Tuesday, April 21, 2015

Transgenic Sweet-Potatoes

One of the first tools available to biologists seeking to make transgenic plants was a natural bacteria called Agrobacterium. The bacteria infects plants and induces the production of auxins and cytokinins, plant hormones that together trigger the growth of a disordered plant tissue called a gall. The gall provides nutrients that the bacteria then uses for its own growth. The bacteria pulls off this trick by inserting genetic information into plant cells. It can do this because it carries a plasmid that can function both in its own cells and in the cells of a plant. When the bacteria infects the plant, the plasmid is transferred into the plant's cells. Once there, the plasmid integrates into the genome of the plant and activates. The bacteria are natural genetic engineers.

Genetic remnants can be left behind whenever the bacteria does this trick and nowadays we can do genome sequencing to find such remnants. Kyndt et al found remnants of this process in sweet-potatoes (Ipomea batatas). In particular, they found such a fragment inserted into an intron of an F-box gene in the sweet-potato genome. Interestingly, this interruption is found in all domesticated sweet-potatoes they examined and not in wild related species.

The insertion contains multiple complete genes and results in the interruption of the F-box gene. F-box genes are generally involved in protein degradation and in plants they're involved in the regulation of development during growth. It isn't clear that the insertion they found results in a change in the development of the plant associated with domestication, however. They are still working on this.

Oh yes, did I mention they found this fragment in all samples they examined of domesticated sweet-potatoes? This means that every single sweet-potato is a transgenic organism, a GMO. We didn't make it a GMO, but there is no way around it, every sweet-potato is a GMO.

Every sweet-potato is a GMO.

Are you against GMOs? Then don't eat any more sweet-potatoes. Are you actually against the business practices of Monsanto surrounding their GMO and herbicide products? Then rail against those business practices instead of the red herring that GMOs are in the overall story.

  1. Agrobacterium: en.wikipedia.org/wiki/Agrobacterium
  2. Kyndt et al, 2015: m.pnas.org/content/early/2015/04/14/1419685112.full.pdf
  3. F-box genes: en.wikipedia.org/wiki/F-box_protein
  4. Red herring: en.wikipedia.org/wiki/Red_herring

Tuesday, April 7, 2015

Glucose Metabolism (Burying the Lead)

1. Glycolysis
The process of glycolysis (Fig 1) breaks down a single 6-carbon glucose molecule into two 3-carbon pyruvate molecules. Glycolysis is the central metabolic pathway for converting sugars into energy for all known living things. Two ATP and two NADH are generated for each glucose molecule processed.

2.  A. Krebs Cycle.  B. Carbons.
If oxygen is available, the resulting pyruvate can then be processed by the Krebs cycle (Fig 2A) to produce two more ATP, as well as eight NADH and two FADH2. The three carbons from each new pyruvate molecule take more than two complete cycles of the Krebs Cycle to be converted into CO2 (Fig 2B).

The NADH and FADH2 can be used in other pathways or they can be used to generate further ATP through the process of oxidative phosphorylation in the mitochondria. Three ATP can be generated from each NADH and two ATP can be generated from each FADH2. The three processes together generate 38 ATP from each glucose molecule metabolized.

3. Fermentation pathways.
When oxygen isn't available, alternate fermentation pathways (Fig 3) are used to get rid of the excess pyruvate that builds up from glycolysis. Because the NADH produced in glycolysis is consumed during ethanol and lactic acid fermentation (fig 3A and 3C), only two ATP are generated in these two fermentation pathways for each glucose molecule metabolized. In acetate fermentation (fig 3B), four ATPs and two NADHs are produced for a total of 10 ATP equivalents.

The net result is that oxidative metabolism can generate 38 ATPs compared to the 2 ATPs of ethanol and lactic acid fermentation and the 10 ATPs in acetate fermentation, for each glucose metabolized. Oxidative metabolism is far more efficient at generating biological energy in the form of ATP.

In the fermentation pathway leading to ethanol, one-third of the carbons are lost as CO2. If a pathway could be engineered to capture that CO2 and incorporate it into another ethanol, the efficiency of the process for creating ethanol could be increased by 50%. This would mean more fuel could be produced more cheaply and ethanol-based fuels would become more cost-effective overall.

4.  A. NOG & EtOH fermentation.  B. Carbon rearrangement.
This is exactly what Igor W. Bogorad, Tzu-Shyang Lin, and James C. Liao argue they have accomplished in what they call non-oxidative glycolysis (NOG). I didn't like their figures because they didn't illustrate the pathways taken by individual carbons or illustrate the final energy balance, so I made my own figure for the first pathway they describe.

In figure 4B, three erythrose 4-phosphate (E4P) molecules are rearranged to make two fructose 6-phosphate molecules (F6P). Each initial E4P molecule is colored distinctly (magenta, red, and blue) and then the carbons in later steps are colored to indicate which E4P they came from. In the end, one F6P is built from three carbons from each of two E4Ps while the other F6P is built from all four carbons of one E4P and the remaining one carbon each from the first two E4Ps.

NOG is able to convert a single glucose molecule into three acetyl-CoA molecules, with no net change in ATP levels or loss of carbon in the form of CO2. Each acetyl-CoA molecule converting to a molecule of ethanol, however, absorbs two NADH molecules (equivalent to 6 ATPs). The final results for this pathway are the consumption of the equivalent of 18 ATPs (3 for each NADH consumed) for each glucose molecule converted to ethanol. This means that the cell would have to process 9 glucose molecules by typical glycolysis paired with anaerobic fermentation for each 1 glucose molecule processed by this version of NOG to maintain a zero energy balance. This isn't a biologically efficient process at all.

5. NOG and acetate fermentation.
They mention integrating this pathway with carbon assimilation pathways to convert CO2 into fuel. Because the ethanolic fermentation pathway after NOG is so energetically unfavorable, I'm not sure how this would work. I'll have to later examine the energetics of the pathway when tied to carbon assimilation pathways to see if the argument actually makes sense.

If instead the acetyl-CoA is fermented to acetate or to acetic acid as a terminal product, there would be a net gain of [3][2] ATPs per glucose. This final version is discussed in short form in Bogorad's paper and is energetically useful, [producing 50% more ATP than the typical glycolysis linked to ethanol or lactic acid fermentation, though still] [producing the same amount of ATP as typical glyclolysis linked to ethanolic or lactic acid fermentation. This is] well below the 10 ATPs per glucose produced through typical glycolysis linked to acetate or acetic acid fermentation.

5. NOG & Krebs Cycle.
What happens if we process the resulting acetyl-CoA by the Krebs Cycle instead of anaerobic fermentation?

The NOG pathway generates 0 ATP compared to the 8 ATP generated during glycolysis. However, the NOG pathway generates 3 acetyl-CoA compared to the 2 acetyl-CoA generated during glycolysis.

Each acetyl-CoA generates the equivalent of 15 ATPs through the Krebs Cycle so the combination of NOG and the Krebs Cycle will generate a total of 45 ATPs for each glucose molecule processed. This is more than the 38 ATPs generated by the combination of glycolysis and the Krebs Cycle.

This pathway produces 25% more biologically usable energy per glucose molecule than what our biology uses, with precisely the same chemical inputs and outputs. This is an amazing result that should have been the headline result of Bogorad's research paper. It would have been the first thing I talked about in this blog post, except that I needed to build the story that provides context for the significance of this result.

NOG-acetic-fermentation is more productive than glycolysis-lactic/ethanolic-fermentation and NOG-Krebs-cycle is more productive than glycolysis-Krebs-cycle in terms of ATP output per glucose metabolized.

Why does our biology use a relatively inefficient method of glycolysis?

Once glycolysis evolved, other metabolic pathways would have evolved to take advantage of the various intermediates of glycolysis. This would have the effect of making dramatic changes to the pathway more costly, locking the pathway into its present form. This appears to be the argument preferred by the authors.

Another possibility is that the NOG pathway was simply too large of a transition from the existing glycolytic pathway to have evolved naturally. Acetic fermentation isn't a common pathway even though it produces far more ATP energy than the common ethanol and lactic acid fermentation pathways. Because acetic fermentation is a prerequisite to NOG being energetically productive, there have been relatively few possibilities for NOG to have evolved naturally.

That pathways with higher efficiency exist but haven't become common is suggestive of limits on how living things can naturally evolve and that other considerations than efficiency at producing ATP are significant.

  1. Non-oxidative glycolysis: www.nature.com/nature/journal/v502/n7473/full/nature12575.html
  2. Alternate source for paper: www.bnl.gov/biosciences/JournalClubDocuments/YuanhengCai-Reprint.pdf
  3. Acetate fermentation: www.vet.ed.ac.uk/clive/cal/rumencal/frames/frmfibro.html
  4. Acetic Acid fermentation: www.pnas.org/content/105/37/13769.figures-only 
  5. Krebs cycle: en.wikipedia.org/wiki/Citric_acid_cycle
  6. Ethanol fermentation: en.wikipedia.org/wiki/Ethanol_fermentation
  7. Lactic acid fermentation: en.wikipedia.org/wiki/Lactic_acid_fermentation
Other pathways of interest: