Ribulose 1,5-bisphosphate explained

Ribulose 1,5-bisphosphate (RuBP) is an organic substance that is involved in photosynthesis, notably as the principal acceptor in plants.[1] 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]

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".[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.[7]

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).[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.[12]

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 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

See also: Photorespiration. Rubisco also catalyzes RuBP with oxygen in an interaction called photorespiration, a process that is more prevalent at high temperatures.[16] [17] During photorespiration RuBP combines with to become 3-PGA and .[18] [19] [20] Like the Calvin-Benson Cycle, the photorespiratory pathway has been noted for its enzymatic inefficiency 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 in the bundle sheath, rates of photorespiration are decreased in plants. 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 and RuBP into glyceraldehyde 3-phosphate.[23] G3P can then be measured using an enzymatic optical assay.[24] 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

Notes and References

  1. Book: Photosynthesis: Physiology and Metabolism . Leegood . R. C. . Sharkey . T. D. . von Caemmerer . S. . 2000 . Kluwer Academic Publishers . Advances in Photosynthesis . 9 . 978-0-7923-6143-5 . 10.1007/0-306-48137-5 .
  2. Book: Nelson . D. L. . Cox . M. M. . Lehninger, Principles of Biochemistry . 3rd . Worth Publishing . New York . 2000 . 1-57259-153-6.
  3. Tabita . F. R. . Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: A different perspective . Photosynthesis Research . 60 . 1–28 . 1999 . 10.1023/A:1006211417981. 21975329 .
  4. Discovery of the canonical Calvin–Benson cycle . Sharkey . T. D. . 2018 . Photosynthesis Research . 140 . 2 . 235–252 . 10.1007/s11120-018-0600-2 . 30374727 . 1607740 . 53092349 .
  5. Identificiation of Ribulose in C14O2 Photosynthesis Products . Benson . A. A. . 1951 . Journal of the American Chemical Society . 73 . 6 . 2971–2972 . 10.1021/ja01150a545.
  6. Book: Benson, A. A. . Discoveries in Photosynthesis . Advances in Photosynthesis and Respiration . 20 . Following the path of carbon in photosynthesis: a personal story . Govindjee . Beatty . J. T. . Gest . H. . Allen . J. F. . 2005 . 10.1007/1-4020-3324-9_71 . 978-1-4020-3324-7 . https://link.springer.com/chapter/10.1007%2F1-4020-3324-9_71 . 795–813.
  7. Wildman . S. G. . Along the trail from Fraction I protein to Rubisco (ribulose bisphosphate carboxylase-oxygenase) . Photosynthesis Research . 73 . 243–250 . 2002 . 1–3 . 10.1023/A:1020467601966 . 16245127 . 7622999 .
  8. 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 . 397–407 . Lorimer . G. H. . Andrews . T. J. . etal . 1986 . 1162 . 10.1098/rstb.1986.0046. 1986RSPTB.313..397L .
  9. CO2 Fixation by Rubisco: Computational Dissection of the Key Steps of Carboxylation, Hydration, and C−C Bond Cleavage . Mauser . H. . King . W. A. . Gready . J. E. . Andrews . T. J. . J. Am. Chem. Soc. . 2001 . 123 . 44 . 10821–10829 . 10.1021/ja011362p. 11686683 .
  10. Web site: Kaiser . G. E. . Light Independent Reactions . Biol 230: Microbiology . 7 May 2021 . The Community College of Baltimore County, Catonsville Campus.
  11. Photosynthetic CO2-Fixation Pathways . Hatch . M. D. . Slack . C. R. . 1970 . 21 . Annual Review of Plant Physiology . 141–162 . 10.1146/annurev.pp.21.060170.001041.
  12. Book: The Light Independent Reactions (aka the Calvin Cycle) . Principles of Biology . L. . Bartee . W. . Shriner . C. . Creech . 2017 . https://openoregon.pressbooks.pub/mhccmajorsbio/chapter/calvin-cycle/ . 978-1-63635-041-7 . Open Oregon Educational Resources .
  13. Jordan . D. B. . Chollet . R. . Inhibition of ribulose bisphosphate carboxylase by substrate ribulose 1,5-bisphosphate . Journal of Biological Chemistry . 258 . 22 . 1983 . 13752–13758 . 10.1016/S0021-9258(17)43982-2 . 6417133. free .
  14. Rubisco: Structure, Regulatory Interactions, and Possibilities for a Better Enzyme . Annual Review of Plant Biology . 53 . 449–475 . 10.1146/annurev.arplant.53.100301.135233 . 2002 . Salvucci . M. E. . Spreitzer . R. J.. 12221984 .
  15. The structure of the complex between rubisco and its natural substrate ribulose 1,5-bisphosphate . Thomas C. . Taylor . Inger . Andersson . Journal of Molecular Biology . 265 . 4 . 1997 . 10.1006/jmbi.1996.0738 . 432–444. 9034362 .
  16. Book: Leegood . R. C. . Edwards . G. E. . Photosynthesis and the Environment . Carbon Metabolism and Photorespiration: Temperature Dependence in Relation to Other Environmental Factors . 191–221 . Baker . N. R. . Kluwer Academic Publishers . 978-0-7923-4316-5 . https://link.springer.com/chapter/10.1007/0-306-48135-9_7 . Advances in Photosynthesis and Respiration . 2004 . 5. 10.1007/0-306-48135-9_7 .
  17. Effect of Temperature on Photosynthesis and Photorespiration of Wheat Leaves . Keys . A. J. . Sampaio . E. V. S. B. . etal . Journal of Experimental Botany . 28 . 3 . 1977 . 525–533 . 10.1093/jxb/28.3.525.
  18. Estimating the rate of photorespiration in leaves . Sharkey . T. D. . 1988 . Physiologia Plantarum . 73 . 1 . 147–152 . 10.1111/j.1399-3054.1988.tb09205.x.
  19. Chloroplastic photorespiratory bypass increases photosynthesis and biomass production in Arabidopsis thaliana . Kebeish . R. . Niessen . M. . etal . Nature Biotechnology . 25 . 593–599 . 2007 . 5 . 10.1038/nbt1299. 17435746 . 22879451 .
  20. The regulation and control of photorespiration . Leegood . R. C. . Lea . P. J. . etal . Journal of Experimental Botany . 46 . 1995 . 1397–1414 . 23694986 . 10.1093/jxb/46.special_issue.1397.
  21. Rubisco is not really so bad . Plant, Cell and Environment . 41 . 4 . 705–716 . Bathellier . C. . Tcherkez . G. . 2018 . etal . 10.1111/pce.13149. 29359811 . 1885/231026 . 3718311 . free .
  22. Book: Niewiadomska . E. . Borland . A. M. . Crassulacean Acid Metabolism: A Cause or Consequence of Oxidative Stress in Planta? . Progress in Botany . 69 . 2008 . 247–266 . 10.1007/978-3-540-72954-9_10 . 978-3-540-72954-9 . Lüttge . U. . Beyschlag . W. . Murata . J..
  23. Book: Latzko . E. . Gibbs . M. . Measurement of the intermediates of the photosynthetic carbon reduction cycle, using enzymatic methods . Photosynthesis and Nitrogen Fixation Part B . Methods in Enzymology . 24 . Academic Press . 1972 . 261–268 . 0076-6879 . 9780121818876 . 10.1016/0076-6879(72)24073-3. 4670193 .
  24. Latzko . E. . Gibbs . M. . Level of Photosynthetic Intermediates in Isolated Spinach Chloroplasts . Plant Physiology . 44 . 3 . 396–402 . 16657074 . 1969 . 10.1104/pp.44.3.396. 396097 .
  25. Sicher . R. C. . Bahr . J. T. . Jensen . R. G. . Measurement of Ribulose 1,5-Bisphosphate from Spinach Chloroplasts . 1979 . Plant Physiology . 64 . 5 . 876–879 . 10.1104/pp.64.5.876 . 16661073. 543382 .

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