Methylation, in the chemistry, is the addition of a methyl group on a substrate, or the substitution of an atom (or group) by a methyl group. Methylation is a form of alkylation, with a methyl group replacing a hydrogen atom. These terms are commonly used in chemistry, biochemistry, soil science, and biology.
In biological systems, methylation is Catalysis by ; such methylation can be involved in modification of heavy metals, regulation of gene expression, regulation of protein function, and RNA processing. In vitro methylation of tissue samples is also a way to reduce some histological staining artifacts. The reverse of methylation is demethylation.
In biology
In biological systems, methylation is accomplished by enzymes. Methylation can modify heavy metals and can regulate gene expression, RNA processing, and protein function. It is a key process underlying
epigenetics. Sources of methyl groups include
S-methylmethionine, methyl folate, methyl B12, trimethylglycine.
Methanogenesis
Methanogenesis, the process that generates methane from CO
2, involves a series of methylation reactions. These reactions are caused by a set of enzymes harbored by a family of anaerobic microbes.
[Thauer, R. K., "Biochemistry of Methanogenesis: a Tribute to Marjory Stephenson", Microbiology, 1998, volume 144, pages 2377-2406.]
In reverse methanogenesis, methane is the methylating agent.
O-methyltransferases
A wide variety of
phenols undergo
O-methylation to give
anisole derivatives. This process, catalyzed by such enzymes as caffeoyl-CoA
O-methyltransferase, is a key reaction in the biosynthesis of
Monolignol, percursors to
lignin, a major structural component of plants.
Plants produce flavonoids and isoflavones with methylations on hydroxyl groups, i.e. methoxy group. This 5- O-methylation affects the flavonoid's water solubility. Examples are 5- O-methylgenistein, 5- O-methylmyricetin, and 5- O-methylquercetin (azaleatin).
Proteins
Along with
Ubiquitin and
phosphorylation, methylation is a major biochemical process for modifying protein function. The most prevalent protein methylations affect arginine and lysine residue of specific histones. Otherwise histidine, glutamate, asparagine, cysteine are susceptible to methylation. Some of these products include
S-Methylcysteine, two isomers of
N-methylhistidine, and two isomers of
N-methylarginine.
Methionine synthase
Methionine synthase regenerates
methionine (Met) from
homocysteine (Hcy). The overall reaction transforms 5-methyltetrahydrofolate (
N5-MeTHF) into
tetrahydrofolate (THF) while transferring a methyl group to Hcy to form Met. Methionine Syntheses can be cobalamin-dependent and cobalamin-independent: Plants have both, animals depend on the methylcobalamin-dependent form.
In methylcobalamin-dependent forms of the enzyme, the reaction proceeds by two steps in a ping-pong reaction. The enzyme is initially primed into a reactive state by the transfer of a methyl group from N5-MeTHF to Co(I) in enzyme-bound cobalamin ((Cob), also known as vitamine B12)), forming methyl-cobalamin (Me-Cob) that now contains Me-Co(III) and activating the enzyme. Then, a Hcy that has coordinated to an enzyme-bound zinc to form a reactive thiolate reacts with the Me-Cob. The activated methyl group is transferred from Me-Cob to the Hcy thiolate, which regenerates Co(I) in Cob, and Met is released from the enzyme.
Heavy metals: arsenic, mercury, cadmium
Biomethylation is the pathway for converting some heavy elements into more mobile or more lethal derivatives that can enter the
food chain. The
biomethylation of
arsenic compounds starts with the formation of
. Thus, trivalent inorganic arsenic compounds are methylated to give methanearsonate.
S-adenosyl methionine is the methyl donor. The methanearsonates are the precursors to dimethylarsonates, again by the cycle of
Redox (to methylarsonous acid) followed by a second methylation.
Related pathways are found in the microbial methylation of mercury to
methylmercury.
Epigenetic methylation
DNA methylation
DNA methylation is the conversion of the cytosine to 5-methylcytosine. The formation of Me-CpG is
Catalysis by the enzyme DNA methyltransferase. In vertebrates, DNA methylation typically occurs at
(cytosine-phosphate-guanine sites—that is, sites where a
cytosine is directly followed by a
guanine in the DNA sequence). In mammals, DNA methylation is common in body cells,
and methylation of CpG sites seems to be the default.
Human DNA has about 80–90% of CpG sites methylated, but there are certain areas, known as CpG islands, that are CG-rich (high cytosine and guanine content, made up of about 65% CG residues), wherein none is methylated. These are associated with the promoters of 56% of mammalian genes, including all ubiquitously expressed genes. One to two percent of the human genome are CpG clusters, and there is an inverse relationship between CpG methylation and transcriptional activity. Methylation contributing to epigenetic inheritance can occur through either DNA methylation or protein methylation. Improper methylations of human genes can lead to disease development,
including cancer.
In Honey bee, DNA methylation is associated with alternative splicing and gene regulation based on functional genomic research published in 2013.
RNA methylation
RNA methylation occurs in different RNA species viz.
tRNA,
rRNA,
mRNA,
tmRNA,
snRNA,
snoRNA,
miRNA, and viral RNA. Different catalytic strategies are employed for RNA methylation by a variety of RNA-methyltransferases. RNA methylation is thought to have existed before DNA methylation in the early forms of life evolving on earth.
N6-methyladenosine (m6A) is the most common and abundant methylation modification in RNA molecules (mRNA) present in eukaryotes. 5-methylcytosine (5-mC) also commonly occurs in various RNA molecules. Recent data strongly suggest that m6A and 5-mC RNA methylation affects the regulation of various biological processes such as RNA stability and mRNA translation,
In social insects such as honey bees, RNA methylation is studied as a possible epigenetic mechanism underlying aggression via reciprocal crosses.
Protein methylation
Protein methylation typically takes place on
arginine or
lysine amino acid residues in the protein sequence.
Arginine can be methylated once (monomethylated arginine) or twice, with either both methyl groups on one terminal nitrogen (asymmetric dimethylarginine) or one on both nitrogens (symmetric dimethylarginine), by protein arginine methyltransferases (PRMTs). Lysine can be methylated once, twice, or three times by lysine methyltransferases. Protein methylation has been most studied in the
. The transfer of methyl groups from
S-adenosyl methionine to histones is catalyzed by enzymes known as histone methyltransferases. Histones that are methylated on certain residues can act
Epigenetics to repress or activate gene expression.
Protein methylation is one type of post-translational modification.
Evolution
Methyl metabolism is very ancient and can be found in all organisms on earth, from bacteria to humans, indicating the importance of methyl metabolism for physiology.
Indeed, pharmacological inhibition of global methylation in species ranging from human, mouse, fish, fly, roundworm, plant, algae, and cyanobacteria causes the same effects on their biological rhythms, demonstrating conserved physiological roles of methylation during evolution.
In chemistry
The term methylation in organic chemistry refers to the
alkylation process used to describe the delivery of a group.
Electrophilic methylation
Methylations are commonly performed using
electrophile methyl sources such as
iodomethane,
,
dimethyl carbonate,
or tetramethylammonium chloride.
Less common but more powerful (and more dangerous) methylating reagents include
methyl triflate,
,
and methyl fluorosulfonate (
magic methyl). These reagents all react via S
N2 nucleophilic substitutions. For example, a
carboxylate may be methylated on oxygen to give a methyl
ester; an
alkoxide salt may be likewise methylated to give an
ether, ; or a ketone
enolate may be methylated on carbon to produce a new
ketone.
- salt and a phenol using iodomethane]]
The Purdie methylation is a specific for the methylation at oxygen of using iodomethane and silver oxide.
Eschweiler–Clarke methylation
The Eschweiler–Clarke reaction is a method for methylation of
.
This method avoids the risk of
quaternization, which occurs when amines are methylated with methyl halides.
Diazomethane and trimethylsilyldiazomethane
Diazomethane and the safer analogue trimethylsilyldiazomethane methylate carboxylic acids, phenols, and even alcohols:
- RCO2H + tmsCHN2 + CH3OH -> RCO2CH3 + CH3Otms + N2
The method offers the advantage that the side products are easily removed from the product mixture.
Nucleophilic methylation
Methylation sometimes involve use of
nucleophile methyl reagents. Strongly nucleophilic methylating agents include
methyllithium ()
or
such as methylmagnesium bromide ().
For example, will add methyl groups to the
carbonyl (C=O) of ketones and aldehyde.:
- by methyl lithium]]
Milder methylating agents include tetramethyltin, dimethylzinc, and trimethylaluminium.
See also
Biology topics
-
Bisulfite sequencing – the biochemical method used to determine the presence or absence of methyl groups on a DNA sequence
-
MethDB DNA Methylation Database
-
Microscale thermophoresis – a biophysical method to determine the methylisation state of DNA
-
Remethylation, the reversible removal of methyl group in methionine and 5-methylcytosine
Organic chemistry topics
External links
-
deltaMasses Detection of Methylations after Mass Spectrometry
