Rubisco also catalyzes photorespiration

The enzyme, rubisco, not only initiates carbon fixation in the Calvin cycle; it also combines with oxygen to initiate photorespiration. As its name suggests (rubsiCO) the enzyme is both a carboxylase and an oxygenase. The active site of rubisco cannot distinguish the two similar substrates: O=C=O and O=O. As we shall see, the two reactions catalyzed by the same enzyme are diametrically oppposed to each other.

Each reaction pathway undoes the other, and both reactions can operate in a cell simultaneously depending upon the environmental conditions. As both substrates combine with the active site of rubisco, they are competitive inhibitors of each other's reactions. One might recall our earlier discussions about competitive inhibition. The relative concentration of the two substrates and the differential affinity of the enzyme for each substrate will determine which of the reactions (Calvin cycle or Photorespiration) predominate. Fortunately for plants (and for us indirectly!) rubisco has an affinity for carbon dioxide that is 80 times higher than its affinity for oxygen. However, the relatively low ratio of CO2 to O2 of mesophyll fluids in contact with air (0.04) means that, in a typical plant, the Calvin cycle only occurs about three times faster than photorespiration. Temperature also influences the relative rates of photorespiration and the Calvin cycle. Because increased temperature more efficiently removes carbon-dioxide from solution than it does oxygen, high temperatures favor photorespiration.

The photorespiration pathway is an enzymatic one that is not coupled to any electron transfer system. It does not generate ATP. It does use oxygen and it does produce carbon dioxide, and it uses a sugar-phosphate as its primary fuel. The complete pathway is depicted here.

It is worthy to note that this diagram, as others of its type, show the organelles tightly appressed to each other. Indeed there are some famous electron micrographs (example above) that show this, but other micrographs do not show them this way. I say this just to comment that this positioning may be more an efficient design for communication to students than a realistic portrayal of life in a typical cell.

In the chloroplast, rubisco, combines with ribulose-1,5-bisphosphate (RuBP) and oxygen. The five-carbon RuBP is split into the two-carbon 2-phosphoglycolate and the three-carbon 3-phosphoglycerate (PGA). The enzymes of this pathway are enumerated in the diagram above.

The 2-phosphoglycolate is converted to glycolate by phosphoglycolate phosphatase in the chloroplast. The phosphate liberated is returned to the local phosphate pool. The glycolate is transported from the chloroplast into a nearby peroxisome.

In the peroxisome, the glycolate is oxidized by oxygen gas to glyoxylate and hydrogen peroxide by glycolate oxidase. The peroxide is converted to water and oxygen gas by catalase. So the consumption of oxygen in the oxidation is replaced by catalase activity in the peroxisome.

The glyoxylate is converted to the amino acid glycine in the peroxisome. The amino group is transferred to the glyoxylate from glutamate (another amino acid) by glyoxylate:glutamate aminotransferase. The glutamate is converted to α-ketoglutarate (we will remember and come back to that later!). The glycine is transported to the mitochondrion.

In the mitochondrion, glycine decarboxylase carves off carbon dioxide gas from the glycine. This requires NAD+ to park the hydrogen atom. It also cleaves off the amino group. If you are paying attention to the chemical structures, you realize that the two-carbon amino acid has had both its amino and acid groups removed! There is only one carbon left! This methylene group is parked on a folate molecule in the mitochondrion.

When a second glycine arrives into the mitochondrion from the peroxisome, it combines with the methylene-folate to release the three-carbon amino acid serine through the action of serine hydroxymethyltransferase. Also released for re-use by this enzyme reaction is the folate. The serine is transported to the peroxisome.

In the peroxisome, the serine loses its amino group to α-ketoglutarate (remember, we would get back to that!) to regenerate the glutamate required in an earlier step in the pathway. This amino-transfer is accomplished by serine aminotransferase. In this reaction the serine is converted to hydroxypyruvate.

The peroxisome reduces the hydroxypyruvate to glycerate by hydroxypyruvate reductase. The reducing power for this comes from NADH; if you recall this was produced in an earlier step in the mitochondrion. The glycerate is transported to the chloroplast.

In the chloroplast, the glycerate is converted by glycerate kinase to 3-phosphoglycerate. The phosphate comes from ATP. Instead of producing ATP, photorespiration uses ATP. The 3-phosphoglycerate from the beginning and this new one from the end of photorespiration enter the chloroplast pool of PGA that is used to regenerate RuBP.

Photorespiration loses 25% of the carbon it takes from the Calvin cycle

The photorespiration pathway siphons carbon away from the Calvin cycle, but it also returns some of what it takes. Because it takes two glycines in photorespiration to complete the pathway, two glycolates must be taken from the Calvin cycle. Of these four carbons taken, one is lost as carbon dioxide and three are returned to the Calvin cycle. This 25% loss of carbon is going to give measurement errors for photosynthesis in whole-cells or leaves. We are probably under-estimating the photosynthetic rate by 25%.

Rubisco evolution

The wastefulness of photorespiration is probably a consequence of just two factors. Early in the evolution of photosynthesis there was a higher carbon dioxide to oxygen gas ratio in the ancient atmosphere. Indeed the atmosphere was likely anaerobic in the earliest times on Earth. Rubisco evolved its active site when oxygen was rare and carbon dioxide was common. Since ancient times, rubisco has not yet evolved a mechanism to discriminate between the two similar substrates (O=C=O and O=O). The reactions are similar too; the substrate is attached at a point along RuBP resulting in its splitting into organo-monophosphates. 3-phosphoglycerate is a common product of both reactions. So the difficulty of a protein to distinguish such similar molecules and to catalyze one reaction but not the other just has not happened yet. Photorespiration losses have not been intolerable either; the selection pressure is probably not severe in most environments. But in hot, dry, heavily-populated environments where plants effectively reduce the local carbon-dioxide content of the atmosphere, selection should have resulted in a few adaptations to overcome photorespiration. Indeed!