Using systems biology to learn how halo respond to their environment

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) Note: other proteins are required for this process, but we will simplify and focus on bR

Retinal Bacteriorhodopsin (bR) is made from a protein called bop and the molecule retinal Bop + retinal = bacteriorhodopsin (bR) Cell membRane Bacteriorhodopsin (bR) Bop protein

Halobacterium cell Halobacterium cell 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

Light 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. + 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: If the enzyme that converts phyotene to lycopene were missing, how would the amount of bacteriorhodopsin (bR) be affected?

Homology

GG-PP phytoene lycopene beta-carotene retinal CrtB1 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 beta-carotene retinal CrtB1 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 beta-carotene retinal CrtB1 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 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 brp CrtY bop bat Overexpressed bat

GG-PP phytoene lycopene beta-carotene retinal CrtB1 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?

GG-PP phytoene lycopene beta-carotene retinal CrtY CrtB1 brp bop bacteriorhodopsin (bR) bat Knocked out bat

GG-PP phytoene lycopene beta-carotene retinal CrtB1 brp CrtY bop bacteriorhodopsin (bR) bat Overexpressed bat

GG-PP phytoene lycopene beta-carotene retinal CrtY CrtB1 brp bop Knocked out bat bacteriorhodopsin (bR) bat GG-PP phytoene lycopene beta-carotene retinal CrtB1 brp CrtY Overexpressed bat 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 beta-carotene retinal CrtB1 CrtY brp bop bacteriorhodopsin (bR) bat LIGHT ATP ADP + P only when light is present

Our hypothesis – Light Absent GG-PP phytoene lycopene beta-carotene retinal CrtB1 CrtY brp bop bacteriorhodopsin (bR) bat LIGHT ATP ADP + P only when light is present

Known Network – bR Production GG-PP phytoene lycopene beta-carotene retinal CrtB1 CrtY brp + bop + + bacteriorhodopsin (bR) bat LIGHT ATP ADP + P only when light is present Where do the other energy pathways fit (e.g. fermentation)?

GG-PP phytoene lycopene beta-carotene retinal CrtB1 CrtY 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

CrtB1 CrtY brp [+] [+] YhdG bop [-] [+] bat [-] [-] [-] [-] [-] ArgH ArcA ArcB ArcC ArgG

GG-PP phytoene lycopene beta-carotene retinal CrtB1 CrtY 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

GG-PP phytoene lycopene beta-carotene retinal 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

GG-PP phytoene lycopene beta-carotene retinal 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

Using systems biology to learn how halo respond to their environment