D. melanogaster

This logical model encompasses 48 components and 82 regulatory interactions controlling mesoderm specification during Drosophila development, thereby integrating all major genetic processes underlying the formation of four mesodermal tissues. The model is based on in vivo genetic data, partly confirmed by functional genomic data.

Model simulations qualitatively recapitulate the expression of the main lineage markers of each mesodermal derivative, from developmental stage 8 to 10, for the wild type case, as well as for over twenty reported mutant genotypes.

This model has been used to systematically predict the effects of over 300 loss- and gain-off unction mutations, and combinations thereof. By generating specific mutant combinations, several novel predictions experimentally could be validated, demonstrating the robustness of model.

VEGF (also called PDGF or PVF) pathway participates in different developmental processes, including border cell migration, hemocyte migration and survival, thorax closure during metamorphosis, the rotation and dorsal closure of the male terminalia. and embryonic salivary gland tissue migration. The ability of PVR to activate the MAP-kinase pathway is important for control of cell growth and differentiation in other tissues. Three genes in the Drosophila genome code for PVR ligands: PVF1, PVF2, and PVF3. Binding of one of the ligands (PVF1, 2 or 3) to the receptor PVR triggers the canonical DRK/SOS/RAS/RAF/DSOR1/RL pathway ([1];[2]; [3]; [4]; [5]). DOF is needed to assemble the PVR receptor and allow it to auto-phosphorylate, likely as an adaptor that links the receptor to RAS pathway. DOF is a cytoplasmic protein which is expressed ubiquitously only in cells that express the FGF receptors. It contains an ankyrin repeat, a coiled-coil structure and many tyrosines within environments that suggest that if phosphorylated they act as binding sites for the SH2 domains of proteins such as DRK or CSW ([6]). The SH2-domain-containing protein DRK recruits the guanine nucleotide exchange factor, Son of sevenless (SOS), to catalyze the exchange of GDP bound to RAS for GTP, thereby activating RAS with the help of activated KSR. RAS promotes the activation of RAF, leading to the activation of DSOR1, and ultimately to that of the MAP kinase Rolled (RL ). Rolled can activate transcription, both through inactivation of transcriptional co-repressors such as AOP, as well as through the activation of transcription factors such as the ETS-domain- containing protein Pointed (PNT) ([7]; [8]). The activation of PNT is a major output of the pathway. It is either phosphorylated by MAP kinase to produce an active transcriptional activator (PointedP2), or transcriptionally induced by MAP kinase to produce a constitutive transcriptional activator (PointedP1). Sprouty (STY) acts downstream of the receptor, but upstream of RAS1 and RAF, by recruiting GAP1 and blocking the ability of DRK to bind to its positive effector. We have considered three typical initial states corresponding to i. ligands binding in wild-type signalling enabling situation (VEGF_signalling), ii. ligand binding in the presence of the inhibitor Sprouty (Sprouty_inhibition), iii. absence of ligand (No_signalling).

References

Processing of HH ligand The precursor of HH is auto-catalytically cleaved to produce an N-terminal (HH-N) and a C- terminal (HH-C) fragments ([1]; [2]). A cholesterol moiety is covalently attached to the last amino acid of HH-N to create HH-Np, that is responsible for the biological activities of HH proteins ([1]; [2]; [3]). The N-terminal region of HH-Np is further modified by addition of palmitate that is essential for its signalling activity ([4]; [5]; [6]; [7]; [8]; [9]). We model these aspects by an AND rule (combining inputs from DLP, IHOG, Rasp, DISP, SHF, Lipophorin, BOI and DALLY) attached to the component representing the secreted HH molecule, denoted Hh in our model. HH Signalling Two integral membrane proteins are involved in HH signal reception: Patched and Smoothened. HH binding to its receptor Patched (PTC) relieves PTC-mediated repression of Smoothened (SMO), a serpentine-like membrane protein required for HH signalling ([10]; [11]). This allows SMO stabilisation, activation, and phosphorylation by Shaggy (SGG), and downstream signalling through the formation of a protein complex including the serine threonine kinase Fused (FU), the kinesin-like protein Costa (COS), and the protein Suppressor of Fused (SU(FU)), ultimately controlling the post-translational processing of the protein Cubitus interruptus (CI) ([12]). In the absence of HH, COS binds CI directly and sequesters it in the cytoplasm with the help of SUFU. The recruitment of different kinases (Casein kinase 1 alpha, Shaggy, Protein kinase A) then leads to the phosphorylation of CI and to its proteolysis by SLMB. The resulting truncated protein (CI_rep) is released and enters the nucleus, where it has a transcriptional repressing activity. Recent evidence further indicates that SMO is inhibited by TOW, which tentatively mediates the effect of PTC on SMO ([13]; [14]). Following SMO activation, the transcription factor CI is phosphorylated and translocated into the nucleus in its entire form, which plays a transcriptional activatory role (CI_act). In the model, a cascade of inhibitions, from HH on PTC, and from PTC on SMO, implements the indirect positive action of HH on SMO. A protein complex including CI, COS, and FU, phosphorylates and thereby inhibits SU(FU), ultimately favouring the CI activatory form and its translocation into the nucleus. We model the roles of the kinases (SGG, PKA, and CK1a), COS and SU(FU) (both needed to recruit the kinases) in the processing of CI in terms of inhibitory interactions on CI_act and activatory interactions on CI_rep ([15]; [16]). Complexes are represented implicitly (they are formed as soon as the components are synthesised or activated), while logical rules define component activity requirements to form CI_act versus CI_rep forms. To explore the dynamic of the pathway, we define two initial states to simulate the presence and the absence of signalling. On one hand, the non binding of HH (level expression 0) triggers a series of signalling cascades that lead to the activation of several kinases (for example SGG, PKA, CK1a, ...) at level of expression 1, which will permit the formation of CI repressor (expressed at level 1), which in turn will inhibit the targets. On the other hand, the presence of HH (level of expression 1) leads to a stable state corresponding to the signalling conditions leading to the formation of CI activator that will activate the targets node (level of expression 1).

References

Notch signaling is involved in the modulation of Twist expression and the subdivision of the mesoderm into high and low domain of Twist. The binding of Delta leads to the cleavage and the release of the Notch intracellular domain NICD. During mesoderm specification, NICD can inhibit Twist by forming a complex with EMC, or in combination with Enhancer of split and Suppressor of hairless proteins. In this regard, we modeled the effect of Notch pathway on Twist expression. Our defined initial states reproduce biological data during mesoderm specification. When Delta is ON (high or medium signaling), the level of Twist expression can decrease from 2 to 1 or 0. When Delta is OFF (no signaling), Twist is expressed at its maximal level 2. For more details on Notch signalling pathway and it's role on Twist expression regulation during Drosophila development, see [1]; [2]; [3]; [4]; [5].

References

Drosophila genome encodes two FGF receptors, HTL (Heartless) and BTL (Breathless), which are required for the morphogenesis of different tissues. BTL is expressed in the tracheae, while HTL is expressed in embryonic mesoderm and was first identified because of its essential role in heart development. BTL ligand, BNL is encoded by the branchless gene ([1]). THS (Thisbe) and PYR (Pyramus) function in a partially redundant fashion to activate heartless (htl). Upon ligand binding receptor dimerization triggers the canonical DRK/SOS/RAS/RAF/DSOR1/RL pathway. In contrast with other RTKs, Stumps is needed to trigger signal transduction (see [2]; [3]). Stumps is a cytoplasmic protein expressed in cells also expressing the FGF receptors. The presence of an ankyrin repeat, a coiled-coil structure and many tyrosines suggests that Stumps could bind SH2 domains of proteins such as DRK or CSW ([4]). As a result, DRK recruits the guanine nucleotide exchange factor SOS (Son of sevenless), which catalyzes the exchange of GDP bound to RAS for GTP. Activated RAS then promotes the activation of RAF (Pole hole), DSOR1, and eventually that of RL (Rolled). RL can activate transcription through the inactivation of transcriptional co-repressors such as Anterior Open (AOP), as well as through the activation of transcriptional activators such as PNT (Pointed, with two forms denote by suffixes P1 and P2) ([5]; [6]). The negative regulator STY (Sprouty) acts downstream of SOS but upstream of RAS and RAF, by recruiting GAP1 and blocking the ability of DRK to bind to its positive effector. Our model enables the simulation of pathway responses to different ligand combinations. In this regard, we define four initial states to simulate different behavior of the pathway. The first initial state reproduces the signalling through the receptor HTL (bound by Pyr and Ths), the second initial state corresponds to the signalling through the receptor BTL, the third initial state corresponds to the involvement of the inhibitor Sprouty during signalling conditions and the fourth initial state corresponds to the absence of signalling (no ligands binding). Each of these initial states lead to a specific stable state representative of in vivo conditions.

References