Biológiai hálózatok reakciókinetikai vizsgálata = Reaction kinetic analysis of biological networks

Az ifjúsági OTKA támogatás lehetőséget nyújtott ahhoz, hogy a biokémiai reakciókinetika módszereit használva több biológiai kérdésen is dolgozzak. A biológiai napi ritmus és a sejtosztódási ciklus biokémiai oszcillációinak kapcsoltságát vizsgáltam matematikai modellekkel. Megállapítottam, hogy kvantált sejtciklusidő eloszláshoz vezethet ha a két oszcillátor eltérő saját periódussal rendelkezik és a modell alapján azt a feltételezést tettük, hogy ez a kapcsoltság fontos szerepet játszhat az emlős sejtek homeosztázisát reguláló méretkontrolljában. Egy másik kapcsolódó munkában azt a meglapítást tettük, hogy a napi ritmus szabályozó reakcióhálózat kísérletesen megfigyelt tulajdonságainak pontos modellezéséhez elengedhetetlen egy pozitív visszacsatolási hurok jelenléte a rendszerben. Más biológiai kérdéseket vizsgáltam élesztők sejtciklusának szabályozásával kapcsolatban: a sarjadzó élesztő sejtciklusának kritikus lépéseinek szabályzó mechanizmusában fontos szerepet játszó előre és visszacsatolási hurkokat találtam a rendszer matematikai modelljeivel, valamint vizsgáltam ezen sejtciklus átmenetek érzékenységét, sztochasztikáját és dinamikáját. Más cikkekben a hasadó élesztő sejtosztódását és növekedésének regulálását és szignalizációs utak egyszerű modelleit is vizsgáltam. A modellezéssel kapott predikciók közül néhányat már kísérletesen igazoltak is, mások jelenleg állnak tesztelés alatt. | The OTKA youth grant allowed me to work on various biology-oriented projects with the tools of biochemical reaction kinetics. I investigated by mathematical modeling the coupling of the biochemical oscillators of the daily rhythm and the cell division cycle. I found that the cell cycle time could show quantized distributions in case the two oscillators run with dissimilar basal periods. Furthermore the model suggests that this coupling might have an important role in homeostasis regulatory size control of mammalian cells. In another related work we showed that the presence of a positive feedback loop in the network of circadian clock regulation is inevitable to properly model some experimental observations on the daily rhythm. Additionally I investigated other biological questions related to the cell cycle regulation of yeast cells: with mathematical modeling of the network of the regulation in budding yeast I identified important feed-forward and feedback loops that control the critical cell cycle transitions, furthermore I investigated the sensitivity, stochasticity and dynamics of these transitions. In other articles I investigated the regulation of cell division and cell growth in fission yeast cells as well as studied simplified models of signaling pathways. Some of the predictions of the models have been already experimentally verified, some are still under experimental tests

Growth Rate as a Direct Regulator of the Start Network to Set Cell Size

Cells are able to adjust their growth and size to external inputs to comply with specific fates and developmental programs. Molecular pathways controlling growth also have an enormous impact in cell size, and bacteria, yeast, or epithelial cells modify their size as a function of growth rate. This universal feature suggests that growth (mass) and proliferation (cell number) rates are subject to general coordinating mechanisms. However, the underlying molecular connections are still a matter of debate. Here we review the current ideas on growth and cell size control, and focus on the possible mechanisms that could link the biosynthetic machinery to the Start network in budding yeast. In particular, we discuss the role of molecular chaperones in a competition framework to explain cell size control by growth at the individual cell level

Response dynamics of phosphorelays suggest their potential utility in cell signalling

Phosphorelays are extended two-component signalling systems found in diverse bacteria, lower eukaryotes and plants. Only few of these systems are characterized, and we still lack a full understanding of their signalling abilities. Here, we aim to achieve a global understanding of phosphorelay signalling and its dynamical properties. We develop a generic model, allowing us to systematically analyse response dynamics under different assumptions. Using this model, we find that the steady-state concentration of phosphorylated protein at the final layer of a phosphorelay is a linearly increasing, but eventually saturating function of the input. In contrast, the intermediate layers can display ultrasensitivity. We find that such ultrasensitivity is a direct result of the phosphorelay biochemistry; shuttling of a single phosphate group from the first to the last layer. The response dynamics of the phosphorelay results in tolerance of cross-talk, especially when it occurs as cross-deactivation. Further, it leads to a high signal-to-noise ratio for the final layer. We find that a relay length of four, which is most commonly observed, acts as a saturating point for these dynamic properties. These findings suggest that phosphorelays could act as a mechanism to reduce noise and effects of cross-talk on the final layer of the relay and enforce its input–response relation to be linear. In addition, our analysis suggests that middle layers of phosphorelays could embed thresholds. We discuss the consequence of these findings in relation to why cells might use phosphorelays along with enzymatic kinase cascades

Unifying the mechanism of mitotic exit control in a spatiotemporal logical model.

The transition from mitosis into the first gap phase of the cell cycle in budding yeast is controlled by the Mitotic Exit Network (MEN). The network interprets spatiotemporal cues about the progression of mitosis and ensures that release of Cdc14 phosphatase occurs only after completion of key mitotic events. The MEN has been studied intensively; however, a unified understanding of how localisation and protein activity function together as a system is lacking. In this paper, we present a compartmental, logical model of the MEN that is capable of representing spatial aspects of regulation in parallel to control of enzymatic activity. We show that our model is capable of correctly predicting the phenotype of the majority of mutants we tested, including mutants that cause proteins to mislocalise. We use a continuous time implementation of the model to demonstrate that Cdc14 Early Anaphase Release (FEAR) ensures robust timing of anaphase, and we verify our findings in living cells. Furthermore, we show that our model can represent measured cell-cell variation in Spindle Position Checkpoint (SPoC) mutants. This work suggests a general approach to incorporate spatial effects into logical models. We anticipate that the model itself will be an important resource to experimental researchers, providing a rigorous platform to test hypotheses about regulation of mitotic exit

Noise Reduction in Complex Biological Switches

Cells operate in noisy molecular environments via complex regulatory networks. It is possible to understand how molecular counts are related to noise in specific networks, but it is not generally clear how noise relates to network complexity, because different levels of complexity also imply different overall number of molecules. For a fixed function, does increased network complexity reduce noise, beyond the mere increase of overall molecular counts? If so, complexity could provide an advantage counteracting the costs involved in maintaining larger networks. For that purpose, we investigate how noise affects multistable systems, where a small amount of noise could lead to very different outcomes; thus we turn to biochemical switches. Our method for comparing networks of different structure and complexity is to place them in conditions where they produce exactly the same deterministic function. We are then in a good position to compare their noise characteristics relatively to their identical deterministic traces. We show that more complex networks are better at coping with both intrinsic and extrinsic noise. Intrinsic noise tends to decrease with complexity, and extrinsic noise tends to have less impact. Our findings suggest a new role for increased complexity in biological networks, at parity of function

Time scale and dimension analysis of a budding yeast cell cycle model

The progress through the eukaryotic cell division cycle is driven by an underlying molecular regulatory network. Cell cycle progression can be considered as a series of irreversible transitions from one steady state to another in the correct order. Although this view has been put forward some time ago, it has not been quantitatively proven yet. Bifurcation analysis of a model for the budding yeast cell cycle has identified only two different steady states (one for G1 and one for mitosis) using cell mass as a bifurcation parameter. By analyzing the same model, using different methods of dynamical systems theory, we provide evidence for transitions among several different steady states during the budding yeast cell cycle. By calculating the eigenvalues of the Jacobian of kinetic differential equations we have determined the stability of the cell cycle trajectories of the Chen model. Based on the sign of the real part of the eigenvalues, the cell cycle can be divided into excitation and relaxation periods. During an excitation period, the cell cycle control system leaves a formerly stable steady state and, accordingly, excitation periods can be associated with irreversible cell cycle transitions like START, entry into mitosis and exit from mitosis. During relaxation periods, the control system asymptotically approaches the new steady state. We also show that the dynamical dimension of the Chen’s model fluctuates by increasing during excitation periods followed by decrease during relaxation periods. In each relaxation period the dynamical dimension of the model drops to one, indicating a period where kinetic processes are in steady state and all concentration changes are driven by the increase of cytoplasmic growth.We apply two numerical methods, which have not been used to analyze biological control systems. These methods are more sensitive than the bifurcation analysis used before because they identify those transitions between steady states that are not controlled by a bifurcation parameter (e.g. cell mass). Therefore by applying these tools for a cell cycle control model, we provide a deeper understanding of the dynamical transitions in the underlying molecular network

Time scale and dimension analysis of a budding yeast cell cycle model

BACKGROUND: The progress through the eukaryotic cell division cycle is driven by an underlying molecular regulatory network. Cell cycle progression can be considered as a series of irreversible transitions from one steady state to another in the correct order. Although this view has been put forward some time ago, it has not been quantitatively proven yet. Bifurcation analysis of a model for the budding yeast cell cycle has identified only two different steady states (one for G1 and one for mitosis) using cell mass as a bifurcation parameter. By analyzing the same model, using different methods of dynamical systems theory, we provide evidence for transitions among several different steady states during the budding yeast cell cycle. RESULTS: By calculating the eigenvalues of the Jacobian of kinetic differential equations we have determined the stability of the cell cycle trajectories of the Chen model. Based on the sign of the real part of the eigenvalues, the cell cycle can be divided into excitation and relaxation periods. During an excitation period, the cell cycle control system leaves a formerly stable steady state and, accordingly, excitation periods can be associated with irreversible cell cycle transitions like START, entry into mitosis and exit from mitosis. During relaxation periods, the control system asymptotically approaches the new steady state. We also show that the dynamical dimension of the Chen's model fluctuates by increasing during excitation periods followed by decrease during relaxation periods. In each relaxation period the dynamical dimension of the model drops to one, indicating a period where kinetic processes are in steady state and all concentration changes are driven by the increase of cytoplasmic growth. CONCLUSION: We apply two numerical methods, which have not been used to analyze biological control systems. These methods are more sensitive than the bifurcation analysis used before because they identify those transitions between steady states that are not controlled by a bifurcation parameter (e.g. cell mass). Therefore by applying these tools for a cell cycle control model, we provide a deeper understanding of the dynamical transitions in the underlying molecular network

Regulation of cluster compactness and resistance to Botrytis cinerea with β-aminobutyric acid treatment in field-grown grapevine

Our paper offers unique information regarding the effects of DL-β-amino-n-butyric acid (BABA) on grape cluster compactness and Botrytis bunch rot development. The impact of treatment was investigated on a native Hungarian grapevine cultivar, Királyleányka (Vitis vinifera L.) during four seasons. The cultivar with dense clusters and with thin skinned berries provided excellent samples for bunch rot studies. In addition, the female sterility effect of BABA in grapevine flowers was examined, which may contribute to looser clusters. Cluster compactness was characterized with two different indexes, bunch rot incidence was assessed in percentages. Ovaries of flowers were examined under epifluorescent microscope. The applied treatments significantly influenced cluster indexes. Bunch rot incidence, however, was highly influenced by the precipitation during ripening. In years 2011 and 2013 reduced bunch rot was detected, while the extremity of rain in 2012 and 2014, resulted in no epidemic or high infection, respectively. Microscopic studies proved that successful treatments on cluster structure can be traced back to the female sterility caused by BABA. Our results presented clear evidence for the effectiveness of BABA treatment on Botrytis bunch rot by promoting looser clusters

Evolution of Opposing Regulatory Interactions Underlies the Emergence of Eukaryotic Cell Cycle Checkpoints

In eukaryotes the entry into mitosis is initiated by activation of cyclin-dependent kinases (CDKs), which in turn activate a large number of protein kinases to induce all mitotic processes. The general view is that kinases are active in mitosis and phosphatases turn them off in interphase. Kinases activate each other by cross- and self-phosphorylation, while phosphatases remove these phosphate groups to inactivate kinases. Crucial exceptions to this general rule are the interphase kinase Wee1 and the mitotic phosphatase Cdc25. Together they directly control CDK in an opposite way of the general rule of mitotic phosphorylation and interphase dephosphorylation. Here we investigate why this opposite system emerged and got fixed in almost all eukaryotes. Our results show that this reversed action of a kinase-phosphatase pair, Wee1 and Cdc25, on CDK is particularly suited to establish a stable G2 phase and to add checkpoints to the cell cycle. We show that all these regulators appeared together in LECA (Last Eukaryote Common Ancestor) and co-evolved in eukaryotes, suggesting that this twist in kinase-phosphatase regulation was a crucial step happening at the emergence of eukaryotes