Acetylation of the DNA-scaffolding-proteins histones and ubiquitination of cell
ID: 101790 • Letter: A
Question
Acetylation of the DNA-scaffolding-proteins histones and ubiquitination of cell cycle regulation proteins cyclins represent two examples of posttranslational covalent modifications. Compare the biochemistry of these modifications to phosphorylation and dephosphorylation. Your answer should mention the specific donor molecules that provide the functional entity, the enzymes (general class/category) catalyzing the modification, bio-chemical effect of the modification on the modified protein, and the regulatory implications and biological significance of the modifications.Explanation / Answer
Histone acetylation occurs by the enzymatic addition of an acetyl group (COCH3) from acetyl coenzyme A. The process of histone acetylation is tightly involved in the regulation of many cellular processes including chromatin dynamics and transcription, gene silencing, cell cycle progression, apoptosis, differentiation, DNA replication, DNA repair, nuclear import, and neuronal repression. The modifying enzymes involved in histone acetylation are called histone acetyltransferases (HATs) and they play a critical role in controlling histone H3 and H4 acetylation. More than 20 HATs have been identified which can be classified into five families: GNAT1, MYST, TAFII250, P300/CBP, and nuclear receptor coactivators such as ACTR. Histone H3 acetylation may be increased by inhibition of histone deacetylases (HDACs) and decreased by HAT inhibition.
The mechanism for acetylation and deacetylation takes place on the NH3+ groups of Lysine amino acid residues. These residues are located on the tails of histones that make up the nucleosome of packaged dsDNA. The process is aided by factors known as Histone Acetyltransferases (HATs). HAT molecules facilitate the transfer of an acetyl group from a molecule of Acetyl Coenzyme-A (Acetyl-CoA) to the NH3+ group on Lysine. When a Lysine is deacetylated, factors known as Histone Deacetylases (HDACs) catalyze the removal of the acetyl group with a molecule of H2O.Acetylation has the effect of changing the overall charge of the histone tail from positive to neutral. Nucleosome formation is dependent on the positive charges of the H4 histones and the negative charge on the surface of H2A histone fold domains. Acetylation of the histone tails disrupts this association, leading to weaker binding of the nucleosomal components.
During ubiquitination, a covalent isopeptide bond is formed between the carboxy-terminus (C-terminus) of ubiquitin and a nucleophilic side chain in the substrate protein. In the vast majority of cases, ubiquitin is linked to the -amino group of lysine residues, but modifications also occur at the amino-terminus, the hydroxyl-group of serine residues, or the thiol-group of cysteine residues.
In order to allow the transfer of ubiquitin to its acceptor, it is first activated by a ubiquitin-activating enzyme, E1 . E1 uses ATP to form a phosphodiester bond between the C-terminus of ubiquitin and AMP, before the ubiquitin is transferred to the active-site cysteine of E1 by thioester formation. At least two human E1 enzymes activate ubiquitin but in most cases, this reaction is carried out by the product of the essential UBE1 gene. In dividing cells, the Ube1 protein localizes to hotspots of cell cycle control, such as the cytoskeleton, the mitotic spindle, or the spindle midzon. Cell lines carrying thermosensitive mutations in UBE1 suffer from cell cycle arrest, and in fact provided early evidence that ubiquitination is crucial for cell cycle control.
The charging with ubiquitin triggers conformational changes in E1 that expose a binding site for the recruitment of one of human ubiquitin conjugating enzymes, or E2s. E2s receive the activated ubiquitin on an active-site cysteine by trans-esterification. Most E2s are single domain proteins, some of which have short extensions at the N- or C-terminus. Several of these E2s, including Ubc13, Cdc34, or UbcH10, have central functions in cell cycle control. In few cases, E2 domains are found in large multifunctional proteins, one of which, localizes to the spindle midzone and functions during the abscission stage of cytokinesis.
Ubiquitin-dependent proteolysis ensures the regulated and unidirectional progression through the cell cycle;and proteolysis orchestrate the function of cell cycle checkpoints;and ubiquitination and endocytosis coordinate proliferation with development.
Phosphorylation refers to an addition of a phosphate group to a phosphate-accepting amino acid, such as Serine and Tyrosine. Aphosphate group added onto a molecule (usually a protein that is an enzyme) activates it or, in some cases, deactivates it. When this phosphate group “falls off,” or is removed, once the protein has performed its function and needs to be deactivated (in the case of phosphorylation-based activation). This is referred to as dephosphorylation.
Many molecules are energy donors that serve to supply the phosphate group; these include Adenosine Triphosphate (ATP, also famous in photosynthesis) and guanosine triphosphate (GTP). Phosphorylation prepares molecules for the tasks they need to perform. This phosphate sticks around as long as the protein needs it and then is lost or dropped. There are different types of phosphorylation.
Kinases, which aid in the transfer of phosphate to another molecule, belong to a group of enzymes called phosphotransferases. (Itis very importantnot to confuse phosphotransferases with another group of enzymes called phosphorylases.)Phosphotransferasesaid in the addition of the phosphate from an inorganic phosphate to the acceptor (for example, glycogen to make glucose-1-PO4). Phosphatase removes the phosphate from the molecule that receivedit with the aid of the kinase. So, in short, the kinase giveth what the phosphatase take away.
If the targeted protein is an enzyme, phosphorylation and dephosphorylation can impact its enzymatic activity, essentially acting like a switch, turning it on and off in a regulated manner.
Another outcome of structural changes to the phosphorylated protein is the facilitation of binding to a partner protein. In this way, phosphorylation can regulate protein-protein interactions. The phosphorylation of a protein can also target it for degradation and removal from the cell by the ubiquitin-proteasome system.
Protein phosphorylation also has a vital role in intracellular signal transduction. Many of the proteins that make up a signaling pathway are kinases, from the tyrosine kinase receptors at the cell surface to downstream effector proteins, many of which are serine/threonine kinases.