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. 2020 Apr 26;21(9):3061.
doi: 10.3390/ijms21093061.

Data-Driven Modeling Identifies TIRAP-Independent MyD88 Activation Complex and Myddosome Assembly Strategy in LPS/TLR4 Signaling

Xiang Li  1   2 , Chuan-Qi Zhong  2 , Zhiyong Yin  1 , Hong Qi  3 , Fei Xu  1 , Qingzu He  1 , Jianwei Shuai  1   2
Affiliations

Data-Driven Modeling Identifies TIRAP-Independent MyD88 Activation Complex and Myddosome Assembly Strategy in LPS/TLR4 Signaling

Xiang Li et al. Int J Mol Sci. .

Abstract

TLR4 complexes are essential for the initiation of the LPS-induced innate immune response. The Myddosome, which mainly contains TLR4, TIRAP, MyD88, IRAK1/4 and TRAF6 proteins, is regarded as a major complex of TLR4. Although the Myddosome has been well studied, a quantitative description of the Myddosome assembly dynamics is still lacking. Furthermore, whether some unknown TLR4 complexes exist remains unclear. In this study, we constructed a SWATH-MS data-based mathematical model that describes the component assembly dynamics of TLR4 complexes. In addition to Myddosome, we suggest that a TIRAP-independent MyD88 activation complex is formed upon LPS stimulation, in which TRAF6 is not included. Furthermore, quantitative analysis reveals that the distribution of components in TIRAP-dependent and -independent MyD88 activation complexes are LPS stimulation-dependent. The two complexes compete for recruiting IRAK1/4 proteins. MyD88 forms higher-order assembly in the Myddosome and we show that the strategy to form higher-order assembly is also LPS stimulation-dependent. MyD88 forms a long chain upon weak stimulation, but forms a short chain upon strong stimulation. Higher-order assembly of MyD88 is directly determined by the level of TIRAP in the Myddosome, providing a formation mechanism for efficient signaling transduction. Taken together, our study provides an enhanced understanding of component assembly dynamics and strategies in TLR4 complexes.

Keywords: LPS signaling; SWATH-MS; TLR4 complexes; higher-order assembly strategy; mathematical modeling; systems biology.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
LPS-induced TLR4 complexes signaling transduction and model construction. (A) Overview of LPS/TLR4 signaling. (B) The stoichiometry of MyD88 and TRAF6 complexes determined by SWATH-MS. Data were obtained from ref [14]. (C) Kinetic mathematical model of the LPS-induced components association and disassociation in Myddosome (Model 1). (D) Simulation using Model 1 (lines) and SWATH-MS data (dots) of the time-course responses. Left and right panels respectively correspond to the major component dynamics in the MyD88 and TRAF6 complexes.
Figure 2
Figure 2
LPS induced the formation of the TIRAP-independent MyD88 activation complex. (A) Discrepancy between the Model 1 simulation results and SWATH-MS data suggest TIRAP-independent MyD88 complex and MyD88-TRAF6 complex formation upon LPS stimulation. (B) Simulation using Model 2 (lines) and SWATH-MS data (dots) of the time-course responses. (C) Comparison results of the R-square values between Model 1 (upper panel) and Model 2 (down panel).
Figure 3
Figure 3
Components distribution strategy in the TLR4 complexes. (A) Percentage of components distribution in TIRAP-dependent and -independent MyD88 complexes. To calculate the total amount of each component recruited into the complexes, we did not consider the components disassociation processes and set the corresponding parameters to 0. The 10-hr LPS stimulation results were calculated as each component reached its maximum amount. (B) Schematic of the components distribution in complexes. (C) Percentage of components distributions in TIRAP-dependent and -independent MyD88 complexes upon different LPS stimulation-strengths.
Figure 4
Figure 4
Higher-order assembly of the components in the Myddosome. (A) Schematic of the higher-order assembly of the components in the TLR4 complexes. There is about 6-fold more MyD88 than TIRAP in the Myddosome. (B) Ratio of the components to TIRAP in the Myddosome upon different LPS stimulation-strength at 30, 60 and 120 min, respectively. (C) The changes of the ratio of MyD88 to TIRAP and the amount of TIRAP in the Myddosome with LPS stimulation-strength (upper panel) and TIRAP initial level (down panel), respectively. (D) Diagram of the three phases that show that MyD88 higher-order behaviors are TIRAP amount-dependent.
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