TY - JOUR A1 - Bartholomäus, Alexander A1 - Fedyunin, Ivan A1 - Feist, Peter A1 - Sin, Celine A1 - Zhang, Gong A1 - Valleriani, Angelo A1 - Ignatova, Zoya T1 - Bacteria differently regulate mRNA abundance to specifically respond to various stresses JF - Geology N2 - Environmental stress is detrimental to cell viability and requires an adequate reprogramming of cellular activities to maximize cell survival. We present a global analysis of the response of Escherichia coli to acute heat and osmotic stress. We combine deep sequencing of total mRNA and ribosome-protected fragments to provide a genome-wide map of the stress response at transcriptional and translational levels. For each type of stress, we observe a unique subset of genes that shape the stress-specific response. Upon temperature upshift, mRNAs with reduced folding stability up-and downstream of the start codon, and thus with more accessible initiation regions, are translationally favoured. Conversely, osmotic upshift causes a global reduction of highly translated transcripts with high copy numbers, allowing reallocation of translation resources to not degraded and newly synthesized mRNAs. KW - transcription KW - translation KW - deep sequencing KW - Escherichia coli KW - copy numbers Y1 - 2016 U6 - https://doi.org/10.1098/rsta.2015.0069 SN - 1364-503X SN - 1471-2962 VL - 374 PB - Royal Society CY - London ER - TY - JOUR A1 - Broeker, Nina K. A1 - Roske, Yvette A1 - Valleriani, Angelo A1 - Stephan, Mareike Sophia A1 - Andres, Dorothee A1 - Koetz, Joachim A1 - Heinemann, Udo A1 - Barbirz, Stefanie T1 - Time-resolved DNA release from an O-antigen-specific Salmonella bacteriophage with a contractile tail JF - The journal of biological chemistry N2 - Myoviruses, bacteriophages with T4-like architecture, must contract their tails prior to DNA release. However, quantitative kinetic data on myovirus particle opening are lacking, although they are promising tools in bacteriophage-based antimicrobial strategies directed against Gram-negative hosts. For the first time, we show time-resolved DNA ejection from a bacteriophage with a contractile tail, the multi-O-antigen-specific Salmonella myovirus Det7. DNA release from Det7 was triggered by lipopolysaccharide (LPS) O-antigen receptors and notably slower than in noncontractile-tailed siphoviruses. Det7 showed two individual kinetic steps for tail contraction and particle opening. Our in vitro studies showed that highly specialized tailspike proteins (TSPs) are necessary to attach the particle to LPS. A P22-like TSP confers specificity for the Salmonella Typhimurium O-antigen. Moreover, crystal structure analysis at 1.63 angstrom resolution confirmed that Det7 recognized the Salmonella Anatum O-antigen via an E15-like TSP, DettilonTSP. DNA ejection triggered by LPS from either host showed similar velocities, so particle opening is thus a process independent of O-antigen composition and the recognizing TSP. In Det7, at permissive temperatures TSPs mediate O-antigen cleavage and couple cell surface binding with DNA ejection, but no irreversible adsorption occurred at low temperatures. This finding was in contrast to short-tailed Salmonella podoviruses, illustrating that tailed phages use common particle-opening mechanisms but have specialized into different infection niches. KW - bacteriophage KW - lipopolysaccharide (YLPS) KW - structural biology KW - DNA viruses KW - glycobiology KW - fluorescence KW - Salmonella enterica KW - contractile tail KW - DNA ejection KW - O-antigen specificity KW - Salmonella myovirus KW - tailspike protein KW - molecular machine Y1 - 2019 U6 - https://doi.org/10.1074/jbc.RA119.008133 SN - 1083-351X VL - 294 IS - 31 SP - 11751 EP - 11761 PB - American Society for Biochemistry and Molecular Biology CY - Bethesda ER - TY - JOUR A1 - Bühning, Martin A1 - Valleriani, Angelo A1 - Leimkühler, Silke T1 - The role of SufS is restricted to Fe-S cluster biosynthesis in escherichia coli JF - Biochemistry N2 - In Escherichia coli, two different systems that are important for the coordinate formation of Fe–S clusters have been identified, namely, the ISC and SUF systems. The ISC system is the housekeeping Fe–S machinery, which provides Fe–S clusters for numerous cellular proteins. The IscS protein of this system was additionally revealed to be the primary sulfur donor for several sulfur-containing molecules with important biological functions, among which are the molybdenum cofactor (Moco) and thiolated nucleosides in tRNA. Here, we show that deletion of central components of the ISC system in addition to IscS leads to an overall decrease in Fe–S cluster enzyme and molybdoenzyme activity in addition to a decrease in the number of Fe–S-dependent thiomodifications of tRNA, based on the fact that some proteins involved in Moco biosynthesis and tRNA thiolation are Fe–S-dependent. Complementation of the ISC deficient strains with the suf operon restored the activity of Fe–S-containing proteins, including the MoaA protein, which is involved in the conversion of 5′GTP to cyclic pyranopterin monophosphate in the fist step of Moco biosynthesis. While both systems share a high degree of similarity, we show that the function of their respective l-cysteine desulfurase IscS or SufS is specific for each cellular pathway. It is revealed that SufS cannot play the role of IscS in sulfur transfer for the formation of 2-thiouridine, 4-thiouridine, or the dithiolene group of molybdopterin, being unable to interact with TusA or ThiI. The results demonstrate that the role of the SUF system is exclusively restricted to Fe–S cluster assembly in the cell. Y1 - 2017 U6 - https://doi.org/10.1021/acs.biochem.7b00040 SN - 0006-2960 VL - 56 SP - 1987 EP - 2000 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Keller, Peter A1 - Roelly, Sylvie A1 - Valleriani, Angelo T1 - On time duality for Markov Chains JF - Stochastic models N2 - For an irreducible continuous time Markov chain, we derive the distribution of the first passage time from a given state i to another given state j and the reversed passage time from j to i, each under the condition of no return to the starting point. When these two distributions are identical, we say that i and j are in time duality. We introduce a new condition called permuted balance that generalizes the concept of reversibility and provides sufficient criteria, based on the structure of the transition graph of the Markov chain. Illustrative examples are provided. KW - Time duality KW - Detailed balance KW - First passage time KW - Reversibility KW - Permuted balance KW - Markov chain Y1 - 2015 U6 - https://doi.org/10.1080/15326349.2014.969736 SN - 1532-6349 SN - 1532-4214 VL - 31 IS - 1 SP - 98 EP - 118 PB - Taylor & Francis Group CY - Philadelphia ER - TY - JOUR A1 - Keller, Peter A1 - Roelly, Sylvie A1 - Valleriani, Angelo T1 - A Quasi Random Walk to Model a Biological Transport Process JF - Methodology and computing in applied probability N2 - Transport molecules play a crucial role for cell viability. Amongst others, linear motors transport cargos along rope-like structures from one location of the cell to another in a stochastic fashion. Thereby each step of the motor, either forwards or backwards, bridges a fixed distance and requires several biochemical transformations, which are modeled as internal states of the motor. While moving along the rope, the motor can also detach and the walk is interrupted. We give here a mathematical formalization of such dynamics as a random process which is an extension of Random Walks, to which we add an absorbing state to model the detachment of the motor from the rope. We derive particular properties of such processes that have not been available before. Our results include description of the maximal distance reached from the starting point and the position from which detachment takes place. Finally, we apply our theoretical results to a concrete established model of the transport molecule Kinesin V. KW - Molecular motor KW - Kinesin V KW - Birth-and-death process KW - Markov Chain KW - Quasi Random Walk Y1 - 2015 U6 - https://doi.org/10.1007/s11009-013-9372-5 SN - 1387-5841 SN - 1573-7713 VL - 17 IS - 1 SP - 125 EP - 137 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Keller, Peter A1 - Valleriani, Angelo T1 - Single-molecule stochastic times in a reversible bimolecular reaction JF - The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr N2 - In this work, we consider the reversible reaction between reactants of species A and B to form the product C. We consider this reaction as a prototype of many pseudobiomolecular reactions in biology, such as for instance molecular motors. We derive the exact probability density for the stochastic waiting time that a molecule of species A needs until the reaction with a molecule of species B takes place. We perform this computation taking fully into account the stochastic fluctuations in the number of molecules of species B. We show that at low numbers of participating molecules, the exact probability density differs from the exponential density derived by assuming the law of mass action. Finally, we discuss the condition of detailed balance in the exact stochastic and in the approximate treatment. Y1 - 2012 U6 - https://doi.org/10.1063/1.4747337 SN - 0021-9606 VL - 137 IS - 8 PB - American Institute of Physics CY - Melville ER - TY - JOUR A1 - Rading, M. Michael A1 - Sandmann, Michael A1 - Steup, Martin A1 - Chiarugi, Davide A1 - Valleriani, Angelo T1 - Weak correlation of starch and volume in synchronized photosynthetic cells JF - Physical review : E, Statistical, nonlinear and soft matter physics N2 - In cultures of unicellular algae, features of single cells, such as cellular volume and starch content, are thought to be the result of carefully balanced growth and division processes. Single-cell analyses of synchronized photoautotrophic cultures of the unicellular alga Chlamydomonas reinhardtii reveal, however, that the cellular volume and starch content are only weakly correlated. Likewise, other cell parameters, e.g., the chlorophyll content per cell, are only weakly correlated with cell size. We derive the cell size distributions at the beginning of each synchronization cycle considering growth, timing of cell division and daughter cell release, and the uneven division of cell volume. Furthermore, we investigate the link between cell volume growth and starch accumulation. This work presents evidence that, under the experimental conditions of light-dark synchronized cultures, the weak correlation between both cell features is a result of a cumulative process rather than due to asymmetric partition of biomolecules during cell division. This cumulative process necessarily limits cellular similarities within a synchronized cell population. Y1 - 2015 U6 - https://doi.org/10.1103/PhysRevE.91.012711 SN - 1539-3755 SN - 1550-2376 VL - 91 IS - 1 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Rusconi, Marco A1 - Valleriani, Angelo A1 - Dunlop, John William Chapman A1 - Kurths, Jürgen A1 - Weinkamer, Richard T1 - Insights into the control of trabecular bone remodelling obtained by a Markov model Y1 - 2009 UR - http://www.sciencedirect.com/science/journal/87563282 U6 - https://doi.org/10.1016/j.bone.2009.03.467 SN - 8756-3282 ER - TY - JOUR A1 - Rusconi, Marco A1 - Valleriani, Angelo A1 - Dunlop, John William Chapman A1 - Kurths, Jürgen A1 - Weinkamer, Richard T1 - Quantitative approach to the stochastics of bone remodeling JF - epl : a letters journal exploring the frontiers of physics N2 - During life bones constantly adapt their structure to their mechanical environment via a mechanically controlled process called bone remodeling. For trabecular bone, this process modifies the thickness of each trabecula leading occasionally to full resorption. We describe the irreversible dynamics of the trabecular thickness distribution (TTD) by means of a Markov chain discrete in space and time. By using thickness data from adult patients, we derive the transition probabilities in the chain. This allows a quantification, in terms of geometrical quantities, of the control of bone remodeling and thus to determine the evolution of the TTD with age. Y1 - 2012 U6 - https://doi.org/10.1209/0295-5075/97/28009 SN - 0295-5075 VL - 97 IS - 2 PB - EDP Sciences CY - Mulhouse ER - TY - JOUR A1 - Stange, Maike A1 - Hintsche, Marius A1 - Sachse, Kirsten A1 - Gerhardt, Matthias A1 - Valleriani, Angelo A1 - Beta, Carsten T1 - Analyzing the spatial positioning of nuclei in polynuclear giant cells JF - Journal of Physics D: Applied Physics N2 - How cells establish and maintain a well-defined size is a fundamental question of cell biology. Here we investigated to what extent the microtubule cytoskeleton can set a predefined cell size, independent of an enclosing cell membrane. We used electropulse-induced cell fusion to form giant multinuclear cells of the social amoeba Dictyostelium discoideum. Based on dual-color confocal imaging of cells that expressed fluorescent markers for the cell nucleus and the microtubules, we determined the subcellular distributions of nuclei and centrosomes in the giant cells. Our two- and three-dimensional imaging results showed that the positions of nuclei in giant cells do not fall onto a regular lattice. However, a comparison with model predictions for random positioning showed that the subcellular arrangement of nuclei maintains a low but still detectable degree of ordering. This can be explained by the steric requirements of the microtubule cytoskeleton, as confirmed by the effect of a microtubule degrading drug. KW - Dictyostelium KW - cell nucleus KW - positioning KW - imaging KW - spatial poisson distribution Y1 - 2017 U6 - https://doi.org/10.1088/1361-6463/aa8da0 SN - 0022-3727 SN - 1361-6463 VL - 50 IS - 46 PB - IOP Publ. Ltd. CY - Bristol ER -