Ribulose 1,5-bisphosphate

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Ribulose 1,5-bisphosphate
RuBP-2D-skeletal.png
The acid form of the RuBP anion
RuBP-3D-balls.png
Names
IUPAC name
1,5-Di-O-phosphono-D-ribulose
Other names
Ribulose 1,5-diphosphate
Identifiers
3D model (JSmol)
ChEBI
ChemSpider
KEGG
PubChem CID
UNII
  • 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 Yes check.svgY
    Key: YAHZABJORDUQGO-NQXXGFSBSA-N Yes check.svgY
  • O=P(O)(OCC(=O)[C@H](O)[C@H](O)COP(=O)(O)O)O
Properties
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).
X mark.svgN  verify  (what is  Yes check.svgYX mark.svgN ?)

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]

Contents

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

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. Calvin-cycle4.svg
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

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 has 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] [a] 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

Related Research Articles

<span class="mw-page-title-main">Photosynthesis</span> Biological process to convert light into chemical energy

Photosynthesis is a system of biological processes by which photosynthetic organisms, such as most plants, algae, and cyanobacteria, convert light energy, typically from sunlight, into the chemical energy necessary to fuel their metabolism. Photosynthesis usually refers to oxygenic photosynthesis, a process that produces oxygen. Photosynthetic organisms store the chemical energy so produced within intracellular organic compounds like sugars, glycogen, cellulose and starches. To use this stored chemical energy, an organism's cells metabolize the organic compounds through cellular respiration. Photosynthesis plays a critical role in producing and maintaining the oxygen content of the Earth's atmosphere, and it supplies most of the biological energy necessary for complex life on Earth.

<span class="mw-page-title-main">RuBisCO</span> Key enzyme of photosynthesis involved in carbon fixation

Ribulose-1,5-bisphosphate carboxylase/oxygenase, commonly known by the abbreviations RuBisCo, rubisco, RuBPCase, or RuBPco, is an enzyme involved in the light-independent part of photosynthesis, including the carbon fixation by which atmospheric carbon dioxide is converted by plants and other photosynthetic organisms to energy-rich molecules such as glucose. It emerged approximately four billion years ago in primordial metabolism prior to the presence of oxygen on Earth. It is probably the most abundant enzyme on Earth. In chemical terms, it catalyzes the carboxylation of ribulose-1,5-bisphosphate.

C<sub>4</sub> carbon fixation Photosynthetic process in some plants

C4 carbon fixation or the Hatch–Slack pathway is one of three known photosynthetic processes of carbon fixation in plants. It owes the names to the 1960s discovery by Marshall Davidson Hatch and Charles Roger Slack.

<span class="mw-page-title-main">Photorespiration</span> Process in plant metabolism

Photorespiration (also known as the oxidative photosynthetic carbon cycle or C2 cycle) refers to a process in plant metabolism where the enzyme RuBisCO oxygenates RuBP, wasting some of the energy produced by photosynthesis. The desired reaction is the addition of carbon dioxide to RuBP (carboxylation), a key step in the Calvin–Benson cycle, but approximately 25% of reactions by RuBisCO instead add oxygen to RuBP (oxygenation), creating a product that cannot be used within the Calvin–Benson cycle. This process lowers the efficiency of photosynthesis, potentially lowering photosynthetic output by 25% in C3 plants. Photorespiration involves a complex network of enzyme reactions that exchange metabolites between chloroplasts, leaf peroxisomes and mitochondria.

C<sub>3</sub> carbon fixation Series of interconnected biochemical reactions

C3 carbon fixation is the most common of three metabolic pathways for carbon fixation in photosynthesis, the other two being C4 and CAM. This process converts carbon dioxide and ribulose bisphosphate (RuBP, a 5-carbon sugar) into two molecules of 3-phosphoglycerate through the following reaction:

<span class="mw-page-title-main">Biological carbon fixation</span> Series of interconnected biochemical reactions

Biological carbon fixation, or сarbon assimilation, is the process by which living organisms convert inorganic carbon to organic compounds. These organic compounds are then used to store energy and as structures for other biomolecules. Carbon is primarily fixed through photosynthesis, but some organisms use chemosynthesis in the absence of sunlight. Chemosynthesis is carbon fixation driven by chemical energy rather than from sunlight.

<span class="mw-page-title-main">Calvin cycle</span> Light-independent reactions in photosynthesis

The Calvin cycle, light-independent reactions, bio synthetic phase, dark reactions, or photosynthetic carbon reduction (PCR) cycle of photosynthesis is a series of chemical reactions that convert carbon dioxide and hydrogen-carrier compounds into glucose. The Calvin cycle is present in all photosynthetic eukaryotes and also many photosynthetic bacteria. In plants, these reactions occur in the stroma, the fluid-filled region of a chloroplast outside the thylakoid membranes. These reactions take the products of light-dependent reactions and perform further chemical processes on them. The Calvin cycle uses the chemical energy of ATP and reducing power of NADPH from the light dependent reactions to produce sugars for the plant to use. These substrates are used in a series of reduction-oxidation (redox) reactions to produce sugars in a step-wise process; there is no direct reaction that converts several molecules of CO2 to a sugar. There are three phases to the light-independent reactions, collectively called the Calvin cycle: carboxylation, reduction reactions, and ribulose 1,5-bisphosphate (RuBP) regeneration.

<span class="mw-page-title-main">Glyceraldehyde 3-phosphate</span> Chemical compound

Glyceraldehyde 3-phosphate, also known as triose phosphate or 3-phosphoglyceraldehyde and abbreviated as G3P, GA3P, GADP, GAP, TP, GALP or PGAL, is a metabolite that occurs as an intermediate in several central pathways of all organisms. With the chemical formula H(O)CCH(OH)CH2OPO32-, this anion is a monophosphate ester of glyceraldehyde.

<span class="mw-page-title-main">Ribulose</span> Monosaccharide with five carbon atoms and a ketone functional group

Ribulose is a ketopentose — a monosaccharide containing five carbon atoms, and including a ketone functional group. It has chemical formula C5H10O5. Two enantiomers are possible, d-ribulose and l-ribulose. d-Ribulose is the diastereomer of d-xylulose.

Methylotrophs are a diverse group of microorganisms that can use reduced one-carbon compounds, such as methanol or methane, as the carbon source for their growth; and multi-carbon compounds that contain no carbon-carbon bonds, such as dimethyl ether and dimethylamine. This group of microorganisms also includes those capable of assimilating reduced one-carbon compounds by way of carbon dioxide using the ribulose bisphosphate pathway. These organisms should not be confused with methanogens which on the contrary produce methane as a by-product from various one-carbon compounds such as carbon dioxide. Some methylotrophs can degrade the greenhouse gas methane, and in this case they are called methanotrophs. The abundance, purity, and low price of methanol compared to commonly used sugars make methylotrophs competent organisms for production of amino acids, vitamins, recombinant proteins, single-cell proteins, co-enzymes and cytochromes.

The light compensation point (Ic) is the light intensity on the light curve where the rate of photosynthesis exactly matches the rate of cellular respiration. At this point, the uptake of CO2 through photosynthetic pathways is equal to the respiratory release of carbon dioxide, and the uptake of O2 by respiration is equal to the photosynthetic release of oxygen. The concept of compensation points in general may be applied to other photosynthetic variables, the most important being that of CO2 concentration – CO2 compensation point (Γ).Interval of time in day time when light intensity is low due to which net gaseous exchange is zero is called as compensation point.

<span class="mw-page-title-main">3-Phosphoglyceric acid</span> Chemical compound

3-Phosphoglyceric acid (3PG, 3-PGA, or PGA) is the conjugate acid of 3-phosphoglycerate or glycerate 3-phosphate (GP or G3P). This glycerate is a biochemically significant metabolic intermediate in both glycolysis and the Calvin-Benson cycle. The anion is often termed as PGA when referring to the Calvin-Benson cycle. In the Calvin-Benson cycle, 3-phosphoglycerate is typically the product of the spontaneous scission of an unstable 6-carbon intermediate formed upon CO2 fixation. Thus, two equivalents of 3-phosphoglycerate are produced for each molecule of CO2 that is fixed. In glycolysis, 3-phosphoglycerate is an intermediate following the dephosphorylation (reduction) of 1,3-bisphosphoglycerate.

<span class="mw-page-title-main">Phosphoenolpyruvate carboxylase</span> Class of enzymes

Phosphoenolpyruvate carboxylase (also known as PEP carboxylase, PEPCase, or PEPC; EC 4.1.1.31, PDB ID: 3ZGE) is an enzyme in the family of carboxy-lyases found in plants and some bacteria that catalyzes the addition of bicarbonate (HCO3−) to phosphoenolpyruvate (PEP) to form the four-carbon compound oxaloacetate and inorganic phosphate:

Carboxylation is a chemical reaction in which a carboxylic acid is produced by treating a substrate with carbon dioxide. The opposite reaction is decarboxylation. In chemistry, the term carbonation is sometimes used synonymously with carboxylation, especially when applied to the reaction of carbanionic reagents with CO2. More generally, carbonation usually describes the production of carbonates.

<span class="mw-page-title-main">Phosphopentose epimerase</span> Class of enzymes

Phosphopentose epimerase encoded in humans by the RPE gene is a metalloprotein that catalyzes the interconversion between D-ribulose 5-phosphate and D-xylulose 5-phosphate.

<span class="mw-page-title-main">Ribose-5-phosphate isomerase</span>

Ribose-5-phosphate isomerase (Rpi) encoded by the RPIA gene is an enzyme that catalyzes the conversion between ribose-5-phosphate (R5P) and ribulose-5-phosphate (Ru5P). It is a member of a larger class of isomerases which catalyze the interconversion of chemical isomers. It plays a vital role in biochemical metabolism in both the pentose phosphate pathway and the Calvin cycle. The systematic name of this enzyme class is D-ribose-5-phosphate aldose-ketose-isomerase.

<span class="mw-page-title-main">Phosphoribulokinase</span> Class of enzymes

Phosphoribulokinase (PRK) (EC 2.7.1.19) is an essential photosynthetic enzyme that catalyzes the ATP-dependent phosphorylation of ribulose 5-phosphate (RuP) into ribulose 1,5-bisphosphate (RuBP), both intermediates in the Calvin Cycle. Its main function is to regenerate RuBP, which is the initial substrate and CO2-acceptor molecule of the Calvin Cycle. PRK belongs to the family of transferase enzymes, specifically those transferring phosphorus-containing groups (phosphotransferases) to an alcohol group acceptor. Along with ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCo), phosphoribulokinase is unique to the Calvin Cycle. Therefore, PRK activity often determines the metabolic rate in organisms for which carbon fixation is key to survival. Much initial work on PRK was done with spinach leaf extracts in the 1950s; subsequent studies of PRK in other photosynthetic prokaryotic and eukaryotic organisms have followed. The possibility that PRK might exist was first recognized by Weissbach et al. in 1954; for example, the group noted that carbon dioxide fixation in crude spinach extracts was enhanced by the addition of ATP. The first purification of PRK was conducted by Hurwitz and colleagues in 1956.

ATP + Mg2+ - D-ribulose 5-phosphate  ADP + D-ribulose 1,5-bisphosphate
<span class="mw-page-title-main">Fractionation of carbon isotopes in oxygenic photosynthesis</span>

Photosynthesis converts carbon dioxide to carbohydrates via several metabolic pathways that provide energy to an organism and preferentially react with certain stable isotopes of carbon. The selective enrichment of one stable isotope over another creates distinct isotopic fractionations that can be measured and correlated among oxygenic phototrophs. The degree of carbon isotope fractionation is influenced by several factors, including the metabolism, anatomy, growth rate, and environmental conditions of the organism. Understanding these variations in carbon fractionation across species is useful for biogeochemical studies, including the reconstruction of paleoecology, plant evolution, and the characterization of food chains.

<span class="mw-page-title-main">Kinetic isotope effects of RuBisCO</span>

The kinetic isotope effect (KIE) of ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO) is the isotopic fractionation associated solely with the step in the Calvin-Benson cycle where a molecule of carbon dioxide is attached to the 5-carbon sugar ribulose-1,5-bisphosphate (RuBP) to produce two 3-carbon sugars called 3-phosphoglycerate. This chemical reaction is catalyzed by the enzyme RuBisCO, and this enzyme-catalyzed reaction creates the primary kinetic isotope effect of photosynthesis. It is also largely responsible for the isotopic compositions of photosynthetic organisms and the heterotrophs that eat them. Understanding the intrinsic KIE of RuBisCO is of interest to earth scientists, botanists, and ecologists because this isotopic biosignature can be used to reconstruct the evolution of photosynthesis and the rise of oxygen in the geologic record, reconstruct past evolutionary relationships and environmental conditions, and infer plant relationships and productivity in modern environments.

<span class="mw-page-title-main">2-Phosphoglycolate</span> Chemical compound

2-Phosphoglycolate (chemical formula C2H2O6P3-; also known as phosphoglycolate, 2-PG, or PG) is a natural metabolic product of the oxygenase reaction mediated by the enzyme ribulose 1,5-bisphosphate carboxylase (RuBisCo).

References

  1. 1 2 3 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. 1 2 3 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. 1 2 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. 1 2 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. 1 2 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. 1 2 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. 1 2 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.
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