This article [MacDonald et al., 2007: (http://www.jbc.org/cgi/content/full/282/42/30596)(http://www.ncbi.nlm.nih.gov/pubmed/17724028?dopt=Abstract)] is interesting, and the authors found that both citrate and acetoacetate could serve as "carriers" or could serve to "transfer" acetyl-CoA from the mitochondria to the cytosol in pancreatic beta cells. Citrate has traditionally been viewed as the only or primary tricarboxylic acid (TCA) cycle intermediate that could be transported across the inner mitochondrial membrane and, fairly directly, serve as a precursor for cytosolic acetyl-CoA and hence for lipogenesis. The authors found that acetoacetate was converted into acetyl-CoA in the cytosol by either of two cytosolic enzymes. Succinate evidently couldn't be converted into succinyl-CoA in the cytosol, but this may not be true in cell types other than beta cells.
This is relevant to an understanding of the ways dietary cholesterol or the cellular cholesterol concentration in general, both in cells within and outside the liver, could exert feedback inhibition of microsomal (endoplasmic-reticulum, cytosolic) HMG-CoA reductase activity, thereby increasing the microsomal/cytosolic HMG-CoA pool, and, in theory, exert some kind of influence on the availability of intramitochondrial HMG-CoA for ketogenesis in the mitochondria [the first page of this pdf is inaccessible, but the rest of the article is fine: Ott and Lachance, 1981: (http://www.ajcn.org/cgi/reprint/34/10/2295)(http://www.ncbi.nlm.nih.gov/pubmed/6170219?dopt=Abstract)]. The cytosolic and mitochondrial HMG-CoA pools are not thought to be interchangeable, and so it's not easy to see an obvious or simple mechanism by which an increase in the overall cellular cholesterol concentration could enhance ketogenesis. Part of the reason for this is that cholesterol biosynthesis and transport within cells are compartmentalized [Ott and Lachance, 1981; Liscum et al., 1995: (http://www.jbc.org/cgi/content/full/270/26/15443)(http://www.ncbi.nlm.nih.gov/pubmed/7797533)]. But the authors of that article mention the relationships between succinate transport across the inner mitochondrial membrane, anaplerosis, and mevalonate biosynthesis. I'll try to read some more about that, but it doesn't look like there's all that much information on it. My point is that, as with glutamine and many other compounds, the compartmentation complicates or makes impossible any attempt to draw simple or easy conclusions about enzyme regulation in response to changes in dietary or intracellular or extracellular cholesterol concentrations. I think there is some mechanism, though, because cholesterol biosynthesis is energetically very demanding, compared to many other small-molecule intermediates or regulatory compounds or whatever one wants to describe cholesterol as being.
Saturday, June 13, 2009
Friday, June 12, 2009
Acute Redox Effects of Butyrate or Propionate in Mitochondria: Stimulation of the Glycine Cleavage System, etc.
This is a really great article [Hampson et al., 1984a: (http://www.ncbi.nlm.nih.gov/pubmed/6498157)], and the authors discuss a lot of things that are not directly related to the glycine cleavage system (GCS). The authors note that butyrate, propionate, or acetate stimulated the overall activity of the GCS multienzyme complex by, in preparations of mitochondria, causing an increase in ATP consumption, as a result of the formation of acyl-CoA thioesters, and thereby decreasing the intramitochondrial NADH/NAD+ ratio. The authors noted that the ATP-depleting effect of the acyl-CoA synthetase reaction in the intact cells of the intact liver had previously been found to be much less pronounced than the effect in mitochondria alone [Hampson et al., 1984b: (http://www.jbc.org/cgi/reprint/259/2/1180.pdf)(http://www.ncbi.nlm.nih.gov/pubmed/6420402)], evidently because intact cells have a supply of glucose and other energy substrates. This article seems strange at first glance, because most of the research has shown that short-chain acyl-CoA's, such as propionyl-CoA, inhibit different enzymes of the GCS [one of many: Hayasaka et al., 1983: (http://www.ncbi.nlm.nih.gov/pubmed/6679320)]. But the initial effects of butyrate and propionate and other free organic anions can be different. The stimulation was not due to an action of propionyl-CoA, because Hampson et al. (1984) added L-carnitine and found a decrease in the levels of propionyl-CoA, formed in response to the exogenous propionate, but not an attenuation of the effect of propionate on the intramitochondrial redox potential.
The way Hampson et al. (1984) present the data on the redox state is potentially confusing, because they keep referring to the transhydrogenase equilibrium. The transhydrogenase enzyme is in the inner mitochondrial membrane and essentially, based on my somewhat limited knowledge of it, serves to buffer changes in the intramitochondrial pyridine (NAD+ based) nucleotide redox couples. The authors discuss the fact that the energy-linked equilibrium constant for the transhydrogenase enzymatic reaction:
NADH + NADP+ <---> NAD+ + NADPH
can be 500, but the Keq can be near 1 in the absence of a proton gradient, such as in response to the presence of an uncoupler. The authors said that propionate had appeared, at first glance, to behave like an uncoupler in the isolated mitochondria but that it had probably just decreased the intramitochondrial NADH/NAD+ ratio via the acyl-CoA-synthetase-dependent consumption of ATP, in the formation of propionyl-CoA. The authors noted that similar experiments had shown the oxygen to be depleted from the media containing isolated mitochondria, in response to propionate. There's similar research in humans that shows that beta-hydroxybutyrate (BHB), a ketone, can increase the oxygen uptake into cells and produce a transient thermal effect, when researchers administer it intravenously [Chiolero et al., 1993: (http://www.ajcn.org/cgi/reprint/58/5/608.pdf)(http://www.ncbi.nlm.nih.gov/pubmed/8237864)]. That effect essentially balances out the acute increase in urinary bicarbonate excretion that evidently results from the oxidation of BHB. Ketone oxidation, even in the absence of ketoacidosis, tends to produce low-level, extracellular acidosis, but the effect can be opposed by the increase in oxygen consumption in response to the oxidation of ketones.
Incidentally, Vamecq et al. (2005) [Vamecq et al., 2005: (http://www.ncbi.nlm.nih.gov/pubmed/15713528)] also discussed the possibility that the formation of acyl-CoA thioesters, in response to a large influx of ketones (similar to the apparent effect of a large influx of propionate or butyrate), could conceivably produce transient ATP depletion. Vamecq et al. (2005) focused a bit too much on the idea that ketones produce anticonvulsant effects by causing mild ATP depletion. Most research has shown the opposite effect, in my view, although I think they make a valid point, to some extent. At very high levels, ketones, upon their metabolism into acetyl-CoA or long-chain acyl-CoA's, will tend to inhibit TCA cycle enzymes by leading to the accumulation of acyl-CoA's. But at lower dosages or levels, the oxidation, in the presence of other substrates, will tend to increase ATP production, in my opinion. But Hampson and colleagues also did some interesting experiments with different combinations of alpha-ketoglutarate and other TCA cycle intermediates and found, from what I can tell, that the additions of excesses of single TCA cycle intermediates produced the opposite effect on the intramitochondrial redox potential and inhibited the stimulatory effects of butyrate and propionate on the overall activity of the GCS. I don't have time to get into this, but it's relevant to anaplerosis and energy metabolism. This and the related articles from 1984 and 1983, by that group (Hampson et al.), have a lot of information that's very relevant to the study of energy metabolism and the ketogenic diet, etc. A lot of these older articles on energy metabolism are really terrific and filled with insights that everyone's forgotten about.
These articles are relevant to the use of sodium butyrate for various purposes, some of which I've discussed in past postings. These types of effects would be another reason, in my opinion, to start at lower dosages of sodium butyrate and not increase to massive dosages, etc. For example, there's research using 4 grams/day of sodium butyrate to treat ulcerative colitis. They've used much higher dosages of arginine butyrate, mainly given intravenously, to treat sickle cell disease, etc. Incidentally, the use of some calcium salts of butyrate could be more problematic than the use of sodium butyrate, in my opinion. Also, some manufacturers are using enteric-coated tablets to administer butyrate, and that's a major mistake, in my opinion. Enteric-coated tablets tend to be quite problematic, in my opinion, and manufacturers seem to be, in many cases, incapable of manufacturing them properly. That's just my opinion, but, in my eyes, it's an intractable problem that people just seem to be incapable of addressing. I've discussed that issue, at length, in past postings.
Incidentally, one approach would be to use small amounts of pantothenic acid (i.e. 100-200 mg/d or something) to partially compensate for any supposed increase in the fatty acyl-CoA/CoA ratio, in response to sodium butyrate, but I don't know how effective that would be. The point of those articles is that pantothenic acid could, by providing more coenzyme A, simply amplify the mild and transient ATP depletion that butyrate could produce. In my opinion (and much as the authors of the first article state), butyrate doesn't appear to behave like something that produces much ATP depletion, even transiently. It behaves like an energy substrate, in my opinion. But the effect of 4 grams/d may be quite different from the effects of higher dosages, both because of the acute effect of butyryl-CoA formation and because of the effects of butyryl-CoA (or longer-chain acyl-CoA's formed from butyrate) on mitochondrial enzymes.
This is also relevant to some research that supposedly rules out or discounts the roles of methylmalonic acid and propionyl-CoA accumulation in subacute combined degeneration and other neuropathic effects of vitamin B12 deficiency. In some of that research, which is summarized in an annual review of nutrition article [Metz, 1992: (http://www.ncbi.nlm.nih.gov/pubmed/1354465)], researchers apparently found that propionate or isoleucine administration or both (I forget the details, and I can't look it up right now) didn't acutely worsen the neurological dysfunction in animals with chronic B12 deficiency. I think some of the conclusions based on that research may have been erroneous, though, because the acute effects of the free organic anions [organic anions, or "ketoacids" (branched-chain fatty acids), formed from isoleucine, for example, could be quite different from the "intermediate-term" effects of the extra 2-methylbutyryl-CoA (formed from isoleucine) or from other acyl-CoA's that could accumulate after the prolonged administration of organic anions.
The way Hampson et al. (1984) present the data on the redox state is potentially confusing, because they keep referring to the transhydrogenase equilibrium. The transhydrogenase enzyme is in the inner mitochondrial membrane and essentially, based on my somewhat limited knowledge of it, serves to buffer changes in the intramitochondrial pyridine (NAD+ based) nucleotide redox couples. The authors discuss the fact that the energy-linked equilibrium constant for the transhydrogenase enzymatic reaction:
NADH + NADP+ <---> NAD+ + NADPH
can be 500, but the Keq can be near 1 in the absence of a proton gradient, such as in response to the presence of an uncoupler. The authors said that propionate had appeared, at first glance, to behave like an uncoupler in the isolated mitochondria but that it had probably just decreased the intramitochondrial NADH/NAD+ ratio via the acyl-CoA-synthetase-dependent consumption of ATP, in the formation of propionyl-CoA. The authors noted that similar experiments had shown the oxygen to be depleted from the media containing isolated mitochondria, in response to propionate. There's similar research in humans that shows that beta-hydroxybutyrate (BHB), a ketone, can increase the oxygen uptake into cells and produce a transient thermal effect, when researchers administer it intravenously [Chiolero et al., 1993: (http://www.ajcn.org/cgi/reprint/58/5/608.pdf)(http://www.ncbi.nlm.nih.gov/pubmed/8237864)]. That effect essentially balances out the acute increase in urinary bicarbonate excretion that evidently results from the oxidation of BHB. Ketone oxidation, even in the absence of ketoacidosis, tends to produce low-level, extracellular acidosis, but the effect can be opposed by the increase in oxygen consumption in response to the oxidation of ketones.
Incidentally, Vamecq et al. (2005) [Vamecq et al., 2005: (http://www.ncbi.nlm.nih.gov/pubmed/15713528)] also discussed the possibility that the formation of acyl-CoA thioesters, in response to a large influx of ketones (similar to the apparent effect of a large influx of propionate or butyrate), could conceivably produce transient ATP depletion. Vamecq et al. (2005) focused a bit too much on the idea that ketones produce anticonvulsant effects by causing mild ATP depletion. Most research has shown the opposite effect, in my view, although I think they make a valid point, to some extent. At very high levels, ketones, upon their metabolism into acetyl-CoA or long-chain acyl-CoA's, will tend to inhibit TCA cycle enzymes by leading to the accumulation of acyl-CoA's. But at lower dosages or levels, the oxidation, in the presence of other substrates, will tend to increase ATP production, in my opinion. But Hampson and colleagues also did some interesting experiments with different combinations of alpha-ketoglutarate and other TCA cycle intermediates and found, from what I can tell, that the additions of excesses of single TCA cycle intermediates produced the opposite effect on the intramitochondrial redox potential and inhibited the stimulatory effects of butyrate and propionate on the overall activity of the GCS. I don't have time to get into this, but it's relevant to anaplerosis and energy metabolism. This and the related articles from 1984 and 1983, by that group (Hampson et al.), have a lot of information that's very relevant to the study of energy metabolism and the ketogenic diet, etc. A lot of these older articles on energy metabolism are really terrific and filled with insights that everyone's forgotten about.
These articles are relevant to the use of sodium butyrate for various purposes, some of which I've discussed in past postings. These types of effects would be another reason, in my opinion, to start at lower dosages of sodium butyrate and not increase to massive dosages, etc. For example, there's research using 4 grams/day of sodium butyrate to treat ulcerative colitis. They've used much higher dosages of arginine butyrate, mainly given intravenously, to treat sickle cell disease, etc. Incidentally, the use of some calcium salts of butyrate could be more problematic than the use of sodium butyrate, in my opinion. Also, some manufacturers are using enteric-coated tablets to administer butyrate, and that's a major mistake, in my opinion. Enteric-coated tablets tend to be quite problematic, in my opinion, and manufacturers seem to be, in many cases, incapable of manufacturing them properly. That's just my opinion, but, in my eyes, it's an intractable problem that people just seem to be incapable of addressing. I've discussed that issue, at length, in past postings.
Incidentally, one approach would be to use small amounts of pantothenic acid (i.e. 100-200 mg/d or something) to partially compensate for any supposed increase in the fatty acyl-CoA/CoA ratio, in response to sodium butyrate, but I don't know how effective that would be. The point of those articles is that pantothenic acid could, by providing more coenzyme A, simply amplify the mild and transient ATP depletion that butyrate could produce. In my opinion (and much as the authors of the first article state), butyrate doesn't appear to behave like something that produces much ATP depletion, even transiently. It behaves like an energy substrate, in my opinion. But the effect of 4 grams/d may be quite different from the effects of higher dosages, both because of the acute effect of butyryl-CoA formation and because of the effects of butyryl-CoA (or longer-chain acyl-CoA's formed from butyrate) on mitochondrial enzymes.
This is also relevant to some research that supposedly rules out or discounts the roles of methylmalonic acid and propionyl-CoA accumulation in subacute combined degeneration and other neuropathic effects of vitamin B12 deficiency. In some of that research, which is summarized in an annual review of nutrition article [Metz, 1992: (http://www.ncbi.nlm.nih.gov/pubmed/1354465)], researchers apparently found that propionate or isoleucine administration or both (I forget the details, and I can't look it up right now) didn't acutely worsen the neurological dysfunction in animals with chronic B12 deficiency. I think some of the conclusions based on that research may have been erroneous, though, because the acute effects of the free organic anions [organic anions, or "ketoacids" (branched-chain fatty acids), formed from isoleucine, for example, could be quite different from the "intermediate-term" effects of the extra 2-methylbutyryl-CoA (formed from isoleucine) or from other acyl-CoA's that could accumulate after the prolonged administration of organic anions.
Tuesday, June 9, 2009
Resistance Exercise vs. Endurance Exercise: Different Effects on AMPK and mTOR Activities
This article [Atherton et al., 2005: (http://www.fasebj.org/cgi/content/full/19/7/786)(http://www.ncbi.nlm.nih.gov/pubmed/15716393?dopt=Abstract)] shows that the high-frequency stimulation of muscles, which supposedly mimics the effects of resistance exercise, does not predominantly activate the often-discussed AMPK-PGC-1alpha pathway but instead leads to increases in protein synthesis by activating the mTOR pathway, by first activating protein kinase B. In contrast, the authors used low-frequency stimulation of muscles to reproduce the effects of endurance exercise, and this did activate the largely-catabolic AMPK-PGC-1alpha pathway that leads to mitochondrial proliferation. One could find fault with the experimental methods, but the findings of the article are very much consistent with my sense of the stark differences between the effects of resistance exercise/strength training and the effects of endurance exercise. There's a lot of other research showing that the activity of mammalian target of rapamycin enzyme(mTOR), a serine-threonine kinase, is negatively regulated by AMPK and hence by the increase in the AMP/ATP ratio [Roe et al., 2006: (http://www.ncbi.nlm.nih.gov/pubmed/16763896)] that tends to occur as a result of endurance exercise. Resistance exercise can also lead to an increase in AMPK activation in the short term, but the long-term effects are quite different from those of endurance exercise. The point is that cell growth, as discussed by Atherton et al. (2005), does not occur in response to the same intracellular conditions (or in response to the same stimuli) as mitochondrial proliferation ("biogenesis") occurs under.
HMB (3-hydroxyisovalerate) increases the phosphorylation and activity of mTOR, by an unknown mechanism [one of multiple articles showing this: Eley et al., 2007: (http://ajpendo.physiology.org/cgi/content/full/293/4/E923)(http://www.ncbi.nlm.nih.gov/pubmed/17609254)], but that's mainly interesting because HMB seems to act, largely or partly, by increasing the plasma membrane or intracellular cholesterol concentration in myocytes and other cell types. It's possible that it's more of a ketogenic substrate than a cholesterol "precursor," given that leucine is known to be ketogenic in astrocytes and hepatocytes and other cell types. I'm not that interested in HMB, because, in my opinion, the potential for problems with phosphate and calcium homeostasis, as a result of calcium salts of HMB that have to include added phosphate, etc., is not a great thing. But it would be interesting to know what the mechanism would be for the increase in mTOR activity in response to HMB. I guess some of the in vitro research would tend to argue against ketogenesis as a primary mechanism, but I would expect that to be one mechanism in vivo. I've suggested other mechanisms in past postings (acylation of proteins or histones by 3-hydroxyisovaleryl-CoA, etc.), but it seems as if the cellular cholesterol concentration might regulate AMPK by some mechanism in extrahepatic cell types. Or it might be that HMB decreases AMPK activity and thereby increase cholesterol biosynthesis, in addition to its role as an HMG-CoA precursor. Alternatively (but not by a mutually-exlusive mechanism), HMB might increase the cellular cholesterol levels in myocytes and, as a result of the feedback inhibition of HMG-CoA reductase activity by that cholesterol, spare acetyl-CoA for entry into the TCA cycle, etc.
HMB (3-hydroxyisovalerate) increases the phosphorylation and activity of mTOR, by an unknown mechanism [one of multiple articles showing this: Eley et al., 2007: (http://ajpendo.physiology.org/cgi/content/full/293/4/E923)(http://www.ncbi.nlm.nih.gov/pubmed/17609254)], but that's mainly interesting because HMB seems to act, largely or partly, by increasing the plasma membrane or intracellular cholesterol concentration in myocytes and other cell types. It's possible that it's more of a ketogenic substrate than a cholesterol "precursor," given that leucine is known to be ketogenic in astrocytes and hepatocytes and other cell types. I'm not that interested in HMB, because, in my opinion, the potential for problems with phosphate and calcium homeostasis, as a result of calcium salts of HMB that have to include added phosphate, etc., is not a great thing. But it would be interesting to know what the mechanism would be for the increase in mTOR activity in response to HMB. I guess some of the in vitro research would tend to argue against ketogenesis as a primary mechanism, but I would expect that to be one mechanism in vivo. I've suggested other mechanisms in past postings (acylation of proteins or histones by 3-hydroxyisovaleryl-CoA, etc.), but it seems as if the cellular cholesterol concentration might regulate AMPK by some mechanism in extrahepatic cell types. Or it might be that HMB decreases AMPK activity and thereby increase cholesterol biosynthesis, in addition to its role as an HMG-CoA precursor. Alternatively (but not by a mutually-exlusive mechanism), HMB might increase the cellular cholesterol levels in myocytes and, as a result of the feedback inhibition of HMG-CoA reductase activity by that cholesterol, spare acetyl-CoA for entry into the TCA cycle, etc.
Monday, June 8, 2009
Squalene as a Potential Cholesterol Precursor or Potential "Vitamin K Mimetic"
This article [Relas et al., 2000: (http://www.sinoas.com/journal/UploadFiles/200706/20070625110816450.pdf)(http://www.ncbi.nlm.nih.gov/pubmed/10998465)] shows that even 500 mg of oral squalene can acutely increase cholesterol biosynthesis, by serving as a precursor of cholesterol. That might be another approach to increasing cholesterol formation extrahepatically (i.e. in the brain or other tissues). Obviously, this is an approach one would want to discuss with one's doctor before implementing. The research generally shows that squalene may or may not acutely increase plasma cholesterol slightly but does not usually elevate it, when given at doses between 500 mg and 1000 mg/d, in the long term. Some squalene is sold in combination with alkylglycerols (a.k.a. alkoxyglycerols), but I can't imagine why anyone would want to mess around with that type of thing. They're incorporated into phospholipids and have mysterious effects, etc., in my opinion, according to the research. People who eat diets high in olive oil (i.e. people who live around the "Mediterranean," etc.) can evidently obtain between 200 and 400 mg of squalene per day, from some types of olive oil [Newmark, 1997: (http://cebp.aacrjournals.org/cgi/reprint/6/12/1101.pdf)(http://www.ncbi.nlm.nih.gov/pubmed/9419410)]. There's research showing "encephaloneuropathy" (abnormalities in the brain, etc.) from massive doses of squalene in rats [Gajkowska et al., 1999: (http://www.ncbi.nlm.nih.gov/pubmed/10048717)] [that dose of 20 grams squalene per kg bw (20,000 mg/kg bw) in rats is like 4,246 mg/kg bw in humans, which is a dose of 297,240 mg squalene per day]. I just mention that to provide basic, toxicological information.
It's not clear if squalene can cross the blood-brain barrier, but I would guess that it can. Free fatty acids can cross lipid bilayers by passive diffusion, by the "flip-flop" type of mechanism of crossing lipid bilayers (http://hardcorephysiologyfun.blogspot.com/2009/04/free-fatty-acid-transport-and.html), and squalene may behave similarly. It's a polymer of 6 isoprene units (30-carbons) but is not nearly as reactive as many polyunsaturated fatty acids, evidently because it does not contain bis-allylic hydrogens [Cho et al., 2009: (http://pt.wkhealth.com/pt/re/cdrm/abstract.00003050-200906000-00011.htm)] (hydrogens that are allylic to two double bonds, meaning that they're on the carbon in between two double bonds). Apart from that, though, it appears to be able to elevate cholesterol levels in the skin of humans (Cho et al., 2009) and, evidently, in the testes in rats, given that squalene supplementation increased plasma testosterone in rats [Liu et al., 2009: (http://icmr.nic.in/ijmr/2009/february/0206.pdf)(http://www.ncbi.nlm.nih.gov/pubmed/19293441)]. That research on testosterone is reminiscent of research showing that serum testosterone concentrations increase as the dietary saturated fat intake increases [one of many articles showing that: Volek et al., 1997: (http://jap.physiology.org/cgi/content/full/82/1/49)(http://www.ncbi.nlm.nih.gov/pubmed/9029197); see some of the articles shown here: (http://scholar.google.com/scholar?q=Testosterone+and+cortisol+in+relationship+to+dietary+volek&hl=en&lr=)], but I don't know how much there is to that. It's probably only true up to a point, but it's consistent with the idea that some saturated fat is "required" for extrahepatic cholesterol biosynthesis. The effect would, in my opinion, eventually or sooner-than-eventually be opposed by, for example, the increase in aromatase activity, in adipocytes, in response to weight gain from massive amounts of saturated fat. Also, one would ask if downregulations in androgen receptor expression occur, etc. Normalizing the membrane or intracellular cholesterol concentration is likely to be possible, but upregulating the whole hypothalamic-pituitary-gonadal axis, in response to something like squalene alone, is unlikely to occur, in my opinion.
One concern would be the potential for induced vitamin K deficiency (in addition to the concern that squalene could, in my opinion, conceivably produce pathological effects by mimicking vitamin K), given the research showing this can occur in rodents and other animals (http://scholar.google.com/scholar?num=100&hl=en&lr=&q=squalene+%22vitamin+K%22), and other potential problems include the possibility that squalene could increase "post-squalene-and-pre-cholesterol" sterols to excessive levels (these can cause problems by exerting inappropriate, feedback inhibition of HMG-CoA reductase and producing all sorts of other effects) or produce direct and "undesirable" regulatory effects (such as by displaying vitamin K activity, in my opinion). There's research showing that geranylgeraniol and related "pre-squalene" isoprenoids can produce apoptotic effects in many cell types (http://scholar.google.com/scholar?q=apoptosis+farnesol+OR+geranylgeraniol&hl=en&lr=), but my sense is that squalene tends to be more of a cholesterol precursor than those isoprenoids (given, in part, that they can be converted into substrates for protein isoprenylation, etc.). But who knows. For all I know, epoxidized squalene could accumulate and exert vitamin K activity or produce some other bizarre effect like that, as discussed below. One reason I throw these suggestions out is that squalene is epoxidized by an enzyme or enzymes that catalyzes a reaction that may be similar to the reaction that produces vitamin K epoxide.
A major reason squalene wouldn't be expected to increase plasma cholesterol much, though, at reasonable dosages, is that dietary cholesterol exerts feedback inhibition of HMG-CoA reductase activity, by various direct and indirect mechanisms, and dietary cholesterol doesn't increase plasma cholesterol in many people, in my opinion (and as shown in various articles, such as the one by McNamara, 2000: (http://hardcorephysiologyfun.blogspot.com/2009/05/hmb-3-hydroxyisovalerate.html)]. But at high doses, cholesterol-laden foods would probably start to contribute to atherosclerosis and other pathological processes, in my opinion.
I sort of doubt, at reasonable dosages, that serious vitamin K deficiency would occur in response to squalene, because, even with high-dose vitamin E supplementation, for example, the plasma under-gamma-carboxylated prothrombin (des-carboxyprothrombin) doesn't increase to anything comparing to the levels that occur with true vitamin K antagonists (such as warfarin). But I don't really know. But at first glance, this article [Booth et al., 2004: (http://www.ajcn.org/cgi/content/full/80/1/143)(http://www.ncbi.nlm.nih.gov/pubmed/15213041?dopt=Abstract)], for example, looks like it's showing that vitamin E behaves like a vitamin K antagonist (they're structurally similar). But there's one key sentence in the article, and it's the one in which the authors say that the PIVKA-II [this is the same as des-gamma-carboxyprothrombin or as des-carboxyprothrombin: (http://scholar.google.com/scholar?num=100&hl=en&lr=&q=%22des-carboxy+prothrombin%22+OR+descarboxyprothrombin+OR+%22carboxyprothrombin%22)] concentrations in response to vitamin E were in the range of 2.4 ng/mL. The authors go on to say that the PIVKA-II levels in people on oral anticoagulants are 750 ng/mL, or 313 times the levels produced by vitamin E. So that's similar to saying warfarin and other anticoagulants are 313 times as potent as vitamin E in producing anticoagulant effects. Of course, vitamin E could, in my opinion, cause bleeding by causing its inhibitory effects on the activation of protein kinase C in platelets, etc. Also, Olestra evidently has been shown to not very readily cause vitamin K deficiency, and some of these articles discuss squalene in relation to compounds like Olestra [Koonsvitsky et al., 1997: (http://jn.nutrition.org/cgi/content/full/127/8/1636S)(http://www.ncbi.nlm.nih.gov/pubmed/9237960)]. I could be wrong about this vitamin K-depleting potential, though. I can't say, with much confidence, what the effects of squalene would be, and I'm just giving my initial impressions and guesses. Vitamin K metabolism is very strange and complex, but the coagulation system is somehow able to sustain itself with tiny, 15-microgram amounts of dietary vitamin K. It's partly that the coagulation cascade is so extremely potent and self-perpetuating and almost totally-unregulated, but I wonder if there isn't some other factor, produced endogenously, that has vitamin K activity.
I mentioned the seemingly-bizarre possibility that squalene could have vitamin K activity, and there's an article showing that geranylgeraniol, which is essentially a 20-carbon chain of 4 isoprene units, appears to have vitamin K activity [Ronden et al., 1997: (http://www.ncbi.nlm.nih.gov/pubmed/9247360)]. Squalene generally doesn't seem to behave in quite the same ways as some of the pre-squalene-and-post-mevalonate isoprenoids, which include geranylgeraniol, do, but the research is very chaotic and difficult to interpret. The authors of that article also discuss the fact that rats have much higher vitamin K requirements than humans, even when one scales the dosages between species (their requirements are 50-100 times those of humans, evidently). That's just one of many totally bizarre aspects of vitamin K metabolism. That article (Ronden et al., 1997), though, as I've discussed in a past posting, shows, in a roudabout way, that increasing the vitamin K intakes of rats does produce thrombogenic effects (the "obstruction time"). The authors suggested that the thrombogenicity might have been secondary to the vitamins-K-induced macrophage apoptosis or osteoclast-precursor-cell apoptosis (programmed cell death). Geranylgeraniol certainly has been shown to produce apoptotic effects in macrophages and osteoclasts in many articles (http://scholar.google.com/scholar?q=geranylgeraniol+apoptosis+osteoclast+OR+macrophage&hl=en&lr=), but it's certainly conceivable that the doses used by the authors of that article (Ronden et al., 1997) are supraphysiological. Some articles have shown, on the other hand, that geranylgeraniol and other free isoprenoids can prevent apoptosis or stimulate cell proliferation and growth in those and other cell types.
In any case, I want to say that, in my opinion, vitamin K supplementation has the potential to be very dangerous, in many cases, especially in the absence of the concomitant use of an anticoagulant (low-dose vitamin K is sometimes given along with vitamin K antagonists, to minimize variation in the INR) or in the absence of instructions from one's doctor. One would obviously want to talk to his or her doctor before making any changes in any supplements or medications. I'm not going to go into a discussion of vitamin K, but, in my opinion, using supplemental vitamin K to compensate for some supposed vitamin-K-deficiency-inducing effect of squalene would be a terrible idea and could, in my opinion, produce life-threatening thrombogenicity or other effects (especially since there's this disturbing, vitamin-K-mimetic effect that some free isoprenoids, such as geranylgeraniol, can have). I've discussed vitamin K in past postings [(http://hardcorephysiologyfun.blogspot.com/2009/01/vitamin-b2-riboflavin-and-vitamin-k.html); (http://hardcorephysiologyfun.blogspot.com/2009/01/half-lives-of-clotting-factor-proteins.html); (http://hardcorephysiologyfun.blogspot.com/2009/01/vitamin-b2-riboflavin-and-vitamin-k.html); (http://hardcorephysiologyfun.blogspot.com/2009/01/another-chilling-article-on-vitamin-k.html); (http://hardcorephysiologyfun.blogspot.com/2009/01/different-perspectives-on-coq10-and.html); (http://hardcorephysiologyfun.blogspot.com/2009/01/vitamin-k-activity-and-coq10-concerns.html)]. Vitamin K compounds can produce macrophage apoptosis and may induce thrombogenicity by that mechanism, in my opinion, as discussed in past postings. It's more likely that it will just increase thrombin formation by increasing prothrombin levels, in my opinion. But the numbers of articles showing these apoptotic effects on osteoclasts, etc., are very disturbing to me (http://scholar.google.com/scholar?q=%22vitamin+K%22+apoptosis+osteoclast+OR+macrophage&hl=en&lr=). I know all about the supposedly-great effects of vitamin K and the way the vitamin-K2-series compounds supposedly act more extrahepatically than vitamin K1 does and supposedly play a role in the prevention of vascular calcification, etc. And some growth factors (http://scholar.google.com/scholar?num=100&hl=en&lr=&q=Gas6+%22vitamin+K%22) and proteins involved in the clearance of apoptotic cells (Mer, etc.) (http://scholar.google.com/scholar?num=100&hl=en&lr=&q=Mer+%22vitamin+K%22) contain glutamate residues that are post-translationally modified by vitamin-K-dependent gamma-carboxylation. But there are things that look good on paper, and then there's reality, in my opinion.
There seem to be lots of things about squalene that are not well-understood, but that's just my opinion. It may increase cholesterol levels and thereby lead to the suppression of the formation pre-squalene isoprenoids and isoprenylated proteins, etc., but then it seems like it might have some mysterious capacity to produce vitamin K activity. It could have the opposite effect and act as a vitamin K antagonist, but there's evidence that some compounds can act as both vitamin K antagonists and vitamin K mimetics. These are just my opinions, though, and squalene isn't sounding all that good to me, at the moment. I'll see if there are other articles showing apparent vitamin K activity or vitamin-K-mimetic effects of geranylgeraniol or other isoprenoids, but it's a really complicated area of research.
It's not clear if squalene can cross the blood-brain barrier, but I would guess that it can. Free fatty acids can cross lipid bilayers by passive diffusion, by the "flip-flop" type of mechanism of crossing lipid bilayers (http://hardcorephysiologyfun.blogspot.com/2009/04/free-fatty-acid-transport-and.html), and squalene may behave similarly. It's a polymer of 6 isoprene units (30-carbons) but is not nearly as reactive as many polyunsaturated fatty acids, evidently because it does not contain bis-allylic hydrogens [Cho et al., 2009: (http://pt.wkhealth.com/pt/re/cdrm/abstract.00003050-200906000-00011.htm)] (hydrogens that are allylic to two double bonds, meaning that they're on the carbon in between two double bonds). Apart from that, though, it appears to be able to elevate cholesterol levels in the skin of humans (Cho et al., 2009) and, evidently, in the testes in rats, given that squalene supplementation increased plasma testosterone in rats [Liu et al., 2009: (http://icmr.nic.in/ijmr/2009/february/0206.pdf)(http://www.ncbi.nlm.nih.gov/pubmed/19293441)]. That research on testosterone is reminiscent of research showing that serum testosterone concentrations increase as the dietary saturated fat intake increases [one of many articles showing that: Volek et al., 1997: (http://jap.physiology.org/cgi/content/full/82/1/49)(http://www.ncbi.nlm.nih.gov/pubmed/9029197); see some of the articles shown here: (http://scholar.google.com/scholar?q=Testosterone+and+cortisol+in+relationship+to+dietary+volek&hl=en&lr=)], but I don't know how much there is to that. It's probably only true up to a point, but it's consistent with the idea that some saturated fat is "required" for extrahepatic cholesterol biosynthesis. The effect would, in my opinion, eventually or sooner-than-eventually be opposed by, for example, the increase in aromatase activity, in adipocytes, in response to weight gain from massive amounts of saturated fat. Also, one would ask if downregulations in androgen receptor expression occur, etc. Normalizing the membrane or intracellular cholesterol concentration is likely to be possible, but upregulating the whole hypothalamic-pituitary-gonadal axis, in response to something like squalene alone, is unlikely to occur, in my opinion.
One concern would be the potential for induced vitamin K deficiency (in addition to the concern that squalene could, in my opinion, conceivably produce pathological effects by mimicking vitamin K), given the research showing this can occur in rodents and other animals (http://scholar.google.com/scholar?num=100&hl=en&lr=&q=squalene+%22vitamin+K%22), and other potential problems include the possibility that squalene could increase "post-squalene-and-pre-cholesterol" sterols to excessive levels (these can cause problems by exerting inappropriate, feedback inhibition of HMG-CoA reductase and producing all sorts of other effects) or produce direct and "undesirable" regulatory effects (such as by displaying vitamin K activity, in my opinion). There's research showing that geranylgeraniol and related "pre-squalene" isoprenoids can produce apoptotic effects in many cell types (http://scholar.google.com/scholar?q=apoptosis+farnesol+OR+geranylgeraniol&hl=en&lr=), but my sense is that squalene tends to be more of a cholesterol precursor than those isoprenoids (given, in part, that they can be converted into substrates for protein isoprenylation, etc.). But who knows. For all I know, epoxidized squalene could accumulate and exert vitamin K activity or produce some other bizarre effect like that, as discussed below. One reason I throw these suggestions out is that squalene is epoxidized by an enzyme or enzymes that catalyzes a reaction that may be similar to the reaction that produces vitamin K epoxide.
A major reason squalene wouldn't be expected to increase plasma cholesterol much, though, at reasonable dosages, is that dietary cholesterol exerts feedback inhibition of HMG-CoA reductase activity, by various direct and indirect mechanisms, and dietary cholesterol doesn't increase plasma cholesterol in many people, in my opinion (and as shown in various articles, such as the one by McNamara, 2000: (http://hardcorephysiologyfun.blogspot.com/2009/05/hmb-3-hydroxyisovalerate.html)]. But at high doses, cholesterol-laden foods would probably start to contribute to atherosclerosis and other pathological processes, in my opinion.
I sort of doubt, at reasonable dosages, that serious vitamin K deficiency would occur in response to squalene, because, even with high-dose vitamin E supplementation, for example, the plasma under-gamma-carboxylated prothrombin (des-carboxyprothrombin) doesn't increase to anything comparing to the levels that occur with true vitamin K antagonists (such as warfarin). But I don't really know. But at first glance, this article [Booth et al., 2004: (http://www.ajcn.org/cgi/content/full/80/1/143)(http://www.ncbi.nlm.nih.gov/pubmed/15213041?dopt=Abstract)], for example, looks like it's showing that vitamin E behaves like a vitamin K antagonist (they're structurally similar). But there's one key sentence in the article, and it's the one in which the authors say that the PIVKA-II [this is the same as des-gamma-carboxyprothrombin or as des-carboxyprothrombin: (http://scholar.google.com/scholar?num=100&hl=en&lr=&q=%22des-carboxy+prothrombin%22+OR+descarboxyprothrombin+OR+%22carboxyprothrombin%22)] concentrations in response to vitamin E were in the range of 2.4 ng/mL. The authors go on to say that the PIVKA-II levels in people on oral anticoagulants are 750 ng/mL, or 313 times the levels produced by vitamin E. So that's similar to saying warfarin and other anticoagulants are 313 times as potent as vitamin E in producing anticoagulant effects. Of course, vitamin E could, in my opinion, cause bleeding by causing its inhibitory effects on the activation of protein kinase C in platelets, etc. Also, Olestra evidently has been shown to not very readily cause vitamin K deficiency, and some of these articles discuss squalene in relation to compounds like Olestra [Koonsvitsky et al., 1997: (http://jn.nutrition.org/cgi/content/full/127/8/1636S)(http://www.ncbi.nlm.nih.gov/pubmed/9237960)]. I could be wrong about this vitamin K-depleting potential, though. I can't say, with much confidence, what the effects of squalene would be, and I'm just giving my initial impressions and guesses. Vitamin K metabolism is very strange and complex, but the coagulation system is somehow able to sustain itself with tiny, 15-microgram amounts of dietary vitamin K. It's partly that the coagulation cascade is so extremely potent and self-perpetuating and almost totally-unregulated, but I wonder if there isn't some other factor, produced endogenously, that has vitamin K activity.
I mentioned the seemingly-bizarre possibility that squalene could have vitamin K activity, and there's an article showing that geranylgeraniol, which is essentially a 20-carbon chain of 4 isoprene units, appears to have vitamin K activity [Ronden et al., 1997: (http://www.ncbi.nlm.nih.gov/pubmed/9247360)]. Squalene generally doesn't seem to behave in quite the same ways as some of the pre-squalene-and-post-mevalonate isoprenoids, which include geranylgeraniol, do, but the research is very chaotic and difficult to interpret. The authors of that article also discuss the fact that rats have much higher vitamin K requirements than humans, even when one scales the dosages between species (their requirements are 50-100 times those of humans, evidently). That's just one of many totally bizarre aspects of vitamin K metabolism. That article (Ronden et al., 1997), though, as I've discussed in a past posting, shows, in a roudabout way, that increasing the vitamin K intakes of rats does produce thrombogenic effects (the "obstruction time"). The authors suggested that the thrombogenicity might have been secondary to the vitamins-K-induced macrophage apoptosis or osteoclast-precursor-cell apoptosis (programmed cell death). Geranylgeraniol certainly has been shown to produce apoptotic effects in macrophages and osteoclasts in many articles (http://scholar.google.com/scholar?q=geranylgeraniol+apoptosis+osteoclast+OR+macrophage&hl=en&lr=), but it's certainly conceivable that the doses used by the authors of that article (Ronden et al., 1997) are supraphysiological. Some articles have shown, on the other hand, that geranylgeraniol and other free isoprenoids can prevent apoptosis or stimulate cell proliferation and growth in those and other cell types.
In any case, I want to say that, in my opinion, vitamin K supplementation has the potential to be very dangerous, in many cases, especially in the absence of the concomitant use of an anticoagulant (low-dose vitamin K is sometimes given along with vitamin K antagonists, to minimize variation in the INR) or in the absence of instructions from one's doctor. One would obviously want to talk to his or her doctor before making any changes in any supplements or medications. I'm not going to go into a discussion of vitamin K, but, in my opinion, using supplemental vitamin K to compensate for some supposed vitamin-K-deficiency-inducing effect of squalene would be a terrible idea and could, in my opinion, produce life-threatening thrombogenicity or other effects (especially since there's this disturbing, vitamin-K-mimetic effect that some free isoprenoids, such as geranylgeraniol, can have). I've discussed vitamin K in past postings [(http://hardcorephysiologyfun.blogspot.com/2009/01/vitamin-b2-riboflavin-and-vitamin-k.html); (http://hardcorephysiologyfun.blogspot.com/2009/01/half-lives-of-clotting-factor-proteins.html); (http://hardcorephysiologyfun.blogspot.com/2009/01/vitamin-b2-riboflavin-and-vitamin-k.html); (http://hardcorephysiologyfun.blogspot.com/2009/01/another-chilling-article-on-vitamin-k.html); (http://hardcorephysiologyfun.blogspot.com/2009/01/different-perspectives-on-coq10-and.html); (http://hardcorephysiologyfun.blogspot.com/2009/01/vitamin-k-activity-and-coq10-concerns.html)]. Vitamin K compounds can produce macrophage apoptosis and may induce thrombogenicity by that mechanism, in my opinion, as discussed in past postings. It's more likely that it will just increase thrombin formation by increasing prothrombin levels, in my opinion. But the numbers of articles showing these apoptotic effects on osteoclasts, etc., are very disturbing to me (http://scholar.google.com/scholar?q=%22vitamin+K%22+apoptosis+osteoclast+OR+macrophage&hl=en&lr=). I know all about the supposedly-great effects of vitamin K and the way the vitamin-K2-series compounds supposedly act more extrahepatically than vitamin K1 does and supposedly play a role in the prevention of vascular calcification, etc. And some growth factors (http://scholar.google.com/scholar?num=100&hl=en&lr=&q=Gas6+%22vitamin+K%22) and proteins involved in the clearance of apoptotic cells (Mer, etc.) (http://scholar.google.com/scholar?num=100&hl=en&lr=&q=Mer+%22vitamin+K%22) contain glutamate residues that are post-translationally modified by vitamin-K-dependent gamma-carboxylation. But there are things that look good on paper, and then there's reality, in my opinion.
There seem to be lots of things about squalene that are not well-understood, but that's just my opinion. It may increase cholesterol levels and thereby lead to the suppression of the formation pre-squalene isoprenoids and isoprenylated proteins, etc., but then it seems like it might have some mysterious capacity to produce vitamin K activity. It could have the opposite effect and act as a vitamin K antagonist, but there's evidence that some compounds can act as both vitamin K antagonists and vitamin K mimetics. These are just my opinions, though, and squalene isn't sounding all that good to me, at the moment. I'll see if there are other articles showing apparent vitamin K activity or vitamin-K-mimetic effects of geranylgeraniol or other isoprenoids, but it's a really complicated area of research.
Sunday, June 7, 2009
Acyl-CoA's as Substrates or Competitive Inhibitors of Histone Deacetylases; Acyl-CoA's as Adenosine-Nucleotide Mimetics
This article [Kasantsev and Thompson, 2008: (http://www.ncbi.nlm.nih.gov/pubmed/18827828)] is interesting, and the authors classify valproic acid (VPA) and sodium butyrate (SB) as "hydroxamate-based" histone deacetylase inhibitors. But SB, VPA, and 4-phenylbutyrate don't have hydroxamate moieties, which are groups in which a carbonyl carbon is bonded to some unspecified group and also to the nitrogen of a hydroxylamine group. And I think 4-phenylbutyrate is metabolized into phenylpyruvate rapidly. The authors say that the hydroxamate moieties of the other drugs that are grouped with SB and VPA bind to an active-site zinc atom on histone deacetylase enzymes. I don't doubt that that's true for those other drugs shown, but VPA and SB only have a carbonyl group in common with those other drugs. That's not a very specific feature (having a carbonyl group).
There are very few articles that even mention butyryl-CoA and histones in the same article, and that tells me that the possibility for the butyrylation or valproylation of histones hasn't really been widely recognized. It's possible that valproyl-CoA and butyryl-CoA just bind to the active sites of HDAC's, produce competitive inhibition, and don't serve as substrates. In any case, histone deacetylase inhibition seems unlikely, in my opinion, to be a major mechanism for the effects of low doses of sodium butyrate. I think it will mainly be ketogenic and be oxidized in the liver and other cell types, but that's just my opinion.
It's interesting that the authors of a review article [Vamecq et al., 2005: (http://www.ncbi.nlm.nih.gov/pubmed/15713528)] on the ketogenic diet suggested that the adenosyl moiety of coenzyme A, in different acyl-CoA's, may mediate some of the effects of acyl-CoA's (whose concentrations increase in the brain, along with ketones, in people who are following the ketogenic (80 percent fat) diet for refractory epilepsy or some other condition) on different types of potassium channels. They basically were saying that some acyl-CoA's could bind to potassium channels by binding to the ATP binding sites. That type of mechanism could also conceivably account for the HDAC inhibition or other effects of some of these short-chain acyl-CoA's, such as butyryl-CoA. If CoA had been named "pantetheinyl-phosphoadenosine," or something along those lines, instead of "coenzyme A," then maybe someone would have mentioned that possibility long ago. Before I read that article, I'd never seen anyone mention the purine moiety of coenzyme A as being potentially important for the toxic effects or regulatory effects of acyl-CoA's (and the possibility had never occurred to me, either).
There are very few articles that even mention butyryl-CoA and histones in the same article, and that tells me that the possibility for the butyrylation or valproylation of histones hasn't really been widely recognized. It's possible that valproyl-CoA and butyryl-CoA just bind to the active sites of HDAC's, produce competitive inhibition, and don't serve as substrates. In any case, histone deacetylase inhibition seems unlikely, in my opinion, to be a major mechanism for the effects of low doses of sodium butyrate. I think it will mainly be ketogenic and be oxidized in the liver and other cell types, but that's just my opinion.
It's interesting that the authors of a review article [Vamecq et al., 2005: (http://www.ncbi.nlm.nih.gov/pubmed/15713528)] on the ketogenic diet suggested that the adenosyl moiety of coenzyme A, in different acyl-CoA's, may mediate some of the effects of acyl-CoA's (whose concentrations increase in the brain, along with ketones, in people who are following the ketogenic (80 percent fat) diet for refractory epilepsy or some other condition) on different types of potassium channels. They basically were saying that some acyl-CoA's could bind to potassium channels by binding to the ATP binding sites. That type of mechanism could also conceivably account for the HDAC inhibition or other effects of some of these short-chain acyl-CoA's, such as butyryl-CoA. If CoA had been named "pantetheinyl-phosphoadenosine," or something along those lines, instead of "coenzyme A," then maybe someone would have mentioned that possibility long ago. Before I read that article, I'd never seen anyone mention the purine moiety of coenzyme A as being potentially important for the toxic effects or regulatory effects of acyl-CoA's (and the possibility had never occurred to me, either).
Note on Histone Butyrylation and Propionylation
What I meant in the last posting (http://hardcorephysiologyfun.blogspot.com/2009/06/histone-butyrylation-and-propionylation.html) is that the transcriptional responses to the butyrylation of histones might be similar to the responses produced by the acetylation of histones, and the butyrylated histones might be poorer substrates for histone deacetylases than acetylated histones are. In the context of histone propionylation, I was thinking that propionylated histones might produce either similar or different transcriptional responses (via the ensuing ATP-dependent, chromatin remodeling) and that those responses (defined in very vague and totally unspecified terms, here) might, by any number of mechanisms, partially account for some of the adverse effects associated with propionyl-CoA accumulation (or, incidentally, some of the "positive" or "desirable" effects that have been associated with treatments with anaplerotic, odd-chain fatty acid supplements). (I mean that histone propionylation could, up to a point, produce therapeutic effects and that those effects might be inappropriately attributed to "anaplerosis" per se.) The fact that histone propionylation can occur might also tend, in my opinion, to call into question the measurements used to assess "propionate overload" in people who are receiving odd-chain fatty acid supplements (such as triheptanoin). Researchers have tended to evaluate the potential for propionyl-CoA overload (and also propionate overload) by measuring plasma or urinary methylcitrate and other organic acids, but it's possible that excesses of propionyl-CoA might be used as substrates for histone acetyltransferases (rather than being cleaved to yield propionate and then its abnormal metabolites) and confound attempts to evaluate the extent of the propionyl-CoA accumulation.
Saturday, June 6, 2009
Histone Butyrylation and Propionylation by Histone Acetyltransferases; Histone Debutyrylation and Depropionylation by Histone Deacetylases
This is a really interesting article [Leemhuis et al., 2008: (http://www.ncbi.nlm.nih.gov/pubmed/18247445)], and it's the first article I've seen that actually sheds some light on the mechanism by which butyrate and its derivatives could produce histone deacetylase inhibition. The authors found that the P/CAF enzyme [P/CAF stands for CBP-associated factor, CBP stands for CREB binding protein, and CREB stands for cyclic adenosine 5'-monophosphate (cAMP) response element binding protein; hence, P/CAF is cAMP response element binding protein binding protein-associated factor: Soutoglou et al., 2001: (http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=125231)(http://www.ncbi.nlm.nih.gov/pubmed/11296231)], a human histone acetyltransferase enzyme, can catalyze the propionylation or butyrylation of the Lys14 residue of the histone H3 protein, using propionyl-CoA or butyryl-CoA, respectively, as substrates. The authors also note that the SIRT2 and SIRT3 histone deacetylase enzymes, which are class I sirtuins, can catalyze histone depropionylation reactions. The authors found that the butyrylation of H3 histones occurred less readily than the propionylation of the H3 histones. Also, the P/CAF enzyme didn't exhibit acyltransferase activity when malonyl-CoA, methylmalonyl-CoA, isovaleryl-CoA, or hexanoyl-CoA were provided as substrates.
It sounds like increases in the percentages of butyrylated histone proteins, in response to sodium butyrate (at, for example, high but not low concentrations), could render those butyrylated histones resistant to deacylation by histone deacetylases. That could be a mechanism for their histone deacetylase inhibition. Who knows, though. It looks like there's some evidence that SIRT2 and SIRT3 can catalyze the debutyrylation of histones (http://scholar.google.com/scholar?num=100&hl=en&lr=&q=histone+debutyrylation+OR+%22butyryl+transferase%22+OR+butyrylation+OR+butyryltransferase). The histone propionylation might be important for understanding some of these genetic disorders (such as for understanding mitochondrial DNA depletion in methylmalonic aciduria, in which propionyl-CoA accumulates), but that process also could be important for understanding vitamin B12 deficiency and the mechanisms underlying all of the pathologies associated with vitamin B12 deficiency (hematological and central-nervous-system-related). Propionyl-CoA also can accumulate intracellularly as a result of biotin deficiency. That's a really important series of articles. That could be a really important mechanism for understanding mitochondrial dysfunction, because acyl-CoA's accumulate in all sorts of disorders. If other histone acetyltransferases can utilize methylmalonyl-CoA or other organic acyl-CoAs as substrates, that would be interesting, too. But it's noteworthy that propionyl-CoA is maybe the most or at least among the most highly toxic of the acyl-CoAs. One reason for that might be its capacity to serve as a good substrate for histone acetyltransferase enzymes, such as P/CAF. It's hard to know, though, because it looks like a lot of different deacetylases can debutyrylate histones. But maybe the butyryllysine residues are poor substrates for those deacetylases.
Butyrate is converted to butyryl-CoA by one or more short chain acyl-CoA synthetase enzymes that display butyryl-CoA synthetase activity [Cremin et al., 2003: (http://ajpgi.physiology.org/cgi/content/full/285/1/G105)(http://www.ncbi.nlm.nih.gov/pubmed/12637251?dopt=Abstract)]. Another possibility is that some transcription factor or other non-histone protein is butyrylated by an acyltransferase enzyme that can use butyryl-CoA as a substrate, and the butyrylated protein might then influence the activity of one or more histone deacetylase enzymes [some hastily-chosen info. on protein acylation: Ozawa et al., 2009: (http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2672172)]. That type of mechanism could account for the effects of HMB (3-hydroxyisovalerate), which is converted into 3-hydroxyisovaleryl-CoA and could then serve as a substrate for the 3-hydroxyisovalerylation of transcription factors, etc. (or it could be that HMG-CoA serves as a substrate for enzymes with histone or non-histone protein acyltransferase activities).
It sounds like increases in the percentages of butyrylated histone proteins, in response to sodium butyrate (at, for example, high but not low concentrations), could render those butyrylated histones resistant to deacylation by histone deacetylases. That could be a mechanism for their histone deacetylase inhibition. Who knows, though. It looks like there's some evidence that SIRT2 and SIRT3 can catalyze the debutyrylation of histones (http://scholar.google.com/scholar?num=100&hl=en&lr=&q=histone+debutyrylation+OR+%22butyryl+transferase%22+OR+butyrylation+OR+butyryltransferase). The histone propionylation might be important for understanding some of these genetic disorders (such as for understanding mitochondrial DNA depletion in methylmalonic aciduria, in which propionyl-CoA accumulates), but that process also could be important for understanding vitamin B12 deficiency and the mechanisms underlying all of the pathologies associated with vitamin B12 deficiency (hematological and central-nervous-system-related). Propionyl-CoA also can accumulate intracellularly as a result of biotin deficiency. That's a really important series of articles. That could be a really important mechanism for understanding mitochondrial dysfunction, because acyl-CoA's accumulate in all sorts of disorders. If other histone acetyltransferases can utilize methylmalonyl-CoA or other organic acyl-CoAs as substrates, that would be interesting, too. But it's noteworthy that propionyl-CoA is maybe the most or at least among the most highly toxic of the acyl-CoAs. One reason for that might be its capacity to serve as a good substrate for histone acetyltransferase enzymes, such as P/CAF. It's hard to know, though, because it looks like a lot of different deacetylases can debutyrylate histones. But maybe the butyryllysine residues are poor substrates for those deacetylases.
Butyrate is converted to butyryl-CoA by one or more short chain acyl-CoA synthetase enzymes that display butyryl-CoA synthetase activity [Cremin et al., 2003: (http://ajpgi.physiology.org/cgi/content/full/285/1/G105)(http://www.ncbi.nlm.nih.gov/pubmed/12637251?dopt=Abstract)]. Another possibility is that some transcription factor or other non-histone protein is butyrylated by an acyltransferase enzyme that can use butyryl-CoA as a substrate, and the butyrylated protein might then influence the activity of one or more histone deacetylase enzymes [some hastily-chosen info. on protein acylation: Ozawa et al., 2009: (http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2672172)]. That type of mechanism could account for the effects of HMB (3-hydroxyisovalerate), which is converted into 3-hydroxyisovaleryl-CoA and could then serve as a substrate for the 3-hydroxyisovalerylation of transcription factors, etc. (or it could be that HMG-CoA serves as a substrate for enzymes with histone or non-histone protein acyltransferase activities).
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