Ribulose 1,5-bisphosphate

History

RuBP was originally discovered by Andrew Benson in 1951 while working in the lab of Melvin Calvin at UC Berkeley. Calvin, who had been away from the lab at the time of discovery and was not listed as a co-author, controversially removed the full molecule name from the title of the initial paper, identifying it solely as "ribulose". At the time, the molecule was known as ribulose diphosphate (RDP or RuDP) but the prefix di- was changed to bis- to emphasize the nonadjacency of the two phosphate groups.

Role in photosynthesis and the Calvin-Benson Cycle

The enzyme ribulose-1,5-bisphosphate carboxylase-oxygenase (rubisco) catalyzes the reaction between RuBP and carbon dioxide. The product is the highly unstable six-carbon intermediate known as 3-keto-2-carboxyarabinitol 1,5-bisphosphate, or 2'-carboxy-3-keto-D-arabinitol 1,5-bisphosphate (CKABP). This six-carbon β-ketoacid intermediate hydrates into another six-carbon intermediate in the form of a gem-diol. This intermediate then cleaves into two molecules of 3-phosphoglycerate (3-PGA) which is used in a number of metabolic pathways and is converted into glucose.

In the Calvin-Benson cycle, RuBP is a product of the phosphorylation of ribulose-5-phosphate (produced by glyceraldehyde 3-phosphate) by ATP.

Interactions with rubisco

RuBP acts as an enzyme inhibitor for the enzyme rubisco, which regulates the net activity of carbon fixation. When RuBP is bound to an active site of rubisco, the ability to activate via carbamylation with and is blocked. The functionality of rubisco activase involves removing RuBP and other inhibitory bonded molecules to re-enable carbamylation on the active site.

Role in photorespiration

Rubisco also catalyzes RuBP with oxygen () in an interaction called photorespiration, a process that is more prevalent at high temperatures. During photorespiration RuBP combines with to become 3-PGA and phosphoglycolic acid.{{cite journal | title = Chloroplastic photorespiratory bypass increases photosynthesis and biomass production in Arabidopsis thaliana

Measurement

RuBP can be measured isotopically via the conversion of and RuBP into glyceraldehyde 3-phosphate. G3P can then be measured using an enzymatic optical assay. Given the abundance of RuBP in biological samples, an added difficulty is distinguishing particular reservoirs of the substrate, such as the RuBP internal to a chloroplast vs external. One approach to resolving this is by subtractive inference, or measuring the total RuBP of a system, removing a reservoir (e.g. by centrifugation), re-measuring the total RuBP, and using the difference to infer the concentration in the given repository.

References

References

1. (2000). "Photosynthesis: Physiology and Metabolism". Kluwer Academic Publishers.
2. (2000). "Lehninger, Principles of Biochemistry". Worth Publishing.
3. Tabita, F. R.. (1999). "Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: A different perspective". Photosynthesis Research.
4. Sharkey, T. D.. (2018). "Discovery of the canonical Calvin–Benson cycle". Photosynthesis Research.
5. Benson, A. A.. (1951). "Identificiation of Ribulose in C14O2 Photosynthesis Products". Journal of the American Chemical Society.
6. Benson, A. A.. (2005). "Discoveries in Photosynthesis".
7. Wildman, S. G.. (2002). "Along the trail from Fraction I protein to Rubisco (''r''ib''u''lose ''bis''phosphate ''c''arboxylase-''o''xygenase)". Photosynthesis Research.
8. (1986). "2´-carboxy-3-keto-D-arabinitol 1,5-bisphosphate, the six-carbon intermediate of the ribulose bisphosphate carboxylase reaction". Phil. Trans. R. Soc. Lond. B.
9. (2001). "CO2 Fixation by Rubisco: Computational Dissection of the Key Steps of Carboxylation, Hydration, and C−C Bond Cleavage". J. Am. Chem. Soc..
10. Kaiser, G. E.. "Light Independent Reactions". The Community College of Baltimore County, Catonsville Campus.
11. (1970). "Photosynthetic CO2-Fixation Pathways". Annual Review of Plant Physiology.
12. (2017). "Principles of Biology". Open Oregon Educational Resources.
13. (1983). "Inhibition of ribulose bisphosphate carboxylase by substrate ribulose 1,5-bisphosphate". Journal of Biological Chemistry.
14. (2002). "Rubisco: Structure, Regulatory Interactions, and Possibilities for a Better Enzyme". Annual Review of Plant Biology.
15. (1997). "The structure of the complex between rubisco and its natural substrate ribulose 1,5-bisphosphate". Journal of Molecular Biology.
16. (2004). "Photosynthesis and the Environment". Kluwer Academic Publishers.
17. (1977). "Effect of Temperature on Photosynthesis and Photorespiration of Wheat Leaves". Journal of Experimental Botany.
18. Sharkey, T. D.. (1988). "Estimating the rate of photorespiration in leaves". Physiologia Plantarum.
19. (1995). "The regulation and control of photorespiration". Journal of Experimental Botany.
20. (2018). "Rubisco is not really so bad". Plant, Cell and Environment.
21. (2008). "Progress in Botany".
22. (1972). "Photosynthesis and Nitrogen Fixation Part B". Academic Press.
23. (1969). "Level of Photosynthetic Intermediates in Isolated Spinach Chloroplasts". Plant Physiology.
24. (1979). "Measurement of Ribulose 1,5-Bisphosphate from Spinach Chloroplasts". Plant Physiology.