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Friday, April 20, 2007

Some Bacteria Don't Need Pyruvate Dehydrogenase

Recall that the pyruvate dehydrogenase complex catalyzes the conversion of pyruvate to acetyl-CoA. This is an important reaction in all living cells because acetyl-CoA is required for fatty acid synthesis. The reaction is important in animals because acetyl-CoA enters the citric acid cycle where it is broken down to carbon dioxide and the energy is captured by the mitochondrial electron transport system in the form of ATP. This step isn't so important in most bacteria because they don't have a citric acid cycle. Most species can also save the two carbon atoms of the acetyl group in acetyl-CoA and use them to build carbohydrates such as glucose. Animals can't do this.

You would think that the pyruvate dehydrogenase complex (PDC) must be ubiquitous since it catalyzes such an important reaction. Not so. PDC is the only enzyme in eukaryotes but some bacteria have another enzyme that can make acetyl-CoA. As you might expect, the bacteria that gave rise to mitochondria do have a PDC that's related to the eukaryotic enzyme. This is because the genes were transferred from those bacteria to their eukaryotic hosts when the endosymbiotic event occurred about two billion years ago.

Lots of different kinds of bacteria have a similar PDC but some have a completely different enzyme called pyruvate:ferredoxin oxidoreducatase (PFOR) (E.C. (Chabrière et al. 2001). This enzyme catalyzes a very similar reaction where pyruvate undergoes an oxidative decarboxylation yielding CO2 and acetyl-CoA. The difference is that instead of having a complicated electron transport chain where electrons are passed to lipoamide, FAD+, and finally NAD+ [Pyruvate Dehydrogenase Reaction], the PFOR reaction is much simpler. Here electrons are transferred to ferredoxin, a small iron-containing protein.

The structure of pyruvate:ferredoxin oxidoreductase has been worked out from a combination of X-ray diffraction data and electron microscopy, just as we saw with the pyruvate dehydrogenase complex [The Structure of the Pyruvate Dehydrogenase Complex]. The structure of one such enzyme, from the bacterium Desulfovibrio vulgaris, is shown in the figure above. This complex consists of eight copies of the enzyme (Garczarek et al. 2007). In other species a simple two-copy complex suffices.

Ferredoxin is a cofactor in many biochemical reactions. As a general rule, enzymes that use ferredoxin are more ancient than enzymes that involve NAD+ as a cofactor. Ferredoxin metabolism doesn't need oxygen and the available evidence suggests that oxygen wasn't present in the ancient atmosphere. Modern bacteria that use pyruvate:ferredoxin oxidoreductase (PFOR) instead of the pyruvate dehydrogenase complex (PDC) are capable of anaerobic growth (without oxygen).

The structure of many ferredoxins have been solved. The one shown on the left is from Pseudomonas aeruginosa. It's a typical example (Giastas et al. 2006). The protein is quite small and most ferredoxins contain two iron-suflur (Fe-S) complexes. These are box-like structures formed from iron molecules (red) and sulfur molecules (yellow). They are bound to the protein through the sulfhydyl groups of the amino acid cysteine. Electrons are carried by the iron ions.
Fe3+ + e- → Fe2+
There's another important reason why PFOR is important in some bacteria. Look at the PDC reaction shown above. The arrow points in one direction indicating that this reaction is essentially irreversible. It can't be used to fix carbon dioxide by combining it with the acetyl group to make pyruvate. That's not true of the much simpler PFOR reaction. In fact, the reverse reaction is the main CO2 fixing reaction in many photosynthetic bacteria and in methanogens (bacteria that use methane as a carbon source).

But we're getting distracted. The point is that the pyruvate dehydrogenase complex probably arose late in evolution after photosynthetic bacteria had transformed the atmosphere into one that contained significant levels of oxygen. Where did such a complicated protein complex come from?

Chabriere, E., Vernede, X., Guigliarelli, B., Charon, M.H., Hatchikian, E.C. and Fontecilla-Camps, J.C. (2001) Crystal structure of the free radical intermediate of pyruvate:ferredoxin oxidoreductase. Science 294:2559-63.

Garczarek, F., Dong, M., Typke, D., Witkowska, H.E., Hazen, T.C., Nogales, E., Biggin, M.D., and Glaeser, R.M..(2007) Octomeric pyruvate-ferredoxin oxidoreductase from Desulfovibrio vulgaris. J Struct Biol. 2007 Feb 17; [Epub ahead of print] .

Giastas, P., Pinotsis, N., Efthymiou, G., Wilmanns, M., Kyritsis, P., Moulis, J.M., and Mavridis, I.M..(2006) The structure of the 2[4Fe-4S] ferredoxin from Pseudomonas aeruginosa at 1.32-Å resolution: comparison with other high-resolution structures of ferredoxins and contributing structural features to reduction potential values. J. Biol. Inorg. Chem. 11:445-58.

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