Table 2 Update rules of model species and supporting literature citations
From: Iron acquisition and oxidative stress response in aspergillus fumigatus
Update rules | Literature support |
|---|---|
1 hapX(t+1) = NOT SreA | |
2 sreA(t+1) = NOT HapX | |
3 HapX(t+1) =hapX AND (NOT LIP) | An ortholog of HapX is inactivated by intracellular iron [58]. |
4 SreA(t+1) =sreA AND LIP | An ortholog of SreA is activated by intracellular iron [59,60]. |
5 RIA(t+1) = NOT SreA | SreA transcriptionally represses RIA genes [13]. |
6 EstB(t+1) = NOT SreA | SreA transcriptionally represses estB [13]. |
7 MirB(t+1) = HapX AND (NOT SreA) | HapX transcriptionally activates mirB [29]. SreA transcriptionally represses mirB [13]. |
8 SidA(t+1) = HapX AND (NOT SreA) | HapX up regulates the SidA substrate ornithine [29]. SreA transcriptionally represses sidA [13]. |
9 TAFC(t+1) = SidA | SidA catalyzes the first step in siderophore biosynthesis [5,8] |
10 ICP(t+1) = (NOT HapX) AND (VAC OR FC +Fe) | HapX represses consumption of intracellular iron [29]. |
11 LIP(t+1) = (TAFC AND MirB AND EstB) OR (Iron AND RIA) | TAFC sequesters iron from the extracellular space [8]. MirB imports ferri-TAFC [54]. EstB |
| Â | degrades ferri-TAFC bonds and releases free iron [55]. RIA compensates for a lack of |
| Â | siderophores when grown in high iron media [33]. |
12 CccA(t+1) = NOT HapX | HapX transcriptionally represses cccA [29]. |
13 FC −Fe(t+1) = SidA | SidA catalyzes the first step in siderophore biosynthesis [5,8] |
14 FC +Fe(t+1) = LIP AND FC −Fe | |
15 VAC(t+1) = LIP AND CccA | CccA mediates import of intracellular iron into the vacuole [56]. |
16 ROS(t+1) = LIP OR | Elevated free iron levels catalyze the formation of ROS [63]. |
\(\left ({\vphantom {\sum \limits ^{1}_{1}}}\; \text {Superoxide AND}\; \left ({\vphantom {\frac {\sum }{\sum }}}\; \text {NOT (SOD3 AND ThP AND Cat1/2)}\; \right)\; \right)\) OR | SODs convert O\(_{2}^{-}\) to H 2 O 2 [20]. Either catalases or thioredoxin |
\(\left ({\vphantom {\sum \limits ^{1}_{1}}}\; \text {ROS AND} \left ({\vphantom {\frac {\sum }{\sum }}}\; \text {NOT} \left ({\vphantom {\frac {1}{2}}}\; \text {SOD3 AND (ThP OR Cat1/2)}\; \right)\; \right)\; \right)\) | |
17 Yap1(t+1) = ROS | |
18 SOD2/3(t+1) = Yap1 | Yap-1 activates transcription of sod2/3 [61]. |
19 Cat1/2(t+1) = Yap1 AND (NOT HapX) | Yap-1 activates transcription of cat1/2 [61]. HapX transcriptionally represses cat1 [29]. |
20 ThP(t+1) = Yap1 | Yap-1 activates transcription of thioredoxin peroxidases [61]. |
21 Iron(t+1) = Iron | External parameter. |
22 Superoxide(t+1) = Superoxide [ = NOT Superoxide, Figure 5 only] | External parameter. |