Ribulose 1,5-bisphosphate

Ribulose 1,5-bisphosphate (RuBP) is an organic substance that is involved in photosynthesis, notably as the principal CO₂ acceptor in plants.^[1]: 2 It is a colourless anion, a double phosphate ester of the ketopentose (ketone-containing sugar with five carbon atoms) called ribulose. Salts of RuBP can be isolated, but its crucial biological function happens in solution.^[2] RuBP occurs not only in plants but in all domains of life, including Archaea, Bacteria, and Eukarya.^[3]

Ribulose 1,5-bisphosphate

The acid form of the RuBP anion
Names
IUPAC name 1,5-Di-O-phosphono-D-ribulose
Other names Ribulose 1,5-diphosphate
Identifiers
CAS Number	2002-28-0 Y
3D model (JSmol)	Interactive image
ChEBI	CHEBI:16710 Y
ChemSpider	110238 Y
KEGG	C01182
PubChem CID	123658
UNII	BR374X7NAH
CompTox Dashboard (EPA)	DTXSID301344111 DTXSID30173837, DTXSID301344111
InChI InChI=1S/C5H12O11P2/c6-3(1-15-17(9,10)11)5(8)4(7)2-16-18(12,13)14/h3,5-6,8H,1-2H2,(H2,9,10,11)(H2,12,13,14)/t3-,5-/m1/s1 Y Key: YAHZABJORDUQGO-NQXXGFSBSA-N Y
SMILES O=P(O)(OCC(=O)[C@H](O)[C@H](O)COP(=O)(O)O)O
Properties
Chemical formula	C5H12O11P2
Molar mass	310.088 g·mol−1
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa). N verify (what is YN ?) Infobox references

History

RuBP was originally discovered by Andrew Benson in 1951 while working in the lab of Melvin Calvin at UC Berkeley.^[4][5] 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".^[4][6] 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.^[4][5][7]

Role in photosynthesis and the Calvin-Benson Cycle

See also: 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).^[8] This six-carbon β-ketoacid intermediate hydrates into another six-carbon intermediate in the form of a gem-diol.^[9] 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.^[10][11]

In the Calvin-Benson cycle, RuBP is a product of the phosphorylation of ribulose-5-phosphate (produced by glyceraldehyde 3-phosphate) by ATP.^[11][12]

The Calvin-Benson cycle showing the role of ribulose-1,5-bisphosphate.

Interactions with rubisco

RuBP acts as an enzyme inhibitor for the enzyme rubisco, which regulates the net activity of carbon fixation.^[13][14][15] When RuBP is bound to an active site of rubisco, the ability to activate via carbamylation with CO₂ and Mg²⁺ is blocked. The functionality of rubisco activase involves removing RuBP and other inhibitory bonded molecules to re-enable carbamylation on the active site.^[1]: 5

Role in photorespiration

See also: Photorespiration

Rubisco also catalyzes RuBP with oxygen (O
₂) in an interaction called photorespiration, a process that is more prevalent at high temperatures.^[16][17] During photorespiration RuBP combines with O
₂ to become 3-PGA and phosphoglycolic acid.^[18][19][20] Like the Calvin-Benson Cycle, the photorespiratory pathway has been noted for its enzymatic inefficiency^[19][20] although this characterization of the enzymatic kinetics of rubisco have been contested.^[21] Due to enhanced RuBP carboxylation and decreased rubisco oxygenation stemming from the increased concentration of CO₂ in the bundle sheath, rates of photorespiration are decreased in C₄ plants.^[1]: 103 Similarly, photorespiration is limited in CAM photosynthesis due to kinetic delays in enzyme activation, again stemming from the ratio of carbon dioxide to oxygen.^[22]

Measurement

RuBP can be measured isotopically via the conversion of ¹⁴CO₂ and RuBP into glyceraldehyde 3-phosphate.^[23] G3P can then be measured using an enzymatic optical assay.^{[23][24][lower-alpha 1]} 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.^[25]

See also

• Rubisco
• Calvin-Benson cycle
• 3-Phosphoglyceric acid
• Photosynthesis

References

1. Leegood, R. C.; Sharkey, T. D.; von Caemmerer, S., eds. (2000). Photosynthesis: Physiology and Metabolism. Advances in Photosynthesis. Vol. 9. Kluwer Academic Publishers. doi:10.1007/0-306-48137-5. ISBN 978-0-7923-6143-5.
2. Nelson, D. L.; Cox, M. M. (2000). Lehninger, Principles of Biochemistry (3rd ed.). New York: Worth Publishing. ISBN 1-57259-153-6.
3. Tabita, F. R. (1999). "Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: A different perspective". Photosynthesis Research. 60: 1–28. doi:10.1023/A:1006211417981. S2CID 21975329.
4. Sharkey, T. D. (2018). "Discovery of the canonical Calvin–Benson cycle" (PDF). Photosynthesis Research. 140 (2): 235–252. doi:10.1007/s11120-018-0600-2. OSTI 1607740. PMID 30374727. S2CID 53092349.
5. Benson, A. A. (1951). "Identificiation of Ribulose in C14O2 Photosynthesis Products". Journal of the American Chemical Society. 73 (6): 2971–2972. doi:10.1021/ja01150a545.
6. Benson, A. A. (2005). "Following the path of carbon in photosynthesis: a personal story". In Govindjee; Beatty, J. T.; Gest, H.; Allen, J. F. (eds.). Discoveries in Photosynthesis. Advances in Photosynthesis and Respiration. Vol. 20. pp. 795–813. doi:10.1007/1-4020-3324-9_71. ISBN 978-1-4020-3324-7.
7. Wildman, S. G. (2002). "Along the trail from Fraction I protein to Rubisco (ribulose bisphosphate carboxylase-oxygenase)" (PDF). Photosynthesis Research. 73 (1–3): 243–250. doi:10.1023/A:1020467601966. PMID 16245127. S2CID 7622999.
8. Lorimer, G. H.; Andrews, T. J.; et al. (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. 313 (1162): 397–407. Bibcode:1986RSPTB.313..397L. doi:10.1098/rstb.1986.0046.
9. Mauser, H.; King, W. A.; Gready, J. E.; Andrews, T. J. (2001). "CO2 Fixation by Rubisco: Computational Dissection of the Key Steps of Carboxylation, Hydration, and C−C Bond Cleavage". J. Am. Chem. Soc. 123 (44): 10821–10829. doi:10.1021/ja011362p. PMID 11686683.
10. Kaiser, G. E. "Light Independent Reactions". Biol 230: Microbiology. The Community College of Baltimore County, Catonsville Campus. Retrieved 7 May 2021.
11. Hatch, M. D.; Slack, C. R. (1970). "Photosynthetic CO2-Fixation Pathways". Annual Review of Plant Physiology. 21: 141–162. doi:10.1146/annurev.pp.21.060170.001041.
12. Bartee, L.; Shriner, W.; Creech, C. (2017). "The Light Independent Reactions (aka the Calvin Cycle)". Principles of Biology. Open Oregon Educational Resources. ISBN 978-1-63635-041-7.
13. Jordan, D. B.; Chollet, R. (1983). "Inhibition of ribulose bisphosphate carboxylase by substrate ribulose 1,5-bisphosphate". Journal of Biological Chemistry. 258 (22): 13752–13758. doi:10.1016/S0021-9258(17)43982-2. PMID 6417133.
14. Spreitzer, R. J.; Salvucci, M. E. (2002). "Rubisco: Structure, Regulatory Interactions, and Possibilities for a Better Enzyme". Annual Review of Plant Biology. 53: 449–475. doi:10.1146/annurev.arplant.53.100301.135233. PMID 12221984.
15. Taylor, Thomas C.; Andersson, Inger (1997). "The structure of the complex between rubisco and its natural substrate ribulose 1,5-bisphosphate". Journal of Molecular Biology. 265 (4): 432–444. doi:10.1006/jmbi.1996.0738. PMID 9034362.
16. Leegood, R. C.; Edwards, G. E. (2004). "Carbon Metabolism and Photorespiration: Temperature Dependence in Relation to Other Environmental Factors". In Baker, N. R. (ed.). Photosynthesis and the Environment. Advances in Photosynthesis and Respiration. Vol. 5. Kluwer Academic Publishers. pp. 191–221. doi:10.1007/0-306-48135-9_7. ISBN 978-0-7923-4316-5.
17. Keys, A. J.; Sampaio, E. V. S. B.; et al. (1977). "Effect of Temperature on Photosynthesis and Photorespiration of Wheat Leaves". Journal of Experimental Botany. 28 (3): 525–533. doi:10.1093/jxb/28.3.525.
18. Sharkey, T. D. (1988). "Estimating the rate of photorespiration in leaves". Physiologia Plantarum. 73 (1): 147–152. doi:10.1111/j.1399-3054.1988.tb09205.x.
19. Kebeish, R.; Niessen, M.; et al. (2007). "Chloroplastic photorespiratory bypass increases photosynthesis and biomass production in Arabidopsis thaliana". Nature Biotechnology. 25 (5): 593–599. doi:10.1038/nbt1299. PMID 17435746. S2CID 22879451.
20. Leegood, R. C.; Lea, P. J.; et al. (1995). "The regulation and control of photorespiration". Journal of Experimental Botany. 46: 1397–1414. doi:10.1093/jxb/46.special_issue.1397. JSTOR 23694986.
21. Bathellier, C.; Tcherkez, G.; et al. (2018). "Rubisco is not really so bad". Plant, Cell and Environment. 41 (4): 705–716. doi:10.1111/pce.13149. hdl:1885/231026. PMID 29359811. S2CID 3718311.
22. Niewiadomska, E.; Borland, A. M. (2008). "Crassulacean Acid Metabolism: A Cause or Consequence of Oxidative Stress in Planta?". In Lüttge, U.; Beyschlag, W.; Murata, J. (eds.). Progress in Botany. Vol. 69. pp. 247–266. doi:10.1007/978-3-540-72954-9_10. ISBN 978-3-540-72954-9.
23. Latzko, E.; Gibbs, M. (1972). "Measurement of the intermediates of the photosynthetic carbon reduction cycle, using enzymatic methods". Photosynthesis and Nitrogen Fixation Part B. Methods in Enzymology. Vol. 24. Academic Press. pp. 261–268. doi:10.1016/0076-6879(72)24073-3. ISBN 9780121818876. ISSN 0076-6879. PMID 4670193.
24. Latzko, E.; Gibbs, M. (1969). "Level of Photosynthetic Intermediates in Isolated Spinach Chloroplasts". Plant Physiology. 44 (3): 396–402. doi:10.1104/pp.44.3.396. PMC 396097. PMID 16657074.
25. Sicher, R. C.; Bahr, J. T.; Jensen, R. G. (1979). "Measurement of Ribulose 1,5-Bisphosphate from Spinach Chloroplasts". Plant Physiology. 64 (5): 876–879. doi:10.1104/pp.64.5.876. PMC 543382. PMID 16661073.

1. Note that G3P is a 3-carbon sugar so its abundance should be twice that of the 6-carbon RuBP, after accounting for rates of enzymatic catalysis.