Histone proteins residues

Histone acetylation is a reversible and covalent modification of histone proteins introduced at the e-amino groups of lysine residues. Histones and DNA form a complex - chromatin - which condenses DNA and controls gene activity. Current models interpret histone acetylation as a means to regulate chromatin activity. 

Acetylation is a reversible modification on proteins that can also contribute to protein localization and function. Acetylation of lysine residues in histone proteins can control the secondary structure of chromatin as well as gene expression levels from certain loci, and chromatin remodeling and its consequences in a variety of molecular and cell biological questions are intensely researched. Many other proteins undergo reversible acetylation, and the functional consequences of these modifications are poorly understood in many cases. 

The first indication that modification of specific tail residues were linked to chromatin functional states, came from immunostaining of Drosophila polytene chromosomes with antibodies specific for H4 acetylated at defined lysines [13]. As shown in Fig. 2A, H4 acetylated at lysine 16 (H4acK16) was found almost exclusively on the transcriptional hyperactive male X chromosome (Fig. 2). (Genes on the Drosophila male X are transcribed twice as fast as their female counterparts so as to equalize levels of X-linked gene products between XY males and XX females.) In addition, H4 lysine 12 was found to remain acetylated in centric heterochromatin, while lysines 5, 8, and 16 were all under-acetylated [13]. These observations led to the suggestion that the histone N-terminal tails constitute nucleosome surface markers that can be recognized by non-histone proteins in a modification-dependent manner to alter the functional state of chromatin [13]. 

Figure 1.1 PTMs found on the first 30 residues of the human histone proteins. Only acetylation, methylation, deimination (formation of citrulline) and phosphorylation are shown.

Dotl proteins and S ET H KMTs illustrate how methyl transfer to a protein Lys side-chain can be done with different structural scaffolding and unrelated local active site spatial arrangements. To date, Dotl proteins are the only nonSET HKMTs and further work and structures are needed to understand the mechanism of methylation of Lys-79, a histone core residue. 

Histone acetyltransferases (H ATs) catalyze the transfer of an acetyl moiety from acetyl-CoA to the E-amino group of certain lysine residues within core histone proteins. This transferase reaction produces acetylated histones and the deacetylated cofactor CoA-SH. As HATs are important enzymes in the regulation of gene expression, there are also a number of assays available to detect acetyltransferases activity. 

Lysine methyltransferases catalyze the transfer of methyl groups from the cosubstrate SAM to certain lysine residues in histone proteins. To characterize modulators of these transferases, the above-mentioned antibody-based assay protocols are also applicable. 

There are demethylases which act like amine oxidases that are dependent in their mechanism on their cosubstrate flavine adenine dinucleotide (FAD). So far, lysine-specific demethylase 1 (LSDl) is the only representative of this class [62]. LSDl, as an amine oxidase leads to oxidation of the methylated lysine residue, generating an imine intermediate, while the protein-bound cosubstrate FAD is reduced to FAD H2. In a second step, the imine intermediate is hydrolyzed to produce the demethylated histone lysine residue and formaldehyde. Importantly the reduced cosubstrate is regenerated to its oxidized form by molecular oxygen, producing hydrogen peroxide (Figure 5.7) [62, 63]. 

The N-terminal tails of histone proteins are rich in arginine and lysine residues and undergo various types of posttranslational modifications. There are small modifications such as acetylation, methylation, phosphorylation but also the attachment of larger peptide groups such as ubiquitinylation and sumoylation [1]. This has an impact on chromatin structure and subsequently on gene transcription and the epigenetic maintenance of altered transcription after cell division [2],... 

As discussed, histones are an integral part of nucleo-somes, the basic repeating structural unit of chromatin. The amino termini of histone proteins can be modified post-translationally by processes that include acetylation, methylation, phosphorylation, and ubiquination. Acetylation of the lysines on the amino termini of histones H3 and H4 by histone acetyltransferases decreases histone-DNA interaction and improves the accessibility of DNA to transcriptional activation. On the contrary, histone deacetylation by histone deacetylases promotes the formation of compact nucleo-somes, leading to repression of transcription. Histone deacetylation is in fact a key component to the assembly of heterochromatin, the transcriptionally inactive chromatin. Methylation of the ninth amino acid residue, lysine, on histone H3 generates a binding site for heterochromatin protein (HP 1) and thus is another key event in heterochromatin formation. Phosphorylation of the tenth amino acid, serine, on histone H3 is important for chromosome condensation and mitosis. 

B. When lysine residues in the A-terminal portion of histones are acetylated, it decreases the positive charge of the histone proteins and weakens the interaction between the histones and the DNA. As a result, the nucleosomes are opened up and lead to gene activation. 

A. Nucleosomes are disk shaped particles that consist of a core of histone protein around which DNA is wrapped. A short linker region of DNA joins nucleosomes. The core of the nucleosomes is made up of two copies each of histones H2A, H2B, H3, and H4. These histone proteins have A-terminal tails that contain lysine residues that can be reversibly acetylated, affecting the electrostatic interaction of the DNA with the histones. Histone HI is not part of the nucleosomes core, therefore acetylation would likely not affect the protein-DNA interaction of the nucleosomes. 

As discussed later, acetyl CoA plays a central role in the oxidation of fatty acids and many amino acids. In addition, it is an intermediate in numerous biosynthetic reactions, such as the transfer of an acetyl group to lysine residues in histone proteins and to the N-terminl of many mammalian proteins. Acetyl CoA also is a biosynthetic precursor of cholesterol and other steroids and of the farnesyl and related groups that form the lipid anchors used to attach some proteins (e.g., Ras) to membranes (see Figure 5-15). In respiring mitochondria, however, the acetyl group of acetyl CoA is almost always oxidized to CO2. 

Each of the histone proteins making up the nucleosome core contains a flexible amino terminus of 11-37 residues extending from the fixed structure of the nucleosome these termini are called histone tails. Each H2A also contains a flexible C-termlnal tall (see Figure 10-20b). The histone tails are required for chromatin to condense from the beads-on-a-string conformation Into the 30-nm fiber. Several positively charged lysine side chains In the histone tails may interact with linker DNA, and the tails of one nucleosome likely interact with neighboring nucleosomes. The histone tail lysines, especially those In H3 and H4, undergo reversible acetylation and deacetylation by enzymes that act on specific lysines In the N-termlnl. In the acetylated form, the positive... 

Protein phosphorylation is a pervasive posttranslational modification in cells. It is reversible and can dramatically affect the activity of a modified protein. Protein phosphorylation is one of the most important mechanisms used for signal transduction by cells. In prokaryotic cells, the best-known reversible protein phosphorylations occur on histidine and aspartate in eukaryotes the best-known occur on the hydroxyl groups of serine, threonine, and tyrosine, although histidine can also be phosphorylated (Fig. 3.9). Other reversible modifications also occur, such as the acetylation of lysine residues in histone proteins. 

Acetylation—the addition of acetate groups to lysine residue as shown in nuclear receptors [22, 23], p53 [6], NF-kB [24], and histone proteins. 

Histone acetylation was one of the first posttranslational histone proteins to be described and demonstrated to function in the regulation of transcriptional activation (Braunstein et al., 1993). To date, this modification of histone is the one best characterized (Workman and Kingston, 1998). Acetylation of a lysine residue on a histone tail can neutralize the positive charge, thus weakening the interaction of the nucleosome with the DNA backbone. This then allows for the remodeling of the nucleosome so that the transcriptional machinery, as well as other proteins, can gain access to previously restricted sites within the DNA... 

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