candida albicanscandida albicans pathogenesis and systems ... · candida albicans enjoys differing...
TRANSCRIPT
Aberdeen Fungal Group
AFG
Candida albicans pathogenesisCandida albicans pathogenesis and systems biology
Alistair BrownAlistair BrownAberdeen Fungal GroupUniversity of Aberdeen
Candida albicans enjoys differing relationships with its human host …
Aberdeen Fungal Group
p
commensalism
systemic infections
mucosal infections
fungus hostg
… and occupies contrasting and complex niches within its human host
How does Candida albicans responddynamically to host niches?
Aberdeen Fungal Group
y y
Major AIM:To understand the
fungus host
adaptation of the fungus to these
complex environmentsg complex environments
Aberdeen Fungal Group
Experimental approaches
l l globallocal global
Dissection of specific target functions:Expression patterns
l l h
Exploration on genome-wide basis:Transcriptomics & ChIP on chip
Molecular phenotypes Cellular phenotypesPhysical interactions
Proteomics Genome-wide phenotypic screens Genome-wide interaction screensPhysical interactions
…Genome wide interaction screens …
Aberdeen Fungal Group
Systems biology approaches
l l globallocal global
modeling of specific modules:Qualitative & semi-quantitative
( )
Network construction:Genetic networks
b d kQuantitative (ODE)Stochastic …
Expression-based networksInteraction networks …… …
LONG TERM AIMS: To define the networks that underpin cell biologyTo define the dynamic behaviour of these systems and how these behaviours contribute to cell adaptation, growth and development To explore the evolution of these biological systems
Aberdeen Fungal GroupMathematical modeling is in its infancy in C. albicansy
l l globallocal global
modeling of specific modules:Qualitative & semi-quantitative
( )Quantitative (ODE)Stochastic ……
Aberdeen Fungal GroupThis talk …
l l globallocal global
modeling of specific modules:Qualitative & semi-quantitative
( )ASPIRATIONS:
I d i i fQuantitative (ODE)Stochastic …
Improve our dynamic views of adaptive responsesIncrease our understanding of the contributions of specific components
GCN System:Rosa De Llanos Tao You… contributions of specific components
to dynamic behavioursExplanations for non-intuitive observations
Laura Selway Priya ChandrasekaranHelene Tournu George Coghill
THREE SHORT STORIES:Amino acid starvation (GCN)Osmotic stress
observationsInsights into the evolution of dynamic systemsInsights into the relevance of
Amino acid starvation (GCN)Osmotic stressHeat shock
Insights into the relevance of regulatory systems to pathogenicity
Aberdeen Fungal GroupAmino Acid Starvation (GCN) System
amino acidstarvation
Gcn2
[uncharged tRNAs]
eIF2α-P
GCN4 mRNA
Gcn4
amino acid
aa genes (HIS3)GCRE
amino acidbiosynthesis
Aberdeen Fungal GroupAmino Acid Starvation (GCN) Model
histidinemRNA
translationmodule
4 modules
module
3AT
histidine
GCN4 mRNA
histidine biosynthesis
GCN4 mRNAtranslational
control moduleGcn4
degradationTao You
Aberdeen Fungal GroupThe process – building the mRNA translation module
mRNA translation module:1. Build a reaction
network
You et al. (2010) Yeast 27, 785
Aberdeen Fungal GroupThe process – building the mRNA translation module
mRNA translation module:1. Build a reaction
network2. Biochemical 2. Biochemical
formulation of the model
You et al. (2010) Yeast 27, 785
Aberdeen Fungal GroupThe process – building the mRNA translation module
mRNA translation module:1. Build a reaction
network2. Biochemical 2. Biochemical
formulation of the model
3. Mathematical formulation of the model
You et al. (2010) Yeast 27, 785
Aberdeen Fungal GroupThe process – building the mRNA translation module
mRNA translation module:1. Build a reaction
network2. Biochemical 2. Biochemical
formulation of the model
3. Mathematical formulation of the model
4. Model t i ti dparameterization and
validation
You et al. (2010) Yeast 27, 785
Aberdeen Fungal GroupThe process – building the mRNA translation module
mRNA translation module:1. Build a reaction
network2. Biochemical 2. Biochemical
formulation of the model
3. Mathematical formulation of the model
4. Model t i ti dparameterization and
validation5. Module predictions
Translation initiation is robust to internal perturbations (e.g. changes in eIF concentrations)Translation initiation is sensitive to external perturbations (e.g. changes in histidine availability)
You et al. (2010) Yeast 27, 785
Aberdeen Fungal GroupThe process – building the Amino Acid Starvation (GCN) Model( )
histidine1 A bl th d l1. Assemble the modules2. Reparameterize and
validate
3AT3AT
3. Apply the model –built using artificial
di iconditions – to simulate a more physiologically relevant situationrelevant situation
Response to histidine starvation imposed by
Tao You
Response to histidine starvation imposed by 3-aminotriazole
Aberdeen Fungal GroupUse model to simulate natural amino acid starvation
1 A bl th d l
Gcn4eIf2αP
1. Assemble the modules2. Reparameterize and
validate
3. Apply the model –built using artificial
di iconditions – to simulate a more physiologically relevant situationrelevant situation
Tao You
Aberdeen Fungal GroupThe GCN Systems behave similarly. However, they operate differently, y p y
GCN4 is transcriptionally
CaGCN4 +/+ +/- -/- -/-/+
GCN43AT +- +- +- +-
GCN4 is transcriptionally activated in C. albicans
GCN4
ACT1HIS4
Gcn2-mediated translational regulation is NOT required for Gcn4-mediated
i d ti i C lbigene induction in C. albicans
Gcn2-mediated translational regulation is NOT essential for gadaptation in C. albicans
Tournu et al. (2005) Eukaryotic Cell, 4, 1687; Tripathi et al. (2002) EMBO J. 21, 5448
Aberdeen Fungal GroupAmino Acid Starvation (GCN) Systems
amino acidstarvation
Gcn2
starvation[uncharged tRNAs]
S. cerevisiaeGcn2
GCN4 geneeIF2α-P
translational regulation
GCN4 mRNA
G 4
GCN4 mRNA
i id
aa genes (HIS3)GCRE
Gcn4
amino acidbiosynthesis
Aberdeen Fungal GroupAmino Acid Starvation (GCN) Systems
amino acidstarvation
C. albicansGcn2
starvation[uncharged tRNAs]
transcriptional regulationGcn2
GCN4 geneeIF2α-P
translational regulation
regulation
GCN4 mRNA
G 4
GCN4 mRNA
In C. albicans:l l
i id
aa genes (HIS3)GCRE
Gcn4Translational regulation less importantT i ti l
Role of uORF spacing in alteringamino acid
biosynthesisTranscriptional regulation more important
altering translational regulation?
Aberdeen Fungal Group
ScGCN4 translational regulation
GCN4 mRNA (A)nuORF1 uORF4
( )n
eIF2·GTPuORF4p v6
GTM
60S mRNAGCN4
mRNA v GTM60S
Gcn4p40S+
TC40S
Met-tRNAiMet Ribosome·mRNAGCN4
(uORF4)
48S RNA
v6
60S
mRNAGCN4
Ribosome·mRNAGCN4(GCN4)
60S
v8GTM
43S
48S·mRNAGCN4
mRNAGCN4
eIF2·GTP TC
48S·mRNAGCN4(<uORF4)
eIF2·GTP TC
48S·mRNAGCN4(<uORF4)
60S
v1GTM
Ribosome·mRNAGCN4(uORF1)
GCN4
60S
40S·mRNAGCN4(<uORF4)v GTM
v3GTM
Met-tRNAiMet
v5GTM
40S·mRNAGCN4( GCN4)
eIF2·GTP TC
Met-tRNAiMet
v7GTM
S. cerevisiae
(uORF1)
uORF1p
60S(<uORF4)v2
GTM
40Sv4
GTM(<GCN4)
Tao You
Aberdeen Fungal Group
ScGCN4 translational regulation
GCN4 mRNA (A)nuORF1 uORF4
( )nn1 n2
Under replete conditions few ribosomes translate the main GCN4 ORF
Under starvation conditionsUnder starvation conditions ~25% ribosomes translate the main GCN4 ORF
G t t l (1994)
S. cerevisiaeTao You
Grant et al. (1994)Mol Cell Biol 14, 2616
Aberdeen Fungal Group
CaGCN4 translational regulation
GCN4 mRNA (A)nuORF1 uORF3uORF2
( )nn1 n2
Could the differential arrangement ofCould the differential arrangement of uORFs in the C. albicans GCN4 mRNA account for the reduced impact of Gcn2-mediated translational regulation?
Under starvation conditions ~40% ribosomes translate the
mediated translational regulation?
40% ribosomes translate the main GCN4 ORF
Simple spatial effects unlikely!Alternative mechanisms probably account for the p yreduced translational regulation in C. albicans
C. albicansPriya Chandrasekaran
Aberdeen Fungal GroupThis talk …
l l globallocal global
modeling of specific modules:Qualitative & semi-quantitative
( )ASPIRATIONS:
I d i i fQuantitative (ODE)Stochastic …
Improve our dynamic views of adaptive responsesIncrease our understanding of the contributions of specific components… contributions of specific components to dynamic behavioursExplanations for non-intuitive observationsTHREE SHORT STORIES:
Amino acid starvation (GCN)Osmotic stress
observationsInsights into the evolution of dynamic systemsInsights into the relevance ofOsmotic stress
Heat shockInsights into the relevance of regulatory systems to pathogenicity
Aberdeen Fungal GroupThis talk …
l l globallocal global
Osmotic Stress:Despoina Kaloriti Tao Youmodeling of specific modules:
Qualitative & semi-quantitative( )
ASPIRATIONS: I d i i f
Despoina Kaloriti Tao YouMette Jacobsen Piers IngramAnna Tillmann Wei PangNeil Gow Mamen RomanoQuantitative (ODE)
Stochastic …
Improve our dynamic views of adaptive responsesIncrease our understanding of the contributions of specific components
Neil Gow Mamen RomanoKen Haynes Marco ThielEmily Cook Alessandro MouraMelanie Putnam Celso Grebogi… contributions of specific components
to dynamic behavioursExplanations for non-intuitive observations
Melanie Putnam Celso GrebogiAndy McDonaghJanet Quinn
THREE SHORT STORIES:Amino acid starvation (GCN)Osmotic stress
observationsInsights into the evolution of dynamic systemsInsights into the relevance ofOsmotic stress
Heat shockInsights into the relevance of regulatory systems to pathogenicity
Aberdeen Fungal GroupOsmotic stress adaptation in C. albicans – the aspirationp
Klipp et al. (2002) Nature Biotechnology 23, 975-982.
Aberdeen Fungal GroupOsmotic stress adaptation in C. albicans – the problemp
Conservation of molecular systems in C. albicansOsmotic stress signalling network
Conservation of molecular systems in C. albicansTranslational apparatus
Many components of the osmotic stress signalling network have
Nikolaou et al. (2009) BMC Evol. Biol. 9, 44.
a y co po e s o e os o c s ess s g a g e o a ediverged significantly
Aberdeen Fungal GroupOsmotic stress adaptation in C. albicans – the problemp
The Ste11/Sho1 module is not required for osmotic stress signalling toHog1 in C. albicansHog1 in C. albicans
Tao You, Piers Ingram Cheetham et al. (2007) Mol Biol Cell 18, 4603
Aberdeen Fungal GroupOsmotic stress adaptation in C. albicans – the solution
Low granularity ODE models that reflect scarcity of information in C. albicans
The models capture essential features of the system, abstracting:Upstream signalling to Hog1Glycerol production machinery and its regulation Tao You, Piers Ingram
Aberdeen Fungal GroupModeling osmotic stress adaptation in C. albicansp
These low granularity models h h l d t
1.0
aCl (
M)
have helped us to understand global features of the system:
0Na
Integral control of glycerol
The existence of memory in the system
Integral control of glycerol production
Tao You, Mette Jacobsen
Aberdeen Fungal GroupModeling osmotic stress adaptation in C. albicansp
These low granularity models do NOT help us to understand the t ib ti f ifi l l t t t b h icontributions of specific molecular components to system behaviours
Aberdeen Fungal GroupThis talk …
l l globallocal global
modeling of specific modules:Qualitative & semi-quantitative
( )ASPIRATIONS:
I d i i fQuantitative (ODE)Stochastic …
Improve our dynamic views of adaptive responsesIncrease our understanding of the contributions of specific components… contributions of specific components to dynamic behavioursExplanations for non-intuitive observationsTHREE SHORT STORIES:
Amino acid starvation (GCN)Osmotic stress
observationsInsights into the evolution of dynamic systemsInsights into the relevance ofOsmotic stress
Heat shockInsights into the relevance of regulatory systems to pathogenicity
Aberdeen Fungal GroupThis talk …
l l globallocal global
modeling of specific modules:Qualitative & semi-quantitative
( )ASPIRATIONS:
I d i i f
Michelle Leach @ 4:35pm on ThursdayQuantitative (ODE)Stochastic …
Improve our dynamic views of adaptive responsesIncrease our understanding of the contributions of specific components
Heat Shock:Michelle LeachKatarzyna Tyc… contributions of specific components
to dynamic behavioursExplanations for non-intuitive observations
y yEdda KlippLeah Cowen
THREE SHORT STORIES:Amino acid starvation (GCN)Osmotic stress
observationsInsights into the evolution of dynamic systemsInsights into the relevance ofOsmotic stress
Heat shockInsights into the relevance of regulatory systems to pathogenicity
Aberdeen Fungal GroupThe heat shock response in Candida albicans
Th H t Sh k T i ti F t (H f1) i ti t d bThe Heat Shock Transcription Factor (Hsf1) is activated by phosphorylation during heat shock Why is Hsf1 not phosphorylated during growth at elevated
Temperature (˚C)
Why is Hsf1 not phosphorylated during growth at elevated temperatures?
15 20 25 3530 40 HSp ( )
Hsf1Hsf1-P
Act1
Nicholls, Leach, et al. (2009) Molec. Micro. 74, 844.
Aberdeen Fungal GroupModeling the heat shock response in Candida albicans
Hsf1heat
HSP90
heatshock
autoregulatorycircuit
Hsp90 unfoldedproteins
Michelle Leach & Katarzyna Tyc
Aberdeen Fungal GroupThe heat shock system displays“Perfect Adaptation”p
simulations experimental datasimulations
P
experimental data
30-42˚C in tet-HSP90 knockdown
Hsf
1 P
- + - + - + - +- +Ppase
0 1 3 42 hrs
30 42 C in tet HSP90 knockdown
Time (min)
30-42˚C+ + + ++
Hsf1Hsf1-P
Hsf1 is activated by phosphorylation during heat shock But this activation is transient, Hsf1-P returning to basal levels
e ( )
, gonce cells have adapted to the elevated temperature“Perfect Adaptation” is dependent upon a negative feedback loopThis explains why Hsf1 is not phosphorylated during
Michelle Leach & Katarzyna Tyc
This explains why Hsf1 is not phosphorylated during protracted growth at elevated temperatures
Aberdeen Fungal GroupThis talk …
l l globallocal global
modeling of specific modules:Qualitative & semi-quantitative
( )ASPIRATIONS:
I d i i fQuantitative (ODE)Stochastic …
Improve our dynamic views of adaptive responsesIncrease our understanding of the contributions of specific components… contributions of specific components to dynamic behavioursExplanations for non-intuitive observationsTHREE SHORT STORIES:
Amino acid starvation (GCN)Osmotic stress
observationsInsights into the evolution of dynamic systemsInsights into the relevance ofOsmotic stress
Heat shockInsights into the relevance of regulatory systems to pathogenicity
Aberdeen Fungal GroupThis talk …
l l globallocal global
modeling of specific modules:Qualitative & semi-quantitative
( )ASPIRATIONS:
I d i i fQuantitative (ODE)Stochastic …
Improve our dynamic views of adaptive responsesIncrease our understanding of the contributions of specific components… contributions of specific components to dynamic behavioursExplanations for non-intuitive observationsTHREE SHORT STORIES:
Amino acid starvation (GCN)Osmotic stress
observationsInsights into the evolution of dynamic systemsInsights into the relevance ofOsmotic stress
Heat shockInsights into the relevance of regulatory systems to pathogenicity
Thanks to …Neil Gow
Aberdeen Fungal Group
Neil GowFrank OddsGordon BrownCarol Munro
AFG
Carol MunroAlex BrandDonna MacCallum
GCN System:Rosa De Llanos Tao YouLaura Selway Priya Chandrasekaran
Heat Shock:Michelle LeachKatarzyna TycLaura Selway Priya Chandrasekaran
Helene Tournu George Coghill
Osmotic Stress:
Katarzyna TycEdda KlippLeah Cowen
Osmotic Stress:Despoina Kaloriti Tao YouMette Jacobsen Piers IngramAnna Tillmann Wei Pang Janet Q inngNeil Gow Mamen RomanoKen Haynes Marco ThielEmily Cook Alessandro Moura
Janet Quinn
Melanie Putnam Celso GrebogiAndy McDonagh