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?