Molecule of the Month: Carbon Capture Mechanisms

Modern agriculture employs many methods to increase the amount of crops that are grown, for use as food and as raw material for generating biofuels. Agricultural improvements include good nutrition, methods to fight pests and disease, and ensuring that there is enough water. However, to support the growing world population and to fight the accumulation of carbon dioxide causing climate change, we need additional ways to enhance agricultural productivity. Scientists are looking to the basic mechanisms of photosynthesis to see if there is room for improvement. One way to supercharge photosynthesis is to ensure that there is plenty of carbon dioxide available.

Cyanobacteria are experts at capturing carbon dioxide for use in photosynthesis. These simple photosynthetic bacteria arose very early in the evolution of life, and have had to face continually dwindling sources of carbon dioxide as the environment of the Earth changed over millennia. Today, cyanobacteria and other phytoplankton fix roughly half of the carbon dioxide on the Earth, and they do so with remarkable efficiency. One way they do this is by selectively transporting carbon dioxide to Rubisco, the enzyme that fixes carbon, using several complementary molecular mechanisms. These mechanisms can increase the concentration of carbon dioxide by a thousand times around the active site of Rubisco. Researchers are currently working to add these same mechanisms to crop plants to improve productivity.

The first carbon-capture mechanism used by cyanobacteria is simple: they transport bicarbonate directly into the cell. In lakes and oceans, much of the carbon dioxide reacts with water molecules to form soluble bicarbonate ions. Bicarbonate transporters traffic these bicarbonate ions into the cytoplasm, later to be converted back to carbon dioxide. Cyanobacteria utilize several types of bicarbonate transporters. BicA, shown here from PDB ID 6ki1 and 6ki2, and SbtA, shown in the interactive JSMol below, both use sodium ions to power the transport.

Cyanobacteria use carboxysomes to concentrate carbon dioxide near the enzymes that use it. Carboxysomes are large protein shells similar to virus capsids, as seen in the electron tomogram at EMDB ID 14377. The inside is packed with Rubisco (PDB ID 7yyo), carbonic anhydrase (PDB ID 8thm), and several other enzymes needed to keep everything functional. When bicarbonate enters the carboxysome, it’s rapidly converted to carbon dioxide by carbonic anhydrase. Rubisco is positioned nearby, ready to fix the carbon dioxide before it diffuses away.

Cyanobacteria also use a modified version of the NDH-1 respiratory complex to trap carbon inside the cell. NDH-1MS (PDB ID 6tjv) has a CO₂-concentrating module that acts as a carbonic anhydrase, converting carbon dioxide to bicarbonate. Carbon dioxide passes freely through cellular membranes, but bicarbonate doesn’t cross as well. So NDH-1MS converts carbon dioxide to bicarbonate, trapping it inside the cell. The bicarbonate can then diffuse into carboxysomes and be converted back to carbon dioxide for use in photosynthesis.