Biology and Evolution. 2011;28(3):1141-1155.
doi:10.1093/molbev/msq301 .

Huvet, M., Toni, T., Sheng, X., Thorne, T., Jovanović, Goran, Engl, C., Buck, M., Pinney, J. W., Stumpf, M. P. H., "The Evolution of the Phage Shock Protein Response System: Interplay between Protein Function, Genomic Organization, and System Function" in Molecular Biology and Evolution, 28, no. 3 (2011):1141-1155,
https://doi.org/10.1093/molbev/msq301 . .

TY  - JOUR
AU  - Toni, Tina
AU  - Jovanović, Goran
AU  - Huvet, Maxime
AU  - Buck, Martin
AU  - Stumpf, Michael P. H.
PY  - 2011
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/511
AB  - Background: Bacteria have evolved a rich set of mechanisms for sensing and adapting to adverse conditions in their environment. These are crucial for their survival, which requires them to react to extracellular stresses such as heat shock, ethanol treatment or phage infection. Here we focus on studying the phage shock protein (Psp) stress response in Escherichia coli induced by a phage infection or other damage to the bacterial membrane. This system has not yet been theoretically modelled or analysed in silico. Results: We develop a model of the Psp response system, and illustrate how such models can be constructed and analyzed in light of available sparse and qualitative information in order to generate novel biological hypotheses about their dynamical behaviour. We analyze this model using tools from Petri-net theory and study its dynamical range that is consistent with currently available knowledge by conditioning model parameters on the available data in an approximate Bayesian computation (ABC) framework. Within this ABC approach we analyze stochastic and deterministic dynamics. This analysis allows us to identify different types of behaviour and these mechanistic insights can in turn be used to design new, more detailed and time-resolved experiments. Conclusions: We have developed the first mechanistic model of the Psp response in E. coli. This model allows us to predict the possible qualitative stochastic and deterministic dynamic behaviours of key molecular players in the stress response. Our inferential approach can be applied to stress response and signalling systems more generally: in the ABC framework we can condition mathematical models on qualitative data in order to delimit e. g. parameter ranges or the qualitative system dynamics in light of available end-point or qualitative information.
PB  - BMC, London
T2  - BMC Systems Biology
T1  - From qualitative data to quantitative models: analysis of the phage shock protein stress response in Escherichia coli
VL  - 5
DO  - 10.1186/1752-0509-5-69
ER  - 

@article{
author = "Toni, Tina and Jovanović, Goran and Huvet, Maxime and Buck, Martin and Stumpf, Michael P. H.",
year = "2011",
abstract = "Background: Bacteria have evolved a rich set of mechanisms for sensing and adapting to adverse conditions in their environment. These are crucial for their survival, which requires them to react to extracellular stresses such as heat shock, ethanol treatment or phage infection. Here we focus on studying the phage shock protein (Psp) stress response in Escherichia coli induced by a phage infection or other damage to the bacterial membrane. This system has not yet been theoretically modelled or analysed in silico. Results: We develop a model of the Psp response system, and illustrate how such models can be constructed and analyzed in light of available sparse and qualitative information in order to generate novel biological hypotheses about their dynamical behaviour. We analyze this model using tools from Petri-net theory and study its dynamical range that is consistent with currently available knowledge by conditioning model parameters on the available data in an approximate Bayesian computation (ABC) framework. Within this ABC approach we analyze stochastic and deterministic dynamics. This analysis allows us to identify different types of behaviour and these mechanistic insights can in turn be used to design new, more detailed and time-resolved experiments. Conclusions: We have developed the first mechanistic model of the Psp response in E. coli. This model allows us to predict the possible qualitative stochastic and deterministic dynamic behaviours of key molecular players in the stress response. Our inferential approach can be applied to stress response and signalling systems more generally: in the ABC framework we can condition mathematical models on qualitative data in order to delimit e. g. parameter ranges or the qualitative system dynamics in light of available end-point or qualitative information.",
publisher = "BMC, London",
journal = "BMC Systems Biology",
title = "From qualitative data to quantitative models: analysis of the phage shock protein stress response in Escherichia coli",
volume = "5",
doi = "10.1186/1752-0509-5-69"
}

Toni, T., Jovanović, G., Huvet, M., Buck, M.,& Stumpf, M. P. H.. (2011). From qualitative data to quantitative models: analysis of the phage shock protein stress response in Escherichia coli. in BMC Systems Biology
BMC, London., 5.
https://doi.org/10.1186/1752-0509-5-69

Toni T, Jovanović G, Huvet M, Buck M, Stumpf MPH. From qualitative data to quantitative models: analysis of the phage shock protein stress response in Escherichia coli. in BMC Systems Biology. 2011;5.
doi:10.1186/1752-0509-5-69 .

Toni, Tina, Jovanović, Goran, Huvet, Maxime, Buck, Martin, Stumpf, Michael P. H., "From qualitative data to quantitative models: analysis of the phage shock protein stress response in Escherichia coli" in BMC Systems Biology, 5 (2011),
https://doi.org/10.1186/1752-0509-5-69 . .