Question

Nucleosome Modification during Transcriptional Activation To prepare genomic regions for transcription, cells acetylate and methylate certain histones in the resident nucleosomes at specific locations. Once transcription is no longer needed, cells need to reverse these modifications. In mammals, peptidylarginine deiminases (PADIs) reverse the methylation of Arg residues in histones. The reaction promoted by these enzymes does not yield unmethylated arginine. Instead, it produces citrulline residues in the histone. What is the other product of the reaction? Suggest a mechanism for this reaction.

Short answer

The other product is ammonia (NH₃). The reaction mechanism involves water, releasing citrulline and ammonia.

Step-by-step solution

Understand the Reaction

The problem deals with the demethylation of arginine in histones by peptidylarginine deiminases (PADIs), which converts methylated arginine to citrulline. This is a deimination reaction where a methylated nitrogen is replaced with an oxygen.

Identify Reactants and Products

In the reaction catalyzed by PADIs, S-adenosylmethionine is not involved as the transfer is reversed. Instead, water (H₂O) is often involved as a nucleophile in hydrolytic reactions, implying water as a possible reactant. Citrulline and ammonia are formed as products.

Mechanistic Proposal

The deimination mechanism involves water attacking the nitrogen of the methylated arginine, leading to its breakdown. The C=N bond in the guanidinium group of arginine reacts, forming a tetrahedral intermediate. As the reaction progresses, it yields citrulline by substituting one amino group with oxygen and releasing ammonia.

Write the Reaction

The chemical equation can be summarized as: Methylated Arginine + H₂O → Citrulline + NH₃. Here, water provides the oxygen to form a carbonyl group in citrulline, while ammonia (NH₃) is released as the other product of the reaction.

Key concepts

Histone Acetylation

Histone acetylation is a crucial modification process for regulating gene expression. It involves the addition of an acetyl group to histone proteins, typically at lysine residues. This process is catalyzed by enzymes known as histone acetyltransferases (HATs). Acetylation changes the charge of histones, which decreases their affinity for DNA. As a result, the chromatin structure becomes more relaxed, allowing transcription factors easier access to the DNA for gene expression. This process is a key step in transcriptional activation, serving as a kind of "on switch" for genes.

• Reduces positive charge on histones
• Results in a more open chromatin structure
• Facilitates gene transcription

To reverse the effects of histone acetylation, cells employ histone deacetylases (HDACs), which remove acetyl groups, re-compacting the chromatin and reducing gene expression. Thus, the balance of acetylation and deacetylation is vital for proper cellular function and gene regulation.

Histone Methylation

Histone methylation involves the transfer of methyl groups to lysine or arginine residues of histone proteins. This is facilitated by enzymes called histone methyltransferases. Unlike acetylation, methylation does not alter the charge of histones, but it does affect how tightly DNA is wrapped around histone proteins. The effects of histone methylation on gene expression can vary depending on the specific residue methylated and the number of methyl groups added. Histone methylation can either activate or repress transcription based on its context and the specific histone being modified.

• Activation: Trimethylation of histone H3 on lysine 4 (H3K4me3) is often associated with transcriptionally active genes.
• Repression: Trimethylation of histone H3 on lysine 27 (H3K27me3) is linked to gene silencing.

Histone demethylases are enzymes responsible for removing methyl groups, thus reverting the methylation marks. This dynamic process plays a fundamental role in regulating chromatin structure and gene expression, sometimes marking regions for repair or other DNA-templated processes.

Transcriptional Activation

Transcriptional activation refers to the process by which a gene's expression is increased, resulting in the production of mRNA and eventually proteins. This involves the orchestrated modification of nucleosomes, a key aspect of which includes both histone acetylation and methylation. During transcriptional activation, specific signals instruct enzymes to modify histones, leading to a more open chromatin state. This is essential for transcription factors and RNA polymerase to access the DNA efficiently.

• Histone Acetylation: Facilitates an open chromatin structure.
• Histone Methylation: Marks genes for activation or repression.

Activation also involves the recruitment of transcription factors to gene promoters and the assembly of the transcriptional machinery. The integrated action of these processes empowers the cell to regulate gene expression in response to various internal and external stimuli. Understanding these mechanisms is crucial for insights into how genes are turned on or off in healthy and disease states.