HOMEBREW Digest #4819 Sun 07 August 2005

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  Crabtree effect and metabolic overflow at pyruvate branch ("Fredrik")
  secondary fermentation in bottle (KEITH R BUSBY)

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---------------------------------------------------------------------- Date: Sun, 7 Aug 2005 21:44:05 +0200 From: "Fredrik" <carlsbergerensis at hotmail.com> Subject: Crabtree effect and metabolic overflow at pyruvate branch Hello everyone. All recent talks on the crabtree discussions is interesting. FWIW I have some comments on which I would like to get some feedback. It seems that many "effects in yeast" take place at different levels. The basic level is the phenomena that can typically appear in any complex dynamical system due to constraints in the metabolic network, like energy and mass balancing. Ontop of this there are regulatory control of enzymes and gene expression. If you consider a really simplified view of the main energy and carbon flow, it seems that at least to principle, the crabtree effect can be understood from (an almost) pure dynamical point of view? though I'm sure the phenomenon is further be tweaked and enhanced by more not so easy to understand regulatory responses in the cell. But OTOH I think that even the not so easy to understand regulatory behaviours often may have a dynamic explanation, at least for triggerings. First there is sugaruptake, then there is glycolysis, then at the pyruvate branch the flow is put to competion with pyruvatedecarboxylase(pdc) (to acetadelhyde/fermentation), pyruvatedehydrogenas(pdh)(to acetyl-CoA) and also some pipelining directly into misc biosynthesis. Each of these pipelines has an affinity, and a capacity, and also a different energy balancing etc. Affect the flow in one pipeline and the flow in remote places in the network might change. I don't find the refenrece now but I know I read a paper claming that, pdh has a factor 10 higher *affinity*(prefenece) for pyruvate as compared to pdc. pdc has a factir 10 higher *capacity* for purvate as comapared to pdh. (If anyone wants it I can look for it, I just have no structure on references atm so I have to wade through lots of htings). But a general good reference is a really nice thesis on the "Physiological Roles of pyruvate decarboxylase in Saccharomyces cerevisiae" by Marcel Flikweert - http://www.xs4all.nl/~marcelf/Thesis.htm Excellent site I found recently where the articles are free to download. Maybe these numbers are from there even (I forgot!?), but it's a great thesis and outstanding bedtime and/or bathtub reading. So already here one would expect that at low glycolysis rates, the respiratory pathways is *preferred*, given that oxidative phosporylation is running and there is O2 etc. (pasteur effect) At higher glycolysis rates, this branch is saturated, and there is an overflow into the pdc. This alone (so far) however, doesn't seem to explain the "suppression" of respiratory pathway, it is just a simple "overflow" - so more is needed. But then at a closer look, what happens if the glycolysis rate increase? Then the growth rate typically increase too right? And so does the demand for building blocks. The puruvate brach is then also more drained for carbon, and the acetyl pool is also drained for carbon to. This seems to imply that, given that the pdh is saturated, then acetyl-CoA production is in a simple estimate, at max. At this point there seems to be a competition for acetyl-CoA between respiratory energy transduction pathways and biosynthesis of for example fatty acids. So, at this point - if the growth rate is to be able to increase - it seems that the respiratory consumption of acetyl-CoA must be not only "saturated and overflowed", it must also be *downregulated* to maintain the mass balance. I have no idea how far this effect lats to explain things when you start to put numbers on it, but it seems to me it could at least help understand the pasteur and crabtree effects, and any additional regulatory things probably enhance these dynamic effects. So from this possibly oversimplified and even incorrect description it seems to me put simple The "Crabtree effect" can be roughly understood the combined effect of 1) saturation of the acetyl-CoA production at high glycolysis rates, causing metabolic overflow at hte pyruvate branch 2) downregulation of the respiratory activity, due to growth related mass flow competition at the acetyl-CoA branch? The "pasteur effect" would as it seems caused by pdh winning the competition for pyruvate, when there is oxygen. The pasteur effect will exist only if pdh is not near saturation, because then in despited of the higher affinity, there is an overflow to alcoholic fermentation. This is admittedly an oversimplification, there are more draining going on in the flow, pentose pathways, and also a shunting via acetate back to acetyl-CoA. But from papers I've read this shunting while highly significant also limited capacity, so it is likely insufficient(?) to regenerate enough acetyl-CoA to prevent biosynthesis from draining the acetyl-CoA pool. Even if you add these things, and the redox balancing I suspect the general conclusion holds to principle. Though if you were to put numbers on things all pathways probably has to be accounted for. Quick simplified pic I made http://hem.bredband.net/frerad/beer/modelling/pictures/crabtree.jpg So it seems to me that the "crabtree" breaking point, seems to be related to the ratio of the pdh pathway "bandwidth" and the rate of glycolysis but also the energy consumption of biosynthesis. So another complication may be thta the cost for growth increases as stress factors accumulate (maybe likely in when alcohol anc acids are produced and osmosis increase?) Too much to keep in the head at once. I'd need a computer. Since glucose as far as I understnad is the quickest sugar to uptake, it is also expected to generate one of the higest glycolytic rates? Of course, if this is not so, the idea fails. Does anyone know if this is so or ot? Once migth wonder, if the capacity of the pdh pathway is so limiting, why doesn't the cell just synthesise more pdh?? I don't know. But I figure that a general thing is that would increase various pool sizes too, and would also probably affect the steady state redox balance? So while I have no idea why, there seems to be many possible understandable reasons?? Comments?? These reasoning may well be flawed, as I'm still no biologist, but it's how I personally currently think of these things where I am constantly trying to improve my understanding. I'd love to get some comments on this or if anyone see any obvious flaws in the reasoning. ( I posted about a simplified computer simulations of metabolism before, and while I'm still working on it. The more I learn the more do I see how much computing power I am going to need due to the :-( So right now, it looks like my original strategy is not going to work so well due to limited computing power. So I am currently trying to figure out how to try to implement even this very limited model in a way that it will work on a normal PC. The basic dynamics will probably be workable, though it is probably going to take many hours on a PC. The other problem I recently found out is that the mimicing of regulation intelligence seems to require probably even more computing power than the "kinetics" alone unless i simplifiy it even more. So it is definitly going to take a little longer than I first thought. I had to make the regulation more intelligent. My first idea to use set regulation functions are not good enough mainly because they would most certainly be able to work, but I would end up with way too many parameters and they would require constant tweaking. ) I'd like comments from the other of you on this list, if you think this makes sense, or you see some flaws I missed? /Fredrik Return to table of contents
Date: Sun, 07 Aug 2005 20:18:22 -0500 From: KEITH R BUSBY <kbusby at wisc.edu> Subject: secondary fermentation in bottle Does anyone have experience of secondary fermentation of Tripels in bottle? While in Brussels last week, I read that Tongerlo adds yeast at bottling to heighten flavors and aromas. Would one use the same yeast as for primary or a different one (the text I read mentioned primary yeasts in the plural)? How would one do it? Add with priming sugar? If so, how much? Or perhaps a drop per bottle? Is there a risk of gushers or bottle bombs? Keith Keith Busby Douglas Kelly Professor of Medieval French Department of French and Italian The University of Wisconsin 618 Van Hise Hall Madison, WI 53706 (608) 262-3941 (608) 265-3892 (fax) Return to table of contents
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