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Using systems biology to learn
how halo respond to their
environment
bR converts light energy into
chemical energy for making ATP
LIGHT
ATP
ATP
ATP
Halobacterium cell
ATP ATP
Bacteriorhodopsin (bR)
Note: other proteins are required for this process, but we will simplify and focus on bR
Bacteriorhodopsin (bR) is made from a
protein called bop and the molecule retinal
Bop + retinal = bacteriorhodopsin (bR)
Cell
membRane
Retinal
Bop protein
Bacteriorhodopsin
(bR)
Halo change the expression of bR in response
to the amount of light in their environment
LIGHT PRESENT
LIGHT ABSENT
(DARK)
LIGHT
Halobacterium cell
When there is more light, halo
respond by making more bR
LIGHT
Halobacterium cell
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
The amount of bR increases
when there is more light.
+
Light
bR
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.
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
GG-PP
phytoene
lycopene
beta-carotene
retinal
bop
bacteriorhodopsin
(bR)
GG-PP
phytoene
lycopene
beta-carotene
retinal
bop
bacteriorhodopsin
(bR)
Question:
How would increasing the amount of GG-PP affect the amount
of bacteriorhodopsin (bR)?
GG-PP
phytoene
lycopene
beta-carotene
retinal
bop
bacteriorhodopsin
(bR)
Question:
How would increasing the amount of GG-PP affect the amount
of bacteriorhodopsin (bR)?
GG-PP
phytoene
lycopene
beta-carotene
retinal
bop
bacteriorhodopsin
(bR)
Question:
If the enzyme that converts phyotene to lycopene were missing,
how would the amount of bacteriorhodopsin (bR) be affected?
GG-PP
phytoene
lycopene
beta-carotene
retinal
bop
bacteriorhodopsin
(bR)
Question:
If the enzyme that converts phyotene to lycopene were missing,
how would the amount of bacteriorhodopsin (bR) be affected?
Homology
GG-PP
phytoene
lycopene
CrtB1
beta-carotene
retinal
CrtY
brp
bop
bacteriorhodopsin
(bR)
bat
Question:
Which enzymes are part of the bacteriorhodopsin network?
What other genes are involved in the system?
GG-PP
phytoene
lycopene
CrtB1
beta-carotene
retinal
CrtY
brp
bop
bacteriorhodopsin
(bR)
bat
LIGHT
Question:
Which protein changes in response to light and affects the
expression of other genes?
Microarray gene expression
GG-PP
phytoene
lycopene
CrtB1
beta-carotene
retinal
CrtY
brp
bop
bacteriorhodopsin
(bR)
bat
To simplify, focus on the genes and gene products (proteins).
Then we’ll see how these affect the metabolites and
bacteriorhodopsin (bR).
CrtB1
CrtY
brp
bop
bat
To simplify, focus on the genes and gene products (proteins).
Then we’ll see how these affect the metabolites and
bacteriorhodopsin (bR).
CrtB1
CrtY
brp
bop
bat
Question:
Which genes does bat affect?
CrtB1
CrtY
brp
bop
bat
Question:
What happens to the expression of the genes when bat is
overexpressed?
CrtB1
CrtY
brp
bop
bat
Question:
What happens to the expression of the genes when bat is
overexpressed?
CrtB1
CrtY
brp
bop
bat
Question:
What happens to the expression of the genes when bat is
knocked out?
CrtB1
CrtY
brp
bop
bat
Question:
What happens to the expression of the genes when bat is
knocked out?
CrtY
CrtB1
brp
bop
bat
Question:
What happens to the expression of the genes when bat is
knocked out?
CrtY
CrtB1
brp
bop
bat
Knocked out bat
CrtB1
CrtY
brp
bop
bat
Overexpressed bat
GG-PP
phytoene
lycopene
CrtB1
beta-carotene
retinal
CrtY
brp
bop
bacteriorhodopsin
(bR)
bat
Question:
Bat affects the amount of proteins in the bR network. How does
this affect the amount of bacteriorhodopsin produced?
phytoene
GG-PP
lycopene
beta-carotene
retinal
CrtY
CrtB1
brp
bop
bacteriorhodopsin
(bR)
bat
Knocked out bat
GG-PP
phytoene
lycopene
CrtB1
beta-carotene
CrtY
retinal
brp
bop
bacteriorhodopsin
(bR)
bat
Overexpressed bat
phytoene
GG-PP
lycopene
beta-carotene
retinal
CrtY
CrtB1
brp
bop
Knocked out bat
bacteriorhodopsin
(bR)
bat
GG-PP
phytoene
lycopene
CrtB1
beta-carotene
CrtY
Overexpressed bat
retinal
brp
bop
bacteriorhodopsin
(bR)
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?
Our hypothesis – Light Present
GG-PP
phytoene
lycopene
CrtB1
beta-carotene
retinal
CrtY
brp
bop
bacteriorhodopsin
(bR)
bat
LIGHT
ADP + P
ATP
only when light is present
Our hypothesis – Light Absent
GG-PP
phytoene
lycopene
CrtB1
beta-carotene
retinal
CrtY
brp
bop
bacteriorhodopsin
(bR)
bat
LIGHT
ADP + P
ATP
only when light is present
Known Network – bR Production
GG-PP
phytoene
lycopene
CrtB1
beta-carotene
retinal
CrtY
+
brp
bop
+
+
bacteriorhodopsin
(bR)
bat
LIGHT
ADP + P
ATP
only when light is present
Where do the other energy pathways fit (e.g. fermentation)?
GG-PP
phytoene
lycopene
beta-carotene
CrtB1
Arginine
retinal
CrtY
brp
YhdG
bop
Arginine
(outside of cell)
(inside cell)
bat
bacteriorhodopsin
(bR)
LIGHT
ADP + P
ATP
only when light is present
ArgH
L-arginosuccinate
ArgG
arginine
ArcA
ornithine
carbamate
CO
2
ArcB
ArcC
citrulline
carbamoyl-PO4
ADP + P
ATP
NH3
CrtB1
CrtY
brp
[+]
[+]
YhdG
bop
[-]
[+]
bat
[-]
[-]
[-]
[-]
[-]
ArgH
ArcA
ArgG
ArcB
ArcC
GG-PP
phytoene
lycopene
beta-carotene
CrtB1
Arginine
retinal
CrtY
brp
YhdG
bop
Arginine
(outside of cell)
(inside cell)
bat
bacteriorhodopsin
(bR)
LIGHT
ADP + P
ArgH
L-arginosuccinate
ArgG
arginine
ArcA
ornithine
carbamate
ATP
CO
2
ArcB
ArcC
citrulline
carbamoyl-PO4
ADP + P
ATP
NH3
GG-PP
phytoene
lycopene
beta-carotene
CrtB1
Arginine
brp
CrtY
YhdG
bop
Arginine
(outside of cell)
retinal
(inside cell)
bat
bacteriorhodopsin
(bR)
LIGHT
ADP + P
ATP
ArgH
L-arginosuccinate
arginine
ArcA
ornithine
carbamate
ArcB
ATP
ArcC
ArgG
CO
2
citrulline
carbamoyl-PO4
ADP + P
NH3
phytoene
GG-PP
lycopene
beta-carotene
CrtY
CrtB1
Arginine
retinal
brp
YhdG
bop
Arginine
(outside of cell)
(inside cell)
bat
bacteriorhodopsin
(bR)
LIGHT
ADP + P
ArgH
L-arginosuccinate
ArgG
arginine
ArcA
ornithine
carbamate
ATP
CO
2
ArcB
ArcC
citrulline
carbamoyl-PO4
ADP + P
ATP
NH3
GG-PP
phytoene
lycopene
beta-carotene
CrtB1
Arginine
brp
CrtY
YhdG
bop
Arginine
(outside of cell)
retinal
(inside cell)
bat
bacteriorhodopsin
(bR)
LIGHT
ADP + P
ATP
ArgH
L-arginosuccinate
arginine
ArcA
ornithine
carbamate
ArcB
ATP
ArcC
ArgG
CO
2
citrulline
carbamoyl-PO4
ADP + P
NH3
phytoene
GG-PP
lycopene
beta-carotene
CrtY
CrtB1
Arginine
retinal
brp
YhdG
bop
Arginine
(outside of cell)
(inside cell)
bat
bacteriorhodopsin
(bR)
LIGHT
ADP + P
ArgH
L-arginosuccinate
ArgG
arginine
ArcA
ornithine
carbamate
ATP
CO
2
ArcB
ArcC
citrulline
carbamoyl-PO4
ADP + P
ATP
NH3
GG-PP
phytoene
lycopene
beta-carotene
CrtB1
Arginine
brp
CrtY
YhdG
bop
Arginine
(outside of cell)
retinal
(inside cell)
bat
bacteriorhodopsin
(bR)
LIGHT
ADP + P
ATP
ArgH
L-arginosuccinate
arginine
ArcA
ornithine
carbamate
ArcB
ATP
ArcC
ArgG
CO
2
citrulline
carbamoyl-PO4
ADP + P
NH3
phytoene
GG-PP
lycopene
beta-carotene
CrtY
CrtB1
Arginine
retinal
brp
YhdG
bop
Arginine
(outside of cell)
(inside cell)
bat
bacteriorhodopsin
(bR)
LIGHT
ADP + P
ArgH
L-arginosuccinate
ArgG
arginine
ArcA
ornithine
carbamate
ATP
CO
2
ArcB
ArcC
citrulline
carbamoyl-PO4
ADP + P
ATP
NH3
GG-PP
phytoene
lycopene
beta-carotene
CrtB1
Arginine
brp
CrtY
YhdG
bop
Arginine
(outside of cell)
retinal
(inside cell)
bat
bacteriorhodopsin
(bR)
LIGHT
ADP + P
ATP
ArgH
L-arginosuccinate
arginine
ArcA
ornithine
carbamate
ArcB
ATP
ArcC
ArgG
CO
2
citrulline
carbamoyl-PO4
ADP + P
NH3
phytoene
GG-PP
lycopene
beta-carotene
CrtY
CrtB1
Arginine
retinal
brp
YhdG
bop
Arginine
(outside of cell)
(inside cell)
bat
bacteriorhodopsin
(bR)
LIGHT
ADP + P
ArgH
L-arginosuccinate
ArgG
arginine
ArcA
ornithine
carbamate
ATP
CO
2
ArcB
ArcC
citrulline
carbamoyl-PO4
ADP + P
ATP
NH3
GG-PP
phytoene
lycopene
beta-carotene
CrtB1
Arginine
brp
CrtY
YhdG
bop
Arginine
(outside of cell)
retinal
(inside cell)
bat
bacteriorhodopsin
(bR)
LIGHT
ADP + P
ATP
ArgH
L-arginosuccinate
arginine
ArcA
ornithine
carbamate
ArcB
ATP
ArcC
ArgG
CO
2
citrulline
carbamoyl-PO4
ADP + P
NH3
phytoene
GG-PP
lycopene
beta-carotene
CrtY
CrtB1
Arginine
retinal
brp
YhdG
bop
Arginine
(outside of cell)
(inside cell)
bat
bacteriorhodopsin
(bR)
LIGHT
ADP + P
ArgH
L-arginosuccinate
ArgG
arginine
ArcA
ornithine
carbamate
ATP
CO
2
ArcB
ArcC
citrulline
carbamoyl-PO4
ADP + P
ATP
NH3
GG-PP
phytoene
lycopene
beta-carotene
CrtB1
Arginine
brp
CrtY
YhdG
bop
Arginine
(outside of cell)
retinal
(inside cell)
bat
bacteriorhodopsin
(bR)
LIGHT
ADP + P
ATP
ArgH
L-arginosuccinate
arginine
ArcA
ornithine
carbamate
ArcB
ATP
ArcC
ArgG
CO
2
citrulline
carbamoyl-PO4
ADP + P
NH3
phytoene
GG-PP
lycopene
beta-carotene
CrtY
CrtB1
Arginine
retinal
brp
YhdG
bop
Arginine
(outside of cell)
(inside cell)
bat
bacteriorhodopsin
(bR)
LIGHT
ADP + P
ArgH
L-arginosuccinate
ArgG
arginine
ArcA
ornithine
carbamate
ATP
CO
2
ArcB
ArcC
citrulline
carbamoyl-PO4
ADP + P
ATP
NH3
GG-PP
phytoene
lycopene
beta-carotene
CrtB1
Arginine
brp
CrtY
YhdG
bop
Arginine
(outside of cell)
retinal
(inside cell)
bat
bacteriorhodopsin
(bR)
LIGHT
ADP + P
ATP
ArgH
L-arginosuccinate
arginine
ArcA
ornithine
carbamate
ArcB
ATP
ArcC
ArgG
CO
2
citrulline
carbamoyl-PO4
ADP + P
NH3
phytoene
GG-PP
lycopene
beta-carotene
CrtY
CrtB1
Arginine
retinal
brp
YhdG
bop
Arginine
(outside of cell)
(inside cell)
bat
bacteriorhodopsin
(bR)
LIGHT
ADP + P
ArgH
L-arginosuccinate
ArgG
arginine
ArcA
ornithine
carbamate
ATP
CO
2
ArcB
ArcC
citrulline
carbamoyl-PO4
ADP + P
ATP
NH3
GG-PP
phytoene
lycopene
beta-carotene
CrtB1
Arginine
brp
CrtY
YhdG
bop
Arginine
(outside of cell)
retinal
(inside cell)
bat
bacteriorhodopsin
(bR)
LIGHT
ADP + P
ATP
ArgH
L-arginosuccinate
arginine
ArcA
ornithine
carbamate
ArcB
ATP
ArcC
ArgG
CO
2
citrulline
carbamoyl-PO4
ADP + P
NH3
phytoene
GG-PP
lycopene
beta-carotene
CrtY
CrtB1
Arginine
retinal
brp
YhdG
bop
Arginine
(outside of cell)
(inside cell)
bat
bacteriorhodopsin
(bR)
LIGHT
ADP + P
ArgH
L-arginosuccinate
ArgG
arginine
ArcA
ornithine
carbamate
ATP
CO
2
ArcB
ArcC
citrulline
carbamoyl-PO4
ADP + P
ATP
NH3
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?