Chapter Three
Methylation Cycle
Methylation involves the attachment of a methyl group composed of three hydrogen elements and one carbon element. The attachment of methyl groups functions like an on-off switch. Methylation can change DNA expression, control excess neurotransmitters, and perform many other important tasks. If the methylation cycle becomes too slow, then the risk of health conditions increases. The internet has images of the methylation cycle and the associated transsulfuration pathway.
The methylation cycle starts with a molecule known as methionine, which contains a methyl group, sulfur, and various other elements. As discussed later, both sulfur and methyl groups are important for good health.
Sulfur molecules are like glue and help to hold together specific molecules. One of the main functions of sulfur is to attach to pollutants, such as heavy metals. Sulfur’s attachment to pollutants helps to remove them from the body. This action of sulfur is important. If this function becomes inefficient, then pollutants could accumulate in the body, which increases inflammation. The following two chapters have a discussion of this concept in greater detail.
There are various intermediate molecules that are part of the methylation cycle pathway. Methionine turns into S-adenosyl methionine (SAMe). SAMe transfers methyl groups to many other molecules, such as DNA. After this process, SAMe becomes S-adenosylhomocysteine (SAH), which later becomes homocysteine.
At this point in the methylation cycle, homocysteine can regenerate into methionine, where the methylation cycle starts all over again. However, the other alternative is homocysteine can redirect into the pathway that generates cysteine, the rate-limiting amino acid needed to produce glutathione, one of the most powerful antioxidants. The transsulfuration pathway is another name for this path.
The section of the methylation cycle where homocysteine occurs is critical. At this point in the cycle, inflammation can direct homocysteine away from the methylation cycle and toward the generation of glutathione, which is one of the most beneficial molecules in the body. Glutathione assists in the elimination of pollutants, such as mercury, cadmium, lead, and dioxins. Glutathione also helps limit hydrogen peroxide, a reactive oxygen species that causes damage when in excess.
The redirection of homocysteine limits methylation cycle efficiency, which causes many changes, especially in how the cells read DNA. These changes are likely purposeful and assist the body during chronic inflammation. There is a further discussion of this idea later.
Importantly, “up to 85% of all methylation reactions and as much as 48% of methionine metabolism occur in the liver, which indicates the crucial importance of this organ in the regulation of blood methionine (54).” If methylation is one of the major pathways for detoxification in the liver, then an inefficient methylation cycle might contribute to increased toxicity in the body.
Considering the massive number of pollutants in the environment, supporting the detoxification pathways of the liver is important. Exercise, fulfilling daily nutrient requirements, and reducing inflammation all help the liver function better. There is a discussion of these ideas later.
ASD and Methylation
If inflammation affects the efficiency of the methylation cycle, and ASD people tend to have more inflammation, then inefficient methylation will likely be more prevalent in autistics. Perhaps unsurprisingly, research found that abnormal DNA methylation significantly correlated with autism symptom scores (55). Research also found that ASD children had “lower baseline plasma concentrations of methionine, SAM, homocysteine, cystathionine, cysteine, and total glutathione and significantly higher concentrations of SAH, adenosine, and oxidized glutathione (56).” These results are consistent with a slower methylation cycle.
In many ASD individuals, the methylation cycle is like a traffic jam. Homocysteine accumulates, which causes the methylation cycle to slow down significantly. This mainly occurs because chronic inflammation depletes nutrients, such as the vitamins B6, B9, and B12. Methylation cycle enzymes need these vitamins to transform homocysteine and keep the cycle going.
The conversion of homocysteine to cysteine depends upon an activated form of vitamin B6, known as pyridoxal-5-phosphate (P5P). Also, the body requires other vitamins, such as vitamin B2, to change vitamin B6 into P5P. A lack of specific nutrients limits this conversion process. If this process is too slow, then homocysteine backs up, which slows down the methylation cycle. Interestingly, researchers found an excessive amount of homocysteine correlates directly how severely ASD communication skills are affected (57).
Methylation Flow
The homocysteine molecular pool is like a splitting of the path. Homocysteine can either regenerate methionine or produce cysteine, which is part of glutathione, a critical detoxification and antioxidant molecule. When trying to reduce inflammation, the requirements for glutathione increase. Therefore, when there is extra inflammation, the body redirects more homocysteine supply toward the production of glutathione. This causes less homocysteine to regenerate back into methionine.
Interestingly, there are two paths for the regeneration of homocysteine to methionine. One path uses betaine-homocysteine methyltransferase (BHMT), which depends on betaine. The other path uses folate, found in many plants, and B12, a vitamin that is mostly found in meats, eggs, and dairy.
One of the enzymes that controls the folate aspect of this cycle is methylenetetrahydrofolate reductase (MTHFR). Inhibition of this enzyme limits the efficient regeneration of methylation from homocysteine. Some people spend a lot of effort trying to increase MTHFR function.
However, the limitation may happen for a useful purpose. As mentioned, the limitation of MTHFR allows more homocysteine to go toward cysteine. This cysteine helps to produce more glutathione, which assists with reducing inflammation. Limiting MTHFR may be a way the body controls inflammation and alters methylation patterns to regulate metabolism.
For multiple reasons, redirecting homocysteine toward cysteine production might be so important that the body limits more than just the MTHFR enzyme. Many other aspects concerning the use of folate in the methylation cycle also change. There are over six different disorders of folate transport and metabolism (58).
The body also inhibits other enzymes that affect the generation of methionine from homocysteine. Amazingly, the construction of multiple enzymes in the methylation cycle is in such a way that excess reactive oxygen species can damage the function of these enzymes.
For example, reactive oxygen species can inhibit betaine homocysteine methyltransferase (BHMT) (59) (60) as well as methionine synthase (MS) (61). These enzymes are critical for efficient methylation cycle function. Limiting them slows down the methylation cycle even further.
Interestingly, reactive oxygen species can also reduce the availability of 5-methyltetrahydrofolate (5-MTHF) used by the MTHR enzyme to regenerate homocysteine into methionine. Research found that reactive oxygen species superoxide and hydrogen peroxide decreased the uptake of 5-MTHF by cells significantly (62). Other researchers also found reactive oxygen species generation may affect the development of 5-MTHF deficiency (63). Less availability of 5-MTHF significantly slows down the methylation cycle.
Additionally, there are genetic changes that reduce the function of the MTHFR enzyme. Since reactive oxygen species and genetic changes can inhibit multiple enzymes designed to regenerate methionine from homocysteine, this means the body wants to slow down the methylation cycle when there are too many reactive oxygen species and inflammation.
Furthering this point, reactive oxygen species also limit methylation by directly damaging DNA. Damage to DNA from the hydroxyl radical, a powerful potential source of inflammation, can interfere with the ability to methylate the damaged DNA (64).
Enzyme Control
Critically, reactive oxygen species can inhibit the activity of many other enzymes besides just the enzymes involved in methylation. This ability to inhibit many enzymes in this way is likely a purposeful design that allows the body to change enzyme functions depending on the number of reactive oxygen species nearby. This permits the cells to precisely adjust many functions according to the amount of inflammation that is happening.
For example, because of reactive oxygen species, some enzymes temporarily form disulfide bonds, which reduce enzyme activity (65). Reactive oxygen species can also inhibit GAPDH and block glycolysis (65). This glycolysis inhibition limits glucose metabolism. Slowing down the metabolism of glucose can limit the creation of more reactive oxygen species. This is a useful redirect if there are already too many reactive oxygen species in the cell. There are further discussions of potentially purposeful redirects such as this in Chapter 6.
Methylation Supplements
Various nutrients can support the methylation cycle. One of these nutrients is trimethylglycine (TMG). Initially found in beetroots, betaine is another name for TMG, and it assists in turning homocysteine into methionine. Some food sources of TMG are quinoa, spinach, and beetroot. Choline, an essential nutrient found in eggs, liver, nuts, and cruciferous vegetables, also helps the body produce more TMG.
A nutrient combination that might assist in regenerating methionine from homocysteine is B12 and folate. Autism researchers have experienced some limited clinical improvements using methylB12 shots injected into the body, which bypasses possible absorption problems in the small intestines (66).
However, rather than unnaturally injecting specific nutrients, the focus of care needs to be on improving health and reducing inflammation naturally. This will improve methylation cycle efficiency because less reactive oxygen species would be available to inhibit methylation cycle enzymes, like MS, BHMT, and MTHFR.
Researchers also found that if there are greater supplies of antioxidant enzymes, then not as much homocysteine gets redirected to cysteine and the eventual creation of glutathione (67). In contrast, toxic metals, such as lead, mercury, and aluminum, which increase inflammation, may inhibit homocysteine transforming into methionine by impairing the enzyme methionine synthase (MS) (68).
Methylation Inefficiency
Methylation cycle inefficiency affects various functions in the body. For example, methylation influences attention because the dopamine receptors in the brain need a methyl group for the receptor to “bind with dopamine, transform lipid membranes, change the frequency of brain waves, and increase our attention (69).” This is relevant since there are many children that cannot maintain attention. Some doctors label these children as having attention deficit hyperactivity disorder (ADHD) and prescribed powerful drugs such as Ritalin™. One way this drug works is by providing extra methyl groups that partially compensate for methylation inefficiency.
However, this drug has negative side effects. Rather than taking medications, which partially compensate for slow methylation, a better choice is to support the methylation cycle through nutritional and lifestyle choices that reduce inflammation naturally.
One of the most significant effects of an inefficient methylation cycle is the limited ability to activate and silence genes, which impacts the epigenetic expression of DNA. Epigenetics, a recent area of study, shows environment factors can change gene expression without changing the DNA itself.
For an analogy, epigenetics is like a website blocker that restricts access to some websites depending on internet browser settings. The websites are technically all there, much like the DNA code, but the browser settings limit access. Like a website blocker, methylation cycle and histone acetylation control access to the DNA code.
Histones are proteins in the cell nucleus upon which the DNA wraps around into tight spools, like winding up a string. Acetylation of these histones causes the DNA to become more loosely wrapped around the histones, which leads to DNA activation. Interestingly, methylation can affect histone acetylation (70). Therefore, methylation is the focus of this discussion.
In general, a well-functioning methylation cycle attaches methyl groups to DNA and stops parts of the genetic code from activating. If the methylation cycle becomes limited, then there is less overall DNA methylation. This changes how cells read DNA for operating instructions.
Altering the DNA readout in this way can eventually lead to severe health conditions. Researchers have found that epigenetics may be a major factor in the development of psychiatric illnesses (71). In addition, epigenetics affects the development of a child in the womb (72). There is further discussion about epigenetics later.
Glutathione
The previously discussed redirection of the methylation cycle indicates the importance of glutathione (GSH). As mentioned, GSH helps to limit inflammation by reducing reactive oxygen species and assisting in the removal of pollutants, such as toxic metals. GSH is one of the main molecules used by the liver for detoxifying.
In the world, where pollution is rapidly increasing due to ignorance and profit-seeking activity, a well-functioning detoxification process is important for good health. Heavy metals, a common pollutant in modern society, deplete glutathione levels intracellularly (73). One of these heavy metals is mercury. Shockingly, multiple types of seafood contain mercury (74) (75).
Critically, chronic inflammation can deplete GSH levels. Research noticed lower GSH levels in ASD people (76) (77) (78). This is unsurprising if ASD people are often dealing with a significant amount of chronic inflammation. Reduced GSH levels are also relevant to other disorders that affect the brain (79) (80). For example, researchers found there is an association between epilepsy and low GSH levels (81).
There are also associations between lower GSH capacity and many other health conditions, such as Alzheimer’s, Parkinson’s, liver disease, cystic fibrosis, sickle cell anemia, HIV, AIDS, cancer, heart attack, stroke, seizure, and diabetes (82) (83). Excitotoxic mechanisms also diminish GSH levels (84). There is a discussion about excitotoxicity in Chapter 8.
Interestingly, astroglia provide precursors of GSH to neurons to assist with controlling reactive oxygen species (85). Neurons need these precursors because completed GSH cannot penetrate the neurons, which must take apart the extracellular GSH and then reassemble the GSH once it is inside the neurons (86). Therefore, if supplementing GSH, a GSH monoester may be better because the monoester likely can penetrate the cells and prevent the decline of GSH (87).
Transdermal or liposomal GSH might also have health benefits. Researchers found that GSH supplementation increased the quantities of sulfate, cysteine, and taurine in ASD children (88). Interestingly, each of these molecules contains sulfur.
GSH can reduce reactive oxygen species by donating electrons, which the reactive oxygen species are seeking. In doing so, the GSH becomes GSSG, which is an oxidized version of glutathione. The ratio of GSH/GSSG is a sign of antioxidant ability in the body (89).
Unlike GSH, GSSG cannot reduce free radicals but can regenerate back into GSH (90). The regeneration of GSH happens through the enzyme glutathione reductase, which transforms one GSSG into two GSH molecules. Physical exercise affects the activity of the glutathione reductase enzyme and is one of the many reasons physical exercise benefits health. Importantly, the function of glutathione reductase depends on cells also having enough cysteine, NADPH, and vitamin B2.
Like GSH, sulfate has anti-inflammatory effects. One way to get more sulfate is to take methylsulfonylmethane (MSM) supplements. Also, fresh fruits, vegetables, and whole grains contain small amounts of MSM.
One of the functions of sulfate is to remove many types of pollutants from the body. As previously mentioned, GSH also performs detoxification functions. If there is a lack of sulfate in the food supply, especially MSM, then this puts more demand on GSH to complete some of the functions normally performed by an adequate sulfate supply.
This higher requirement lowers GSH levels and worsens inflammation. Although the body can make sulfate from cysteine, this process is not as reliable as getting sulfate from food. This is because inflammation can inhibit the enzyme that creates sulfate from cysteine.
Besides, getting sulfate from cysteine sometimes involves removing homocysteine from the methylation cycle. As mentioned, a loss of homocysteine from the methylation cycle can reduce methylation efficiency. Due to sulfate’s detoxification and anti-inflammatory potential, the next chapter focuses on sulfate and other recent changes that increase inflammation.