Using systems biology to learn how halo respond to their environment

1
Using systems biology to learn how halo respond
to their environment
2
bR converts light energy into chemical energy for
making ATP
LIGHT
Halobacterium cell
ATP
ATP
ATP
ATP
ATP
Bacteriorhodopsin (bR)
Note other proteins are required for this
process, but we will simplify and focus on bR
3
Bacteriorhodopsin (bR) is made from a protein
called bop and the molecule retinal
Bop retinal bacteriorhodopsin (bR)
Cell membRane
Bacteriorhodopsin (bR)
Bop protein
4
Halo change the expression of bR in response to
the amount of light in their environment
LIGHT PRESENT
LIGHT ABSENT (DARK)
LIGHT
LIGHT
When there is more light, halo respond by making
more bR
When there is less light, halo make less bR
5
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.

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.
6
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?

7
Metabolic data group
8
GG-PP
lycopene
beta-carotene
retinal
phytoene
bop
bacteriorhodopsin (bR)
9
GG-PP
lycopene
beta-carotene
retinal
phytoene
bop
bacteriorhodopsin (bR)
Question How would increasing the amount of
GG-PP affect the amount of bacteriorhodopsin (bR)?
10
GG-PP
lycopene
beta-carotene
retinal
phytoene
bop
bacteriorhodopsin (bR)
Question How would increasing the amount of
GG-PP affect the amount of bacteriorhodopsin (bR)?
11
GG-PP
lycopene
beta-carotene
retinal
phytoene
bop
bacteriorhodopsin (bR)
Question If the enzyme that converts phyotene to
lycopene were missing, how would the amount of
bacteriorhodopsin (bR) be affected?
12
GG-PP
lycopene
beta-carotene
retinal
phytoene
bop
bacteriorhodopsin (bR)
Question If the enzyme that converts phyotene to
lycopene were missing, how would the amount of
bacteriorhodopsin (bR) be affected?
13
Homology
14
GG-PP
lycopene
beta-carotene
retinal
phytoene
CrtY
CrtB1
brp
bop
bacteriorhodopsin (bR)
bat
Question Which enzymes are part of the
bacteriorhodopsin network? What other genes are
involved in the system?
15
GG-PP
lycopene
beta-carotene
retinal
phytoene
CrtY
CrtB1
brp
bop
bacteriorhodopsin (bR)
bat
LIGHT
Question Which protein changes in response to
light and affects the expression of other genes?
16
Microarray gene expression
17
GG-PP
lycopene
beta-carotene
retinal
phytoene
CrtY
CrtB1
brp
bop
bacteriorhodopsin (bR)
bat
To simplify, focus on the genes and gene products
(proteins). Then well see how these affect the
metabolites and bacteriorhodopsin (bR).
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CrtY
CrtB1
brp
bop
bat
To simplify, focus on the genes and gene products
(proteins). Then well see how these affect the
metabolites and bacteriorhodopsin (bR).
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CrtY
CrtB1
brp
bop
bat
Question Which genes does bat affect?
20
CrtY
CrtB1
brp
bop
bat
Question What happens to the expression of the
genes when bat is overexpressed?
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CrtY
CrtB1
brp
bop
bat
Question What happens to the expression of the
genes when bat is overexpressed?
22
CrtY
CrtB1
brp
bop
bat
Question What happens to the expression of the
genes when bat is knocked out?
23
CrtY
CrtB1
brp
bop
bat
Question What happens to the expression of the
genes when bat is knocked out?
24
CrtY
CrtB1
brp
bop
bat
Question What happens to the expression of the
genes when bat is knocked out?
25
CrtY
CrtB1
brp
bop
bat
Knocked out bat
26
CrtB1
brp
CrtY
bop
bat
Overexpressed bat
27
GG-PP
lycopene
beta-carotene
retinal
phytoene
CrtY
CrtB1
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?
28
GG-PP
lycopene
beta-carotene
retinal
phytoene
CrtY
CrtB1
brp
bop
bacteriorhodopsin (bR)
bat
Knocked out bat
29
GG-PP
lycopene
beta-carotene
retinal
phytoene
CrtB1
brp
CrtY
bop
bacteriorhodopsin (bR)
bat
Overexpressed bat
30
GG-PP
lycopene
beta-carotene
retinal
phytoene
CrtY
CrtB1
brp
bop
Knocked out bat
bacteriorhodopsin (bR)
bat
lycopene
beta-carotene
retinal
GG-PP
phytoene
CrtB1
brp
CrtY
Overexpressed bat
bop
bacteriorhodopsin (bR)
bat
31
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?

32
Our hypothesis Light Present
lycopene
beta-carotene
retinal
GG-PP
phytoene
CrtY
CrtB1
brp
bop
bacteriorhodopsin (bR)
bat
LIGHT
ATP
ADP P
only when light is present
33
Our hypothesis Light Absent
lycopene
beta-carotene
retinal
GG-PP
phytoene
CrtY
CrtB1
brp
bop
bacteriorhodopsin (bR)
bat
LIGHT
ATP
ADP P
only when light is present
34
Known Network bR Production
lycopene
beta-carotene
retinal
GG-PP
phytoene
CrtY
CrtB1
brp
bop



bacteriorhodopsin (bR)
bat
LIGHT
ATP
ADP P
only when light is present
Where do the other energy pathways fit (e.g.
fermentation)?
35
lycopene
beta-carotene
retinal
GG-PP
phytoene
CrtY
CrtB1
brp
YhdG
bop
Arginine (outside of cell)
Arginine (inside cell)
bat
bacteriorhodopsin (bR)
LIGHT
ATP
ADP P
only when light is present
arginine
ornithine
ArgH
carbamate
CO2
L-arginosuccinate
ArcA
ArcB
ATP
NH3
ArcC
ArgG
citrulline
carbamoyl-PO4
ADP P
36
CrtY
CrtB1
brp


YhdG
bop
-

bat
-
-
-
-
-
ArgH
ArcA
ArcB
ArcC
ArgG
37
lycopene
beta-carotene
retinal
GG-PP
phytoene
CrtY
CrtB1
brp
YhdG
bop
Arginine (outside of cell)
Arginine (inside cell)
bat
bacteriorhodopsin (bR)
LIGHT
ATP
ADP P
arginine
ornithine
ArgH
carbamate
CO2
L-arginosuccinate
ArcA
ArcB
ATP
NH3
ArcC
ArgG
citrulline
carbamoyl-PO4
ADP P
38
lycopene
beta-carotene
retinal
GG-PP
phytoene
CrtB1
brp
CrtY
YhdG
bop
Arginine (outside of cell)
Arginine (inside cell)
bat
bacteriorhodopsin (bR)
LIGHT
ATP
ADP P
arginine
ornithine
ArgH
carbamate
CO2
L-arginosuccinate
ArcA
ArcB
ATP
NH3
ArcC
ArgG
citrulline
carbamoyl-PO4
ADP P
39
lycopene
beta-carotene
retinal
GG-PP
phytoene
CrtY
CrtB1
brp
YhdG
bop
Arginine (outside of cell)
Arginine (inside cell)
bat
bacteriorhodopsin (bR)
LIGHT
ATP
ADP P
arginine
ornithine
ArgH
carbamate
CO2
L-arginosuccinate
ArcA
ArcB
ATP
NH3
ArcC
ArgG
citrulline
carbamoyl-PO4
ADP P
40
lycopene
beta-carotene
retinal
GG-PP
phytoene
CrtB1
brp
CrtY
YhdG
bop
Arginine (outside of cell)
Arginine (inside cell)
bat
bacteriorhodopsin (bR)
LIGHT
ATP
ADP P
arginine
ornithine
ArgH
carbamate
CO2
L-arginosuccinate
ArcA
ArcB
ATP
NH3
ArcC
ArgG
citrulline
carbamoyl-PO4
ADP P
41
lycopene
beta-carotene
retinal
GG-PP
phytoene
CrtY
CrtB1
brp
YhdG
bop
Arginine (outside of cell)
Arginine (inside cell)
bat
bacteriorhodopsin (bR)
LIGHT
ATP
ADP P
arginine
ornithine
ArgH
carbamate
CO2
L-arginosuccinate
ArcA
ArcB
ATP
NH3
ArcC
ArgG
citrulline
carbamoyl-PO4
ADP P
42
lycopene
beta-carotene
retinal
GG-PP
phytoene
CrtB1
brp
CrtY
YhdG
bop
Arginine (outside of cell)
Arginine (inside cell)
bat
bacteriorhodopsin (bR)
LIGHT
ATP
ADP P
arginine
ornithine
ArgH
carbamate
CO2
L-arginosuccinate
ArcA
ArcB
ATP
NH3
ArcC
ArgG
citrulline
carbamoyl-PO4
ADP P
43
lycopene
beta-carotene
retinal
GG-PP
phytoene
CrtY
CrtB1
brp
YhdG
bop
Arginine (outside of cell)
Arginine (inside cell)
bat
bacteriorhodopsin (bR)
LIGHT
ATP
ADP P
arginine
ornithine
ArgH
carbamate
CO2
L-arginosuccinate
ArcA
ArcB
ATP
NH3
ArcC
ArgG
citrulline
carbamoyl-PO4
ADP P
44
lycopene
beta-carotene
retinal
GG-PP
phytoene
CrtB1
brp
CrtY
YhdG
bop
Arginine (outside of cell)
Arginine (inside cell)
bat
bacteriorhodopsin (bR)
LIGHT
ATP
ADP P
arginine
ornithine
ArgH
carbamate
CO2
L-arginosuccinate
ArcA
ArcB
ATP
NH3
ArcC
ArgG
citrulline
carbamoyl-PO4
ADP P
45
lycopene
beta-carotene
retinal
GG-PP
phytoene
CrtY
CrtB1
brp
YhdG
bop
Arginine (outside of cell)
Arginine (inside cell)
bat
bacteriorhodopsin (bR)
LIGHT
ATP
ADP P
arginine
ornithine
ArgH
carbamate
CO2
L-arginosuccinate
ArcA
ArcB
ATP
NH3
ArcC
ArgG
citrulline
carbamoyl-PO4
ADP P
46
lycopene
beta-carotene
retinal
GG-PP
phytoene
CrtB1
brp
CrtY
YhdG
bop
Arginine (outside of cell)
Arginine (inside cell)
bat
bacteriorhodopsin (bR)
LIGHT
ATP
ADP P
arginine
ornithine
ArgH
carbamate
CO2
L-arginosuccinate
ArcA
ArcB
ATP
NH3
ArcC
ArgG
citrulline
carbamoyl-PO4
ADP P
47
lycopene
beta-carotene
retinal
GG-PP
phytoene
CrtY
CrtB1
brp
YhdG
bop
Arginine (outside of cell)
Arginine (inside cell)
bat
bacteriorhodopsin (bR)
LIGHT
ATP
ADP P
arginine
ornithine
ArgH
carbamate
CO2
L-arginosuccinate
ArcA
ArcB
ATP
NH3
ArcC
ArgG
citrulline
carbamoyl-PO4
ADP P
48
lycopene
beta-carotene
retinal
GG-PP
phytoene
CrtB1
brp
CrtY
YhdG
bop
Arginine (outside of cell)
Arginine (inside cell)
bat
bacteriorhodopsin (bR)
LIGHT
ATP
ADP P
arginine
ornithine
ArgH
carbamate
CO2
L-arginosuccinate
ArcA
ArcB
ATP
NH3
ArcC
ArgG
citrulline
carbamoyl-PO4
ADP P
49
lycopene
beta-carotene
retinal
GG-PP
phytoene
CrtY
CrtB1
brp
YhdG
bop
Arginine (outside of cell)
Arginine (inside cell)
bat
bacteriorhodopsin (bR)
LIGHT
ATP
ADP P
arginine
ornithine
ArgH
carbamate
CO2
L-arginosuccinate
ArcA
ArcB
ATP
NH3
ArcC
ArgG
citrulline
carbamoyl-PO4
ADP P
50
lycopene
beta-carotene
retinal
GG-PP
phytoene
CrtB1
brp
CrtY
YhdG
bop
Arginine (outside of cell)
Arginine (inside cell)
bat
bacteriorhodopsin (bR)
LIGHT
ATP
ADP P
arginine
ornithine
ArgH
carbamate
CO2
L-arginosuccinate
ArcA
ArcB
ATP
NH3
ArcC
ArgG
citrulline
carbamoyl-PO4
ADP P
51
lycopene
beta-carotene
retinal
GG-PP
phytoene
CrtY
CrtB1
brp
YhdG
bop
Arginine (outside of cell)
Arginine (inside cell)
bat
bacteriorhodopsin (bR)
LIGHT
ATP
ADP P
arginine
ornithine
ArgH
carbamate
CO2
L-arginosuccinate
ArcA
ArcB
ATP
NH3
ArcC
ArgG
citrulline
carbamoyl-PO4
ADP P
52
lycopene
beta-carotene
retinal
GG-PP
phytoene
CrtB1
brp
CrtY
YhdG
bop
Arginine (outside of cell)
Arginine (inside cell)
bat
bacteriorhodopsin (bR)
LIGHT
ATP
ADP P
arginine
ornithine
ArgH
carbamate
CO2
L-arginosuccinate
ArcA
ArcB
ATP
NH3
ArcC
ArgG
citrulline
carbamoyl-PO4
ADP P
53
lycopene
beta-carotene
retinal
GG-PP
phytoene
CrtY
CrtB1
brp
YhdG
bop
Arginine (outside of cell)
Arginine (inside cell)
bat
bacteriorhodopsin (bR)
LIGHT
ATP
ADP P
arginine
ornithine
ArgH
carbamate
CO2
L-arginosuccinate
ArcA
ArcB
ATP
NH3
ArcC
ArgG
citrulline
carbamoyl-PO4
ADP P
54
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?

55
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?