Protein Acetylation

Question 1

Histone acetyltransferases (HATs) transfer the acetyl moiety from acetyl-CoA to the ε-amino group of a lysine residue on a substrate protein
TRUE

Answer 1

TRUE

Question 2

Writers, erasers, and readers for acetylation:

Answer 2

Writers:
Histone acetyl transferases (HATs)

Erasers:
Classical histone deacetylases (HDACs)
Sirtuins (NAD+-dependent)

Readers:
Bromodomains bind onto acetyl-lysine-containing proteins (in nucleus).

Question 3

3 Major classes of eukaryotic HATs:

Answer 3

1. GNAT (Gcn5-related N-acetyltransferases)
2. MYST
3. Others e.g. (CBP/p300)

Question 4

What determines which lysines are acetylated by any given HAT?

Answer 4

1. Docking domains in the HAT
   - HATs containing bromodomains dock onto specific acetyl-lysine residues. HATs containing chromodomains dock onto specific methylated lysines which means that the HAT can acetylate another nearby lysine residue (in cis or trans, where cis means in the same protein as the docking acetyl-lysine, and trans means that a lysine in another associated protein becomes acetylated)
2. Most HATs exist within multisubunit complexes in vivo,
   many of which are transcriptional coactivator complexes. Affects the HATs in 3 ways:
   - Targeting/localisation
   - Substrate specificity
   - Regulation of HAT activity

Question 5

The major classes of eukaryotic HDACs:

Answer 5

Class I: (HDACs 1,2,3, and 8)
Class II: (HDACs 4, 5, 6, 7, 9, and 10)
Class III: (Sirtuins, SIRT 1-7)
Class IV: (HDAC 11)

Question 6

Sirtuins:

Answer 6

Class III HDACs
Originally identified as Sir2 (silencing information regulator)
Their HDAC activity couples histone deacetylation to cleavage of a high-energy bond in nicotimamide adenine dinucleotide (NAD+) to generate O-acetyl-ADP-ribose and nicotinamide
Nicotinamide inhibits SIRTs linking the NAD+ salvage pathway to regulation of SIRT activity
SIRTs regulate aging, fat metabolism and cell proliferation

Question 7

How does histone acetylation make DNA accessible?

Answer 7

1. Decreases interactions of histones with DNA –CONTROVERSIAL. +ve charge of K neutralised by acetylation and prevents binding of histones to DNA and chromatin compaction (H4K16ac prevents 30 nm fibre formation)
2. Recruits chromatin proteins with bromodomains
3. Prevents methylation of same lysine residues (competitive antagonism). Lysines can be methylated once, twice or three times by methyltransferases. Depending on residue and number of methyl groups, methylation can be associated with repression or activation of transcription.

Question 8

HDACs are often in transcriptional coactivator complexes

TRUE OR FALSE

Answer 8

FALSE

HDACs are often in transcriptional COREPRESSOR complexes.

Question 9

HATs are often in transcriptional corepressor complexes

TRUE OR FALSE

Answer 9

FALSE

HATs are often in transcriptional COACTIVATOR complexes.

Question 10

HATs roles as transcriptional coactivators:

Answer 10

In response to signalling pathways, certain DNA-binding transcription factors (TFs) can bind to coactivator complexes containing acetyltransferases (such as CDP/p300 and PCAF) and recruit them to specific recognition sequences in DNA (enhancers etc). The coactivator is unable to bind to DNA by itself.

The HAT within the coactivator complex acetylates specific lysine residues in core histones.

The DNA is made accessible to RNA polymerase II and other proteins that promote gene transcription.

Question 11

The histone code:

Answer 11

Different combinations of histone modifications affect chromatin structure in different ways.

Histone modifications are interdependent: Histone modifications influence one another by steric hindrance or by creating PTMs such as Ac-Lys and Me-Lys that act as docking sites for bromodomain and chromodomain proteins, respectively.

Histones can be combinatorially modified to elicit a specific nuclear response. (e.g. H3K4 methylation and H3K9 acetylation are hallmarks of active chromatin)

Question 12

Acetylation sites are conserved across vertebrate species.

TRUE OR FALSE

Answer 12

TRUE

Question 13

Acetylation regulates the amount of metabolic enzymes (Give example)

Answer 13

Acetylation can regulate the steady-state levels of metabolic enzymes by promoting their degradation through either the ubiquitin–proteasomal system in the case of phosphoenolpyruvate carboxykinase (PCK1; A) or CMA in the case of PK M2 isoform (PKM2; B). Metabolic enzymes and acetylated lysine residues (K) are colored in light green and purple, respectively. Active sites are indicated by three red radial dashes.