Comprehensive Logic Based Analyses of Toll-Like Receptor 4 Signal Transduction Pathway

<div><p>Among the 13 TLRs in the vertebrate systems, only TLR4 utilizes both Myeloid differentiation factor 88 (MyD88) and Toll/Interleukin-1 receptor (TIR)-domain-containing adapter interferon-β-inducing Factor (TRIF) adaptors to transduce signals triggering host-protective immune responses. Earlier studies on the pathway combined various experimental data in the form of one comprehensive map of TLR signaling. But in the absence of adequate kinetic parameters quantitative mathematical models that reveal emerging systems level properties and dynamic inter-regulation among the kinases/phosphatases of the TLR4 network are not yet available. So, here we used reaction stoichiometry-based and parameter independent logical modeling formalism to build the TLR4 signaling network model that captured the feedback regulations, interdependencies between signaling kinases and phosphatases and the outcome of simulated infections. The analyses of the TLR4 signaling network revealed 360 feedback loops, 157 negative and 203 positive; of which, 334 loops had the phosphatase PP1 as an essential component. The network elements' interdependency (positive or negative dependencies) in perturbation conditions such as the phosphatase knockout conditions revealed interdependencies between the dual-specific phosphatases MKP-1 and MKP-3 and the kinases in MAPK modules and the role of PP2A in the auto-regulation of Calmodulin kinase-II. Our simulations under the specific kinase or phosphatase gene-deficiency or inhibition conditions corroborated with several previously reported experimental data. The simulations to mimic <i>Yersinia pestis</i> and <i>E. coli</i> infections identified the key perturbation in the network and potential drug targets. Thus, our analyses of TLR4 signaling highlights the role of phosphatases as key regulatory factors in determining the global interdependencies among the network elements; uncovers novel signaling connections; identifies potential drug targets for infections.</p></div

TLR4 Signal Transduction pathway map.

<p>Logical model of the TLR4 signal transduction network built in CellDesigner. The input species are shown by arrow pointing to the species while output species are shown by arrow going away from a species. Final outputs of model are represented as yellow colored boxes. Black dot in picture indicates AND gate. Black colors of the edges represent the activatory signals to the downstream node while the inhibitions are represented in red color.</p

Influence of ERK1/2 on various kinases in wild type and MKP3 knockout condition.

<p>A. ERK1/2 regulates MEKK3both positively as well as negatively in wild type condition. In the MKP3 knockout condition the regulation of MEKK3 by ERK1/2 is only positive; similarly the effect of the ERK1/2 on IKK (B), p38MAPK (C), Akt (D) and CAMKII (E), in wild type and MKP3 knockout condition is shown. Black arrow represents positive and red arrow represents negative influence respectively.</p

Conversion of reactions from the comprehensive map to the logical reactions.

<p>Set of representative interactions extracted from comprehensive map of TLR signaling and represented as interaction graph and interaction hypergraph.</p

MISs for inhibiting production of the IL-10 in <i>Yersinia</i> infection.

<p>! Denote the permanent inactivation of the species and the species without ! sign are species which should be permanently activated for fulfilling target goal.</p><p>* Shows activated form of the IRAK1 complex.</p

Shortest positive and negative signaling path from ERK1/2 to IL-10.

<p>Positive and negative signaling path from the ERK1/2 to IL-10 is shown. Red bar show inhibition and black shows activatory signal.</p

Self-regulation of CAMKII.

<p>(A) CAMKII and Akt (B) in the wild type and PP2A knockout out condition are shown. Black arrow shows positive influence; red arrow shows the inhibitory effect and cross mark shows no effect.</p

Auto regulation of MEKK3 and its influence on different kinases/phosphatase in wild type and knockout conditions.

<p>Influence of MEKK3 on PP2A (A), Akt (B), MEKK3 (C), CAMKII (D) and IKK (E), in wild type and PP1 knockout condition is shown. Black arrow shows positive and red arrow represents the inhibitory influences respectively.</p

Relative participation of phosphatases in feedback loops.

<p>Figures show number of remaining feedback loops in different phosphatases knockout conditions.</p

Shortest positive path form ERK1/2 to IL-12.

<p>Positive signal path from the ERK1/2 to the IL-12 is shown.</p