Genome-scale network model of metabolism and histone acetylation reveals metabolic dependencies of histone deacetylase inhibitors

Table 1 Functional significance of the 24 metabolic genes predicted by the model to impact acetylation

Gene	Gene description	1. Acetylated?	2. Interacts with acetylase?	3. Interacts with deacetylase?	4. Sirtuin target?
AASS	Aminoadipate-semialdehyde synthase	X
ACLY	ATP citrate lyase	X	X	X
ACO2	Aconitase 2, mitochondrial	X	X	X
ALDH1L1	Aldehyde dehydrogenase 1 family, member L1	X
CS	Citrate synthase	X	X	X
FAH	Fumarylacetoacetate hydrolase (fumarylacetoacetase)	X
FH	Fumarate hydratase	X	X	X
GOT1	Glutamic-oxaloacetic transaminase 1, soluble (aspartate aminotransferase 1)	X
GSTZ1	Glutathione transferase zeta 1	X
HGD	Homogentisate 1,2-dioxygenase	X
HPD	4-Hydroxyphenylpyruvate dioxygenase
IDH2	Isocitrate dehydrogenase 2 (NADP+), mitochondrial	X		X	X
PC	Pyruvate carboxylase	X	X
OAT	Ornithine aminotransferase	X	X	X
RBKS	Ribokinase
RPE	Ribulose-5-phosphate-3-epimerase
SDHA	Succinate dehydrogenase complex, subunit A, flavoprotein	X	X	X	X
SDHB	Succinate dehydrogenase complex, subunit B, iron sulfur (Ip)		X	X	X
SDHC	Succinate dehydrogenase complex, subunit C				X
SDHD	Succinate dehydrogenase complex, subunit D				X
SHMT1	Serine hydroxymethyltransferase 1 (soluble)	X	X
SLC25A1	Solute carrier family 25 (mitochondrial carrier; citrate transporter)	X	X	X
SUOX	Sulfite oxidase	X
TALDO1	Transaldolase 1	X	X

Column 1 shows acetylation status based on protein acetylation database. Column 2 shows proteins that are found to physically interact with an acetylase. Column 3 shows proteins that are found to physically interact with a deacetylase enzyme. Column 4 shows predicted targets of sirtuins, a major class of deacetylases (X mark implies true)

ISSN: 1474-760X