Pathway Component. Domain Architecture dc24. GpaI. Ste4. Ste18. Cdc24.
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sbm 2: synbio of protein networks
ppi: common motives
BMN a real example: the pheromone pathway
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Fus3 kinases in red Jan 2010 Science - W. Lim et al
modularity 1 - domain split
t Mating Pathway
e18
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Pathway Component Domain Architecture
Domain Recombination (66 variants)
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Ga
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Gb
Ste4
Ste18
Gg
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GTPase
Ste20
PBD
DH
PH
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PBD
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MAPKK
Ste50
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SAM
Fus3
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Ste11
SAM
Kinase
Ste11
SAM
Ste5
PM
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Ste7
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Kinase
Downstream Effects
Fus3
of the recombination library of belonging to the yeast mating yeast mating pathway is activated
PH
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targeting/regulatory domain
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PM
Ste7
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Fus3 catalytic domain
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Domain Recombination Library modularity 2 - domain recombination (66 variants) Ga
GpaI Gb
Ste4
Gg
Ste18 PB1
VWA
omain
Cdc24
CH
Cdc42
GTPase
Ste20
PBD
Kinase
Ste50
SAM
RA
Ste11
SAM
Ste5 Ste7 Fus3
PM
RING N-t
DH
PH
Kinase PH
PB1
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C
t
VWA
Kinase Kinase
66 synthetics?
5
PM
RING
7
N-t
Kinase
3
PH
VWA
PM
Ste7
PH
RING N-t
targeting/regulatory domain
catalytic domain
VWA
Kinase
Fus3
Kinase
D
Ste5
Kinase
recombination junction
Types of Genetic Changes Analyzed in this Study full gene duplication
domain duplication
ding to the small 1 near its upstream hosphorylates Ste7, translocates to the on factors, leading nd cell morphology
wt gene (two-domains)
domain recombination
domain co-expression
architecture of the yeast mating signaling pathway components. Regulator domains are shown in green; catalytic domains are shown in orange. Full annotated domain maps are given in fig. S8. (C) Domain recombination library. Recombination junctions are depicted as white circles; all possibl recombinations are shown as red connecting lines. (D) Possible evolutionar events analyzed in this work. Gene duplication, domain duplication, domain
lation of subfunctionalized duplicates (17, 18); see fig. S2]. In contrast, shuffling of domains promorphospace vides a more direct path to functional divergence
al domain blocks had y activation (Fig. 2E). nd signaling pathway
pFus1-GFP
alpha-factor added
Slope Baseline
2 WT
3 Time
1 WT
3 Whole Gene Duplication (11) N
C
2 3
Baseline (rel.)
C WT)
WT)
1
Time (min)
B
Response Morphospace
Possible Behaviors Slope (rel.)
Mating Pathway
alpha factor
Pathway Output (GFP Fluorescence)
OUTPUT
Pathway Output
A INPUT
3 Domain Duplication (12) N
Time
Baseline (rel.)
Slope (relative to WT)
C 3 Domain Duplication (12) N 2 1 0 0
E
Slope (relative to WT)
Slope (relative to WT)
Slope (relative to WT)
(G
from the Fus1 (min) responds to resultsTime - signalling tivation, in an B r1 strain. Time 3 Whole Gene Duplication (11) asurements of N C escence were 2 calculate the and slope of 1 tivation under of linear path0 nse. Baseline 0 1 2 3 s were then Baseline (relative to WT) d relative to D alues, and the Recombination (66) 3 C N values were pathway mor2 B) Gene duplid minor effects 1 pathway reynamics, with 0 ues clustered 0 1 2 3 ild type. (C) Baseline (relative to WT) duplications minor effects on mating pathway response dynamics; Ste5[N] (which includes Ste5’s RING domain), and
1
2
3
2
3
Baseline (relative to WT) Co-Expression (66)
3
C
N
2 1 0 0
1
Baseline (relative to WT)
duplication of Ste50[N] (Ste50’s SAM Ste11[N] (Ste11’s SAM domain) are
centage of “a” when coincuba strains expressi iants with slope than that of wi than did wild-ty The same was baseline of path slope (Ste4[N]-S expressing varia than that of wil observed chang appeared to dep because there w the mating effic bination and co Thus, domain r pathway output morphological c least under labo of protein doma more efficiently work is needed t in mating efficie
. S3) are shown in red. (E) These alters the regulation of the cell cycle (16). In corresponding pairs of domains. addition, the mating pathway shares several proteins with other signaling pathways, such as nts, each time in triplicate. Error results - mating the high osmolarity pathway. Thus, domain
Circle Area=Mating Efficiency (relative to WT)
gs. S3 ts are s. (B)
B Ste50 [N]-Ste7 [C] Ste5 [N]-Ste11 [C]
Co-expression
Ste50 [N]-Cdc24 [C] Ste4 [N]-Ste5 [C]
Recombination
Ste50 [N]-Ste11 [C] Cdc42 [N]-Ste18 [C]
0
1 2 3 4 Mating Efficiency (relative to WT)
acts with the Ste11 (MAPKKK) N-terminal SAM domain, facilitating the interaction of Ste11 with Ste20, its upstream activator. Thus, it is possible that, as an isolated domain, Ste50[N] (as well as Ste11[N]) act as dom-
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