Upload
remy
View
14
Download
0
Tags:
Embed Size (px)
DESCRIPTION
Using systems biology to learn how halo respond to their environment. bR converts light energy into chemical energy for making ATP. LIGHT. Halobacterium cell. ATP. ATP. ATP. ATP. ATP. Bacteriorhodopsin (bR). - PowerPoint PPT Presentation
Citation preview
Using systems biology to learn how halo respond to their environment
bR converts light energy into chemical energy for making ATP
Halobacterium cell
Note: other proteins are required for this process, but we will simplify and focus on bR
Bacteriorhodopsin (bR)
LIGHT
ATP
ATP
ATP
ATP
ATP
Bacteriorhodopsin(bR)
Cell membRane
Bacteriorhodopsin (bR) is made from a protein called bop and the molecule retinal
Bop protein
Bop + retinal = bacteriorhodopsin (bR)
Retinal
Halobacterium cell
LIGHT PRESENT LIGHT ABSENT(DARK)
Halobacterium cell
LIGHT
When there is more light, halo respond by making more bR
LIGHT
When there is less light, halo make less bR
Halo change the expression of bR in response to the amount of light in their environment
Light bR+
The amount of bR increases when there is more light.
Note that the size of nodes in this diagram relates to the amount of light and bR, not the actual size. In other words, the size of bR does not change; a larger node for bR indicates a larger amount of bR.
Halo change the expression of bR in response to the amount of light in their environment
OUR QUESTION:
How do Halobacterium cells control the amount of bR expressed in response to light? What is the gene and protein network that regulates the expression of bR?
Metabolic data group
lycopene beta-carotene retinal
bacteriorhodopsin(bR)
GG-PP phytoene
bop
lycopene beta-carotene retinal
bacteriorhodopsin(bR)
GG-PP phytoene
bop
Question:How would increasing the amount of GG-PP affect the amount of bacteriorhodopsin (bR)?
lycopene beta-carotene retinal
bacteriorhodopsin(bR)
GG-PP phytoene
bop
Question:How would increasing the amount of GG-PP affect the amount of bacteriorhodopsin (bR)?
lycopene beta-carotene retinal
bacteriorhodopsin(bR)
GG-PP phytoene
bop
Question:If the enzyme that converts phyotene to lycopene were missing, how would the amount of bacteriorhodopsin (bR) be affected?
lycopene beta-carotene retinal
bacteriorhodopsin(bR)
GG-PP phytoene
bop
Question:If the enzyme that converts phyotene to lycopene were missing, how would the amount of bacteriorhodopsin (bR) be affected?
Homology
lycopene beta-carotene retinal
bacteriorhodopsin(bR)
GG-PP phytoene
bop
CrtYCrtB1 brp
Question:Which enzymes are part of the bacteriorhodopsin network?What other genes are involved in the system?
bat
lycopene beta-carotene retinal
bacteriorhodopsin(bR)
GG-PP phytoene
bop
CrtYCrtB1 brp
Question:Which protein changes in response to light and affects the expression of other genes?
bat
LIGHT
Microarray gene expression
lycopene beta-carotene retinal
bacteriorhodopsin(bR)
GG-PP phytoene
bop
CrtYCrtB1 brp
bat
To simplify, focus on the genes and gene products (proteins). Then we’ll see how these affect the metabolites and bacteriorhodopsin (bR).
bop
CrtYCrtB1 brp
bat
To simplify, focus on the genes and gene products (proteins). Then we’ll see how these affect the metabolites and bacteriorhodopsin (bR).
bop
CrtYCrtB1 brp
bat
Question:Which genes does bat affect?
bop
CrtYCrtB1 brp
bat
Question:What happens to the expression of the genes when bat is overexpressed?
bop
CrtYCrtB1 brp
bat
Question:What happens to the expression of the genes when bat is overexpressed?
bop
CrtYCrtB1 brp
bat
Question:What happens to the expression of the genes when bat is knocked out?
bop
CrtYCrtB1 brp
bat
Question:What happens to the expression of the genes when bat is knocked out?
bop
CrtYCrtB1 brp
bat
Question:What happens to the expression of the genes when bat is knocked out?
bop
CrtYCrtB1 brp
bat
Knocked out bat
bop
CrtYCrtB1 brp
bat
Overexpressed bat
bop
CrtYCrtB1 brp
bat
lycopene beta-carotene retinal
bacteriorhodopsin(bR)
GG-PP phytoene
Question:Bat affects the amount of proteins in the bR network. How does this affect the amount of bacteriorhodopsin produced?
bop
CrtYCrtB1 brp
bat
Knocked out bat
lycopene beta-carotene retinal
bacteriorhodopsin(bR)
GG-PP phytoene
bop
CrtYCrtB1 brp
bat
Overexpressed bat
lycopene beta-carotene retinal
bacteriorhodopsin(bR)
GG-PP phytoene
bop
CrtYCrtB1 brp
bat
lycopene beta-carotene retinal
bacteriorhodopsin(bR)
GG-PP phytoene
bop
CrtYCrtB1 brp
bat
lycopene beta-carotene retinal
bacteriorhodopsin(bR)
GG-PP phytoene
Knocked out bat
Overexpressed bat
OUR QUESTION:
How do Halobacterium cells control the amount of bR expressed in response to light? What is the gene and protein network that regulates the expression of bR?
ADP + P
ATP
LIGHT
bop
CrtYCrtB1 brp
bat
lycopene beta-carotene retinal
bacteriorhodopsin(bR)
GG-PP phytoene
Our hypothesis – Light Present
only when light is present
ADP + P
ATP
LIGHT
bop
CrtYCrtB1 brp
bat
lycopene beta-carotene retinal
bacteriorhodopsin(bR)
GG-PP phytoene
Our hypothesis – Light Absent
only when light is present
Known Network – bR Production
ADP + P
ATP
LIGHT
bop
CrtYCrtB1 brp
bat
lycopene beta-carotene retinal
bacteriorhodopsin(bR)
GG-PP phytoene
only when light is present
Where do the other energy pathways fit (e.g. fermentation)?
+ +
+
bop
CrtYCrtB1 brp
bat
lycopene beta-carotene retinal
bacteriorhodopsin(bR)
GG-PP phytoene
L-arginosuccinate
ArgG
ArgHarginine
citrulline
ornithine
carbamoyl-PO4
carbamate CO2
NH3
ADP + P
ArcA ArcB
ArcC ATP
Arginine
(inside cell)
Arginine
(outside of cell)
YhdG
ADP + P
ATP
LIGHT
only when light is present
bop
CrtYCrtB1 brp
bat
ArgG
ArgH
ArcA ArcB
ArcC
YhdG
[+]
[+][+]
[-]
[-]
[-][-] [-]
[-]
bop
CrtYCrtB1 brp
bat
lycopene beta-carotene retinal
bacteriorhodopsin(bR)
GG-PP phytoene
L-arginosuccinate
ArgG
ArgHarginine
citrulline
ornithine
carbamoyl-PO4
carbamate CO2
NH3
ADP + P
ArcA ArcB
ArcC ATP
Arginine
(inside cell)
Arginine
(outside of cell)
YhdG
ADP + P
ATP
LIGHT
L-arginosuccinate
arginine
citrulline
ornithine
carbamoyl-PO4
carbamate CO2
NH3
ADP + P
ATP
Arginine
(inside cell)
Arginine
(outside of cell)
ArgG
ArgH
ArcA ArcB
ArcC
YhdG bop
CrtYCrtB1 brp
lycopene beta-carotene retinal
bacteriorhodopsin(bR)
GG-PP phytoene
bat
LIGHTADP + P
ATP
L-arginosuccinate
ArgG
ArgHarginine
citrulline
ornithine
carbamoyl-PO4
carbamate CO2
NH3
ADP + P
ArcA ArcB
ArcC
ATP
Arginine
(inside cell)
Arginine
(outside of cell)
YhdG bop
CrtYCrtB1 brp
lycopene beta-carotene retinal
bacteriorhodopsin(bR)
GG-PP phytoene
bat
ADP + P
ATP
LIGHT
L-arginosuccinate
arginine
citrulline
ornithine
carbamoyl-PO4
carbamate CO2
NH3
ADP + P
ATP
Arginine
(inside cell)
Arginine
(outside of cell)
ArgG
ArgH
ArcA ArcB
ArcC
YhdG bop
CrtYCrtB1 brp
lycopene beta-carotene retinal
bacteriorhodopsin(bR)
GG-PP phytoene
bat
LIGHTADP + P
ATP
L-arginosuccinate
ArgG
ArgHarginine
citrulline
ornithine
carbamoyl-PO4
carbamate CO2
NH3
ADP + P
ArcA ArcB
ArcC
ATP
Arginine
(inside cell)
Arginine
(outside of cell)
YhdG bop
CrtYCrtB1 brp
lycopene beta-carotene retinal
bacteriorhodopsin(bR)
GG-PP phytoene
bat
ADP + P
ATP
LIGHT
L-arginosuccinate
arginine
citrulline
ornithine
carbamoyl-PO4
carbamate CO2
NH3
ADP + P
ATP
Arginine
(inside cell)
Arginine
(outside of cell)
ArgG
ArgH
ArcA ArcB
ArcC
YhdG bop
CrtYCrtB1 brp
lycopene beta-carotene retinal
bacteriorhodopsin(bR)
GG-PP phytoene
bat
LIGHTADP + P
ATP
L-arginosuccinate
ArgG
ArgHarginine
citrulline
ornithine
carbamoyl-PO4
carbamate CO2
NH3
ADP + P
ArcA ArcB
ArcC
ATP
Arginine
(inside cell)
Arginine
(outside of cell)
YhdG bop
CrtYCrtB1 brp
lycopene beta-carotene retinal
bacteriorhodopsin(bR)
GG-PP phytoene
bat
ADP + P
ATP
LIGHT
Why is it so complicated?
• Why does the cell use this network of genes, enzymes, other proteins, and metabolites to make bR?
• Why does the cell go through the trouble of regulating the network for bR?
What could we do to test our network model?
• How could we validate our network?
• What other types of experiments could we do?
• What other types of information could we use?
• Would we have been able to define this network without multiple data types? Why or why not?