Rubisco and Crop Output

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You may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue.

Function

Rubisco or ribulose- 1,5- bisphosphate carboxylase oxygenase is an enzyme that is involved in photosynthesis in plants and is specifically found in chloroplasts. (Harel, et. al) Rubisco is used in the light dependent part of the Calvin cycle. In this cycle, it catalyzes the first step of carbon fixation. It converts atmospheric carbon dioxide into useable sugar. It does this by using carbon dioxide to make an intermediate- an Enediolate intermediate, then a unstable intermediate, and then finally, 3-Phosphoglycerate. Most all of this 3-Phosphoglycerate is recycled and able to use again. It adds carbons to ribulose bisphosphate and then cleaves the 6 carbons into 2 chains with 3 carbons. Rubisco can also help to oxidize RuBP (Ribulose 1,5-bisphosphate), a sugar.

Structure

Rubisco is composed of 8 large subunits and 8 small subunits. The large subunits house the binding/active sites. In Rubisco, the active site of bonding is centered around a magnesium ion. However, depending on the organism, Rubisco can also have a different shape. on the large subunit. This, in turn, further helps with the Calvin cycle. (Harel, et. al) “The types of residues involved are acidic residues that interact with Mg2+, basic residues and histidines that interact with phosphate and hydroxyl groups, polar residues that interact with hydroxyl groups, one hydrophobic residue, and backbone atoms of several residues.” (Harel, et. al) This enzyme, Rubisco, only works during the day, or when there is a light source, and is turned off at night when it is dark. Carbon dioxide is attached to the binding site which turns it off and then back on again.

is Rubisco’s “chaperone” or “regulator”. It turns Rubisco on and off based off of the amount of carbon intake. ATP is used by rubisco activase to change rubisco structurally, which turns it on and off. “The activase is now recognized to be a member of the AAA(+) family, whose members participate in macromolecular complexes that perform diverse chaperone-like functions. The conserved nucleotide-binding domain of AAA(+) family members appears to have a common fold that when applied to the activase is generally consistent with previous site-directed mutagenesis studies of the activase.” (Portis Jr.)

Effect on Crop Output

Scientists can and have used Rubisco to make advances in plant technology. With the ever-changing problems going on in this world, some plant proteins can help change food scarcity. Some plant proteins, including Rubisco, can be even more useful and sustainable than proteins found in animals. It also has a lot of nutritional value, along with amino acids. For example, lysine is the most common amino acid found. Lysine may reduce anxiety by blocking stress response receptors, and it can also improve the absorption/retention of calcium. “Highly purified Rubisco is a tasteless, odourless white powder with a nutritional value reported to be equal to or superior to that of other food proteins. Rubisco also possesses some desirable functional properties which might enable food processors to successfully incorporate the protein into a number of different food products (desserts, composite meat products, ice cream, beverages). Further developments are to come to test Rubisco into food systems such as desserts / yogurt for texturing and flavouring improvements.” (van de Velde, et. al)

Problems

Rubisco is the most common protein in the world! Although this is true, just because it is the most abundant doesn’t mean it’s the most useful. Rubisco has some problems working correctly. The rate of the carboxylation reaction with Rubisco is 3 s-1. This is extremely slow. Another problem with Rubisco is that oxygen, as well as carbon dioxide, can fit into the binding site. This is because they both are similar in size and shape. It is difficult for Rubisco to distinguish which is which. (Goodsell) If this happens, and it does, phosphoglycolate can be made, and this is very toxic. This is Rubisco’s wasteful side reaction. To fix these mistakes, is very costly to the plant, meaning, it costs ATP to fix this. Now the plant has to transport the glycolate across multiple membranes, losing CO and making more of these wasteful reactions occur. Depending on varying temperatures Rubisco is working with, its error rate can range from 20- 40%! (Alber, et. Al) Most plants are C3 or C4 plants. This is based off whether they use C3 or C4 intermediates. C3 plants are more accustomed to cooler temperatures, as opposed to C4 plants that are found in warmer temperatures. is more likely to occur in C4 plants than C3 plants, because C4 plants grow in warmer climates. As temperatures begin to increase, so does photorespiration. Plants are more likely to dehydrate in the warm weather. This forces them to close the stomata in order to conserve water. When the plant closes the stomata, CO2 is prevented from entering the leaf. Photorespiration is when Rubisco binds O2 instead of CO2. This is contrary to the general pattern of photosynthesis, where Rubisco binds to CO2 instead of O2. Rubisco acts differently in C4 than C3 plants. To reduce photorespiration, C4 plants can “harvest” CO2 in bundle sheath cells. They also are useful at collecting carbon and using less water in warmer climates.

The major problem researchers have been working to change with Rubisco is the oxygenation instead of the carboxylation. The reason this is a problem is because the plant has to undergo a wasteful side reaction, making this energetically unfavorable, by losing around 30% of the plants ATP in that step. When Rubisco binds oxygen instead, crop yield becomes lower, this is because it only makes half the amount of 3-Phosphoglycerate. This limits how many times a plant can undergo the Calvin Cycle to make sugar. When temperatures begin to increase it is even more of an inconvenience and much more difficult for a plant to fix this problem. If we can fix kinetically competitive side reaction, Rubisco can not only be more successful with photosynthesis, but extremely successful with changing crop growth and quantity.

“In recent times, major advances in Rubisco engineering have been achieved through improvement of our knowledge of Rubisco synthesis and assembly, and identifying amino acid catalytic switches in the L-subunit responsible for improvements in catalysis. in crops such as rice will require further advances in chloroplast bioengineering and Rubisco biogenesis.”Carefully modifying genes in specific major functioning subunits can help change Rubisco to adjust the Calvin cycle and save ATP. This all starts in the chloroplasts, where Rubisco works. Improvements can also be made in C3 plants as well. They can be engineered to harvest Co2 as well, just like C4 plants. There are also alternative pathways that can be created to avoid oxygenation. ^[3]

Success of Rubisco

RCA plays an important part in maintaining Rubisco activity. RCA is a nuclear gene that encodes a chloroplast protein. It is a member of the AAA(+) protein superfamily. Without RCA, plants would need a high amount of CO2 because Rubisco activity wouldn’t be maintained. Sugar phosphate molecules inhibit catalysis and prevent carbamylation. RCA removes these sugar phosphate molecules. “In most plants, RCA comprises two isoforms, an α isoform equipped with a C-terminal extension containing two cysteine residues that confer redox regulation and a shorter b isoform (Carmo-Silva et al., 2015). In Arabidopsis, the b isoform does not contain the redoxsensitive cysteine residues and is less sensitive to ADP inhibition (Carmo-Silva & Salvucci, 2013). However, the b form of tobacco RCA is sensitive to ADP inhibition, which may be explained by the absence of the α isoform (Carmo-Silva & Salvucci, 2013).” ^[3]

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