Tag Archives: 8 oxo guanine

Why antioxidants may be bad for you

Antioxidants (vitamin E, beta carotene, vitamin C etc. etc. ) were very big a while ago. They were held to prevent all sorts of bad things (heart attack, stroke). However one pretty good study done years and years ago (see the bottom) showed that they increased the risk of lung cancer in 29,000 Finnish male smokers by 18%. People still take them however.

Now we are beginning to find out the good things that oxidation does for you. One oxidation product is 8-oxo-guanine–https://en.wikipedia.org/wiki/8-Oxoguanine — and it is estimated that it occurs 100,000 time a day in every cell in our body. This isn’t very often as we have .24 x 3,200,000 = 768,000,000 guanines in our genome.

One good thing 8-oxo-guanine may do for you is turn on gene transcription [ Proc. Natl. Acad. Sci. vol. 114 pp. 2788 – 2790, 2604 – 2609 ’17 ].This occurs when the guanine occurs in an elegant DNA structure called a G-quartet (G quadruplex) — https://en.wikipedia.org/wiki/G-quadruplex. Oxidation recruits an enzyme to remove it (8-oxo-guanine glycosylase — aka OGG1 ) generating a DNA lesion — a sugar in the backbone without a nucleotide attach. This causes the binding of Apurinic/Apyrmidic Endonuclease 1 (APE1) which recruits other things to repair the DNA.

As you know DNA in our cells is compacted 100,000 fold to fit its 1 meter length into a nucleus .00001 meters in size. Compaction involves wrapping the helix around all nucleosomes and then binding the nucleosomes together.

It’s pretty hard for RNA polymerase to even get to a gene to transcribe it into mRNA, and DNA lesions cause opening up of this compaction so repair enzymes can actually get to the double helix.

One such gene is Vascular Endothelial Growth Factor (VEGF), a gene induced by low oxygen (hypoxia). The promoter of VEGF has a potential G quadruplex sequence. If the authors put 8-oxo-guanine at 5 different positions in the G quartet, transcription of the VEGF gene was increased 2 – 3 times over the next few days. Showing the importance of the DNA lesion, if OGG1 levels were decreased this didn’t happen — showing that guanine oxidation and with the subsequent formation of a DNA lesion is required for increased transcription of VEGF.

Aside from being another mechanism for gene activation under oxidative stress, 8-oxo-guanine may actually be another epigenetic DNA modification, like 5 methyl cytosine.

So this may explain the result immediately below.

[ New England J. Med. vol. 330 pp. 1029 – 1035 ’94 ] The Alpha-Tocopherol, Beta-Carotene Trial (ATBC trial) randomized double blind placebo controlled of daily supplementation with alpha-tocopherol (a form of vitamin E), beta carotene or both to see if it reduced the incidence of lung cancer was done in 29,000 Finnish male smokers ages 50 – 69 (when most of the damage had been done). They received either alpha tocopherol 50 mg/day, beta carotene 20 mg/day or both. There was a high incidence of lung cancer (876/29000) during the 5 – 8 year period of followup. Alpha tocopherol didn’t decrease the incidence of lung cancer, and there was a higher incidence among the men receiving beta carotene (by 18%). Alpha tocopherol had no benefit on mortality (although there were more deaths from hemorrhagic stroke among the men receiving the supplement). Total mortality was 8% higher among the participants on beta carotene (more deaths from lung cancer and ischemic heart disease). It is unlikely that the dose was too low, since it was much higher than the estimated intake thought to be protective in the uncontrolled dietaryt studies. The trial organizers were so baffled by the results that they even wondered whether the beta-carotene pills used in the study had become contaminated with some known carcinogen during the manufacturing process. However, tests have ruled out that possibility.

Needless to say investigators in other beta carotene clinical trials (the Women’s Health Study, the Carotene and Retinoid Efficacy Trial) are upset. [ Science vol. 264 pp. 501 – 502 ’94 ] “In our heart of hearts, we don’t believe [ beta carotene is ] toxic” says one researcher. Touching isn’t it. Such faith in a secular age, particularly where other people’s lives are at stake. I love it when ecology, natural vitamins and pseudoscience take it in the ear.

Maybe there is something to it after all

Nearly 8 years ago I wrote a post (see below) about a rather fantastic paper, that said that in order to turn on gene transcription, the DNA had to be damaged first. This caused all sorts of repair enzymes to rush to the damaged site, opening up the chromatin there and allowing RNA polymerase II (which is large) to get to the DNA and transcription to proceed. I wrote the original author who was Italian, who said he was ill, but nothing further appeared about the idea (as far as I know). Remember what Carl Sagan said “Extraordinary claims require extraordinary evidence.”

Now Science (vol. 351 p. 147 ’16 ) has an abstract of an article in Nat. Commun. 6, 10191 (2015). “Curiously, DNA repair factors have been found associated with tran- scriptionally paused, inducible genes. Bunch et al. show that the activation of paused and inducible genes in human tissue culture cells triggers DNA breaks at the RNA polymerase pause site. The subsequent recruitment and signaling activity of DNA repair factors is critical for DNA repair, release of the RNA polymerase, and the transition to the transcrip- tion elongation phase of gene expression.”

Here’s the relevant portion of the post from 2/08. How about that ! ! ! DNA breaks are even more spectacular than 8 oxo-guanine

An incredible article appeared last month in the journal Science. (see below for the abstract). If it can be verified and if it applies generally, our conception of just how genes coding for protein are turned on will be radically changed (yes, there are many other kinds of genes other than those coding for proteins). If DNA compaction, nucleosomes, histones, lysine methylation and demethylation, the histone code, nuclear hormone receptors (particularly the estrogen receptor), DNA glycosylase and topoisomerase aren’t old friends have a look at the first comment on this post for the background you need (it’s back on the Skeptical Chymist). Don’t worry, there is plenty of chemistry to follow.

Some histone code modifications are reversible, particularly acetylation of the epsilon amino group of lysine. Enzymes acetylating histone lysines are called histone acetylases, those removing it are called histone deacetylatases (HDACs). However, lysine methylation was thought to be permanent until ’04 when several enzymes able to demethylate lysine were found. One such enzyme is called LSD1 (it has nothing to do with the hallucinogen). It removes the two methyl groups from lysine #9 of histone #3 (H3K9me2). If this modification is present on a nucleosome near a gene, the gene is silenced, so the methyls must be removed so the protein it codes for can be made.

The estrogen receptor + estrogen complex bound to the ERE (the estrogen response element – a 15 nucleotide DNA sequence) triggers H3K9me2 removal. The process of demethylation is oxidative (how else would you split a nitrogen to hydrocarbon bond?). Hydrogen peroxide is produced, a loose cannon which oxidizes the juicy electron-rich bases of DNA nearby, forming in particular 8 oxo-guanine, as guanine is the most easily oxidized DNA base. Since 21% of the DNA bases in our genome are guanine, H2O2 doesn’t have far to look. This calls in some fairly heavy artillery (DNA glycosylase to remove the 8 oxo-guanine, topoisomerase IIbeta to unwind the DNA so it can be repaired, the repair enzymes, etc, etc…). Naturally this opens up the compacted DNA structure around the gene allowing RNA polymerase II to do its work transcribing the estrogen responsive gene into mRNA (once the damage is repaired).

So according to this paper, estrogen turns on gene transcription by damaging DNA. This is fantastic (if true). There’s more. The estrogen receptor is but one member of a group of proteins called nuclear hormone receptors. The name comes from the fact that other hormones (progesterone, androgen, thyroid, glucocorticoids, mineralocorticoids) have their own proteins that turn on (or turn off) genes the same way. Subsequently it was found that some vitamin metabolites (vitamin D3, vitamin A) have similar receptors even though they aren’t hormones. The human genome contains 48 such proteins. Less than half of them have known ligands. Those with known ligands have their finger in just about every metabolic pie in the cell.

One final point. It has been estimated that 8-oxoguanine is formed 100,000 times each day in every cell. Perhaps its formation is physiologic rather than pathologic. Where does that leave antioxidant therapy, which has been touted to do everything but cure hemorrhoids? Well, one such trial was done on 29,000 Finnish men at high risk for lung cancer (they were smokers) [New England J. Med. vol. 330 pp. 1029-1035 (1994)] Alpha tocopherol (one antioxidant used in the study) didn’t decrease the incidence of lung cancer, and there was an 18% higher incidence of lung cancer among the men receiving beta carotene (another antioxidant). In medicine, theory is great but data trumps it every time.

Science vol. 301 pp. 202 – 206 ’08, B. Perillo et. al.

Modifications at the N-terminal tails of nucleosomal histones are required for efficient transcription in vivo. We analyzed how H3 histone methylation and demethylation control expression of estrogen-responsive genes and show that a DNA-bound estrogen receptor directs transcription by participating in bending chromatin to contact the RNA polymerase II recruited to the promoter. This process is driven by receptor-targeted demethylation of H3 lysine 9 at both enhancer and promoter sites and is achieved by activation of resident LSD1 demethylase. Localized demethylation produces hydrogen peroxide, which modifies the surrounding DNA and recruits 8-oxoguanine–DNA glycosylase 1 and topoisomeraseIIβ, triggering chromatin and DNA conformational changes that are essential for estrogen-induced transcription. Our data show a strategy that uses controlled DNA damage and repair to guide productive transcription.