RuBisCO

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Ribulose-1,5-bisphosphate carboxylase oxygenase
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Ribulose-1,5-bisphosphate carboxylase/oxygenase, commonly known by the abbreviations RuBisCo, rubisco,

ribulose-1,5-bisphosphate (also known as RuBP).[5][6][7]

Alternative carbon fixation pathways

RuBisCO is important

3-hydroxypropionate cycle, or the reverse Krebs cycle, these pathways are relatively small contributors to global carbon fixation compared to that catalyzed by RuBisCO. Phosphoenolpyruvate carboxylase, unlike RuBisCO, only temporarily fixes carbon. Reflecting its importance, RuBisCO is the most abundant protein in leaves, accounting for 50% of soluble leaf protein in C3 plants (20–30% of total leaf nitrogen) and 30% of soluble leaf protein in C4 plants (5–9% of total leaf nitrogen).[7] Given its important role in the biosphere, the genetic engineering of RuBisCO in crops is of continuing interest (see below
).

Structure

Active site of RuBisCO of Galdieria sulphuraria with CO2: Residues involved in both the active site and stabilizing CO2 for enzyme catalysis are shown in color and labeled. Distances of the hydrogen bonding interactions are shown in angstroms. Mg2+ ion (green sphere) is shown coordinated to CO2, and is followed by three water molecules (red spheres). All other residues are placed in grayscale.
chloroplast genome of Arabidopsis thaliana
(positions ca. 55-56.4 kb). rbcL is one of the 21 protein-coding genes involved in photosynthesis (green boxes).

In plants,

substrate (ribulose 1,5-bisphosphate) binding sites are located in the large chains that form dimers in which amino acids from each large chain contribute to the binding sites. A total of eight large chains (= four dimers) and eight small chains assemble into a larger complex of about 540,000 Da.[10] In some Pseudomonadota and dinoflagellates, enzymes consisting of only large subunits have been found.[a]

Magnesium ions (Mg2+) are needed for enzymatic activity. Correct positioning of Mg2+ in the active site of the enzyme involves addition of an "activating" carbon dioxide molecule (CO2) to a lysine in the active site (forming a carbamate).[12] Mg2+ operates by driving deprotonation of the Lys210 residue, causing the Lys residue to rotate by 120 degrees to the trans conformer, decreasing the distance between the nitrogen of Lys and the carbon of CO2. The close proximity allows for the formation of a covalent bond, resulting in the carbamate.[13] Mg2+ is first enabled to bind to the active site by the rotation of His335 to an alternate conformation. Mg2+ is then coordinated by the His residues of the active site (His300, His302, His335), and is partially neutralized by the coordination of three water molecules and their conversion to −OH.[13] This coordination results in an unstable complex, but produces a favorable environment for the binding of Mg2+. Formation of the carbamate is favored by an alkaline pH. The pH and the concentration of magnesium ions in the fluid compartment (in plants, the stroma of the chloroplast) increases in the light. The role of changing pH and magnesium ion levels in the regulation of RuBisCO enzyme activity is discussed below. Once the carbamate is formed, His335 finalizes the activation by returning to its initial position through thermal fluctuation.[13]

RuBisCO large chain,
catalytic domain
Identifiers
SymbolRuBisCO_large
SCOP2
3rub / SCOPe / SUPFAM
CDDcd08148
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary
PDB1aa1​, 1aus​, 1bwv​, 1bxn​, 1ej7​, 1geh​, 1gk8​, 1ir1​, 1ir2​, 1iwa​, 1rba​, 1rbl​, 1rbo​, 1rco​, 1rcx​, 1rld​, 1rsc​, 1rus​, 1rxo​, 1svd​, 1tel​, 1upm​, 1upp​, 1uw9​, 1uwa​, 1uzd​, 1uzh​, 1wdd​, 1ykw​, 2cwx​, 2cxe​, 2d69​, 2qyg​, 2rus​, 2v63​, 2v67​, 2v68​, 2v69​, 2v6a​, 3rub​, 4rub​, 5rub​, 8ruc​, 9rub​
RuBisCO, N-terminal domain
Identifiers
SymbolRuBisCO_large_N
SCOP2
3rub / SCOPe / SUPFAM
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary
PDB1aa1​, 1aus​, 1bwv​, 1bxn​, 1ej7​, 1geh​, 1gk8​, 1ir1​, 1ir2​, 1iwa​, 1rba​, 1rbl​, 1rbo​, 1rco​, 1rcx​, 1rld​, 1rsc​, 1rus​, 1rxo​, 1svd​, 1tel​, 1upm​, 1upp​, 1uw9​, 1uwa​, 1uzd​, 1uzh​, 1wdd​, 1ykw​, 2cwx​, 2cxe​, 2d69​, 2qyg​, 2rus​, 2v63​, 2v67​, 2v68​, 2v69​, 2v6a​, 3rub​, 4rub​, 5rub​, 8ruc​, 9rub​
RuBisCO, small chain
Identifiers
SymbolRuBisCO_small
SCOP2
3rub / SCOPe / SUPFAM
CDDcd03527
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary
PDB1aa1​, 1aus​, 1bwv​, 1bxn​, 1ej7​, 1gk8​, 1ir1​, 1ir2​, 1iwa​, 1rbl​, 1rbo​, 1rco​, 1rcx​, 1rlc​, 1rld​, 1rsc​, 1rxo​, 1svd​, 1upm​, 1upp​, 1uw9​, 1uwa​, 1uzd​, 1uzh​, 1wdd​, 2v63​, 2v67​, 2v68​, 2v69​, 2v6a​, 3rub​, 4rub​, 8ruc​

Enzymatic activity

Two main reactions of RuBisCo: CO2 fixation and oxygenation.

RuBisCO is one of many enzymes in the

enolisation, carboxylation, hydration, C-C bond cleavage, and protonation.[14][15][16]

Substrates

ribulose-1,5-bisphosphate and carbon dioxide (distinct from the "activating" carbon dioxide). RuBisCO also catalyses a reaction of ribulose-1,5-bisphosphate and molecular oxygen (O2) instead of carbon dioxide (CO2).[17]
Discriminating between the substrates CO2 and O2 is attributed to the differing interactions of the substrate's
dielectric constant.[18] This isolation has a significant entropic
cost, and results in the poor turnover rate.

Binding RuBP

Carbamylation of the ε-amino group of Lys210 is stabilized by coordination with the Mg2+.[19] This reaction involves binding of the carboxylate termini of Asp203 and Glu204 to the Mg2+ ion. The substrate RuBP binds Mg2+ displacing two of the three aquo ligands.[14][20][21]

Enolisation

Enolisation of RuBP is the conversion of the keto tautomer of RuBP to an enediol(ate). Enolisation is initiated by deprotonation at C3. The enzyme base in this step has been debated,[20][22] but the steric constraints observed in crystal structures have made Lys210 the most likely candidate.[14] Specifically, the carbamate oxygen on Lys210 that is not coordinated with the Mg ion deprotonates the C3 carbon of RuBP to form a 2,3-enediolate.[20][21]

Carboxylation

A 3D image of the active site of spinach RuBisCO complexed with the inhibitor 2-carboxyarabinitol-1,5-bisphosphate, CO2, and Mg2+. (PDB: 1IR1; Ligand View [CAP]501:A)

Carboxylation of the 2,3-enediolate results in the intermediate 3-keto-2-carboxyarabinitol-1,5-bisphosphate and Lys334 is positioned to facilitate the addition of the CO2 substrate as it replaces the third Mg2+-coordinated water molecule and add directly to the enediol. No Michaelis complex is formed in this process.[14][22] Hydration of this ketone results in an additional hydroxy group on C3, forming a gem-diol intermediate.[20][23] Carboxylation and hydration have been proposed as either a single concerted step[20] or as two sequential steps.[23] Concerted mechanism is supported by the proximity of the water molecule to C3 of RuBP in multiple crystal structures. Within the spinach structure, other residues are well placed to aid in the hydration step as they are within hydrogen bonding distance of the water molecule.[14]

C-C bond cleavage

The gem-diol intermediate cleaves at the C2-C3 bond to form one molecule of glycerate-3-phosphate and a negatively charged carboxylate.[14] Stereo specific protonation of C2 of this carbanion results in another molecule of glycerate-3-phosphate. This step is thought to be facilitated by Lys175 or potentially the carbamylated Lys210.[14]

Products

When carbon dioxide is the substrate, the product of the carboxylase reaction is an unstable six-carbon phosphorylated intermediate known as 3-keto-2-carboxyarabinitol-1,5-bisphosphate, which decays rapidly into two molecules of

glycerate-3-phosphate. This product, also known as 3-phosphoglycerate, can be used to produce larger molecules such as glucose
.

When molecular oxygen is the substrate, the products of the oxygenase reaction are

metabolite repair). In this process, two molecules of phosphoglycolate are converted to one molecule of carbon dioxide and one molecule of 3-phosphoglycerate, which can reenter the Calvin cycle. Some of the phosphoglycolate entering this pathway can be retained by plants to produce other molecules such as glycine. At ambient levels of carbon dioxide and oxygen, the ratio of the reactions is about 4 to 1, which results in a net carbon dioxide fixation of only 3.5. Thus, the inability of the enzyme to prevent the reaction with oxygen greatly reduces the photosynthetic capacity of many plants. Some plants, many algae, and photosynthetic bacteria have overcome this limitation by devising means to increase the concentration of carbon dioxide around the enzyme, including C4 carbon fixation, crassulacean acid metabolism, and the use of pyrenoid
.

Rubisco side activities can lead to useless or inhibitory by-products. Important inhibitory by-products include xylulose 1,5-bisphosphate and glycero-2,3-pentodiulose 1,5-bisphosphate, both caused by "misfires" halfway in the enolisation-carboxylation reaction. In higher plants, this process causes RuBisCO self-inhibition, which can be triggered by saturating CO2 and RuBP concentrations and solved by Rubisco activase (see below).[24]

Rate of enzymatic activity

Overview of the Calvin cycle and carbon fixation.

Some enzymes can carry out thousands of chemical reactions each second. However, RuBisCO is slow, fixing only 3-10 carbon dioxide molecules each second per molecule of enzyme.[25] The reaction catalyzed by RuBisCO is, thus, the primary rate-limiting factor of the Calvin cycle during the day. Nevertheless, under most conditions, and when light is not otherwise limiting photosynthesis, the speed of RuBisCO responds positively to increasing carbon dioxide concentration.

RuBisCO is usually only active during the day, as ribulose 1,5-bisphosphate is not regenerated in the dark. This is due to the regulation of several other enzymes in the Calvin cycle. In addition, the activity of RuBisCO is coordinated with that of the other enzymes of the Calvin cycle in several other ways:

By ions

Upon illumination of the chloroplasts, the

driven by light and is fundamental to ATP synthesis in chloroplasts (Further reading: Photosynthetic reaction centre; Light-dependent reactions
). To balance ion potential across the membrane, magnesium ions (Mg2+) move out of the thylakoids in response, increasing the concentration of magnesium in the stroma of the chloroplasts. RuBisCO has a high optimal pH (can be >9.0, depending on the magnesium ion concentration) and, thus, becomes "activated" by the introduction of carbon dioxide and magnesium to the active sites as described above.

By RuBisCO activase

In plants and some algae, another enzyme, RuBisCO activase (Rca, GO:0046863, P10896), is required to allow the rapid formation of the critical

CA1P-phosphatase. Even without these strong inhibitors, once every several hundred reactions, the normal reactions with carbon dioxide or oxygen are not completed; other inhibitory substrate analogs are still formed in the active site. Once again, RuBisCO activase can promote the release of these analogs from the catalytic sites and maintain the enzyme in a catalytically active form. However, at high temperatures, RuBisCO activase aggregates and can no longer activate RuBisCO. This contributes to the decreased carboxylating capacity observed during heat stress.[30][31]

By activase

The removal of the inhibitory RuBP, CA1P, and the other inhibitory substrate analogs by activase requires the consumption of ATP. This reaction is inhibited by the presence of ADP, and, thus, activase activity depends on the ratio of these compounds in the chloroplast stroma. Furthermore, in most plants, the sensitivity of activase to the ratio of ATP/ADP is modified by the stromal reduction/oxidation (redox) state through another small regulatory protein, thioredoxin. In this manner, the activity of activase and the activation state of RuBisCO can be modulated in response to light intensity and, thus, the rate of formation of the ribulose 1,5-bisphosphate substrate.[32]

By phosphate

In cyanobacteria, inorganic phosphate (Pi) also participates in the co-ordinated regulation of photosynthesis: Pi binds to the RuBisCO active site and to another site on the large chain where it can influence transitions between activated and less active conformations of the enzyme. In this way, activation of bacterial RuBisCO might be particularly sensitive to Pi levels, which might cause it to act in a similar way to how RuBisCO activase functions in higher plants.[33]

By carbon dioxide

Since carbon dioxide and oxygen

C3 photosynthesis
then decarboxylated, releasing CO2 to boost the concentration of CO2.

Calvin Cycle) from taking place, since these reactions require CO2 to pass by gas exchange through these openings. Evaporation through the upper side of a leaf is prevented by a layer of wax
.

Genetic engineering

Since RuBisCO is often rate-limiting for photosynthesis in plants, it may be possible to improve

chloroplast DNA, and altering RuBisCO genes to increase specificity for carbon dioxide or otherwise increase the rate of carbon fixation.[39][40]

Mutagenesis in plants

In general, site-directed mutagenesis of RuBisCO has been mostly unsuccessful,[38] though mutated forms of the protein have been achieved in tobacco plants with subunit C4 species,[41] and a RuBisCO with more C4-like kinetic characteristics have been attained in rice via nuclear transformation.[42] Robust and reliable engineering for yield of RuBisCO and other enzymes in the C3 cycle was shown to be possible,[43] and it was first achieved in 2019 through a synthetic biology approach.[37]

One avenue is to introduce RuBisCO variants with naturally high specificity values such as the ones from the

cyanobacterium Synechococcus elongatus PCC7942 (Se7942) were created by replacing the RuBisCO with the large and small subunit genes of the Se7942 enzyme, in combination with either the corresponding Se7942 assembly chaperone, RbcX, or an internal carboxysomal protein, CcmM35. Both mutants had increased CO2 fixation rates when measured as carbon molecules per RuBisCO. However, the mutant plants grew more slowly than wild-type.[46]

A recent theory explores the trade-off between the relative specificity (i.e., ability to favour CO2 fixation over O2 incorporation, which leads to the energy-wasteful process of photorespiration) and the rate at which product is formed. The authors conclude that RuBisCO may actually have evolved to reach a point of 'near-perfection' in many plants (with widely varying substrate availabilities and environmental conditions), reaching a compromise between specificity and reaction rate.[47] It has been also suggested that the oxygenase reaction of RuBisCO prevents CO2 depletion near its active sites and provides the maintenance of the chloroplast redox state.[48]

Since photosynthesis is the single most effective natural regulator of

carbon dioxide in the Earth's atmosphere,[49]
a biochemical model of RuBisCO reaction is used as the core module of climate change models. Thus, a correct model of this reaction is essential to the basic understanding of the relations and interactions of environmental models.

Expression in bacterial hosts

There currently are very few effective methods for expressing functional plant Rubisco in bacterial hosts for genetic manipulation studies. This is largely due to Rubisco's requirement of complex cellular machinery for its biogenesis and metabolic maintenance including the nuclear-encoded RbcS subunits, which are typically imported into chloroplasts as unfolded proteins.[50][51] Furthermore, sufficient expression and interaction with Rubisco activase are major challenges as well.[39] One successful method for expression of Rubisco in E. coli involves the co-expression of multiple chloroplast chaperones, though this has only been shown for Arabidopsis thaliana Rubisco.[52]

Depletion in proteomic studies

Due to its high abundance in plants (generally 40% of the total protein content), RuBisCO often impedes analysis of important signaling proteins such as transcription factors, kinases, and regulatory proteins found in lower abundance (10-100 molecules per cell) within plants.[53] For example, using mass spectrometry on plant protein mixtures would result in multiple intense RuBisCO subunit peaks that interfere and hide those of other proteins.

Recently, one efficient method for precipitating out RuBisCO involves the usage of protamine sulfate solution.[54] Other existing methods for depleting RuBisCO and studying lower abundance proteins include fractionation techniques with calcium and phytate,[55] gel electrophoresis with polyethylene glycol,[56][57] affinity chromatography,[58][59] and aggregation using DTT,[60] though these methods are more time-consuming and less efficient when compared to protamine sulfate precipitation.[53]

Evolution of RuBisCO

Phylogenetic studies

The chloroplast gene rbcL, which codes for the large subunit of RuBisCO has been widely used as an appropriate locus for analysis of phylogenetics in plant taxonomy.[61]

Origin

Non-carbon-fixing proteins similar to RuBisCO, termed RuBisCO-like proteins (RLPs), are also found in the wild in organisms as common as Bacillus subtilis. This bacterium has a rbcL-like protein with a 2,3-diketo-5-methylthiopentyl-1-phosphate enolase function, part of the methionine salvage pathway.[62] Later identifications found functionally divergent examples dispersed all over bacteria and archaea, as well as transitionary enzymes performing both RLP-type enolase and RuBisCO functions. It is now believed that the current RuBisCO evolved from a dimeric RLP ancestor, acquiring its carboxylase function first before further oligomerizing and then recruiting the small subunit to form the familiar modern enzyme.[15] The small subunit probably first evolved in anaerobic and thermophilic organisms, where it enabled RuBisCO to catalyze its reaction at higher temperatures.[63] In addition to its effect on stabilizing catalysis, it enabled the evolution of higher specificities for CO2 over O2 by modulating the effect that substitutions within RuBisCO have on enzymatic function. Substitutions that do not have an effect without the small subunit suddenly become beneficial when it is bound. Furthermore, the small subunit enabled the accumulation of substitutions that are only tolerated in its presence. Accumulation of such substitutions leads to a strict dependence on the small subunit, which is observed in extant Rubiscos that bind a small subunit.

C4

With the mass convergent evolution of the

Calvin cycle. Laboratory-based phylogenetic studies have shown that this evolution was constrained by the trade-off between stability and activity brought about by the series of necessary mutations for C4 RuBisCO.[65] Moreover, in order to sustain the destabilizing mutations, the evolution to C4 RuBisCO was preceded by a period in which mutations granted the enzyme increased stability, establishing a buffer to sustain and maintain the mutations required for C4 RuBisCO. To assist with this buffering process, the newly-evolved enzyme was found to have further developed a series of stabilizing mutations. While RuBisCO has always been accumulating new mutations, most of these mutations that have survived have not had significant effects on protein stability. The destabilizing C4 mutations on RuBisCO has been sustained by environmental pressures such as low CO2 concentrations, requiring a sacrifice of stability for new adaptive functions.[65]

History of the term

The term "RuBisCO" was coined humorously in 1979, by

Sam Wildman, and also alluded to the snack food trade name "Nabisco" in reference to Wildman's attempts to create an edible protein supplement from tobacco leaves.[66][67]

The capitalization of the name has been long debated. It can be capitalized for each letter of the full name (Ribulose-1,5 bisphosphate carboxylase/oxygenase), but it has also been argued that is should all be in lower case (rubisco), similar to other terms like scuba or laser.[1]

See also

References

  1. bacterial RuBisCO is shown in the Protein Data Bank "Molecule of the Month" #11.[11]
  1. ^
    S2CID 53092349
    .
  2. PMID 16663341
    .
  3. PMID 16666327
    .
  4. ^ Back to the future of photosynthesis: Resurrecting billon-year-old enzymes reveals how photosynthesis adapted to the rise of oxygen., News from the Max Planck Society, October 13, 2022
  5. ISBN 978-0-87893-106-4
    . , one of the subunits of ribulose bisphosphate carboxylase (rubisco) is encoded by chloroplast DNA. Rubisco is the critical enzyme that catalyzes the addition of CO2 to ribulose-1,5-bisphosphate during the Calvin cycle. It is also thought to be the single most abundant protein on Earth, so it is noteworthy that one of its subunits is encoded by the chloroplast genome.
  6. ^
    PMID 15067115
    . (Rubisco) is the most prevalent enzyme on this planet, accounting for 30–50% of total soluble protein in the chloroplast;
  7. ^
    PMID 17975207
    .
  8. PMID 29594130
    .
  9. PMID 11401297
    .
  10. ISBN 978-0-7167-3051-4
    . Figure 20.3. Structure of Rubisco.] (Color-coded ribbon diagram)
  11. doi:10.2210/rcsb_pdb/mom_2000_11
    .
  12. ^ Lodish H, Berk A, Zipursky SL, Matsudaira P, Baltimore D, Darnell JE (2000). "Molecular Cell Biology" (4th ed.). New York: W. H. Freeman & Co. Figure 16-48 shows a structural model of the active site, including the involvement of magnesium.
  13. ^
    PMID 23112176
    .
  14. ^
    PMID 18417482
    .
  15. ^
    PMID 28843191
    .
  16. PMID 1905726
    .
  17. doi:10.2210/rcsb_pdb/mom_2000_11
    .
  18. PMID 18664299
    .
  19. PMID 6778504
    .
  20. ^
    PMID 11848907
    .
  21. ^
    S2CID 4370073
    .
  22. ^
    PMID 7979237
    .
  23. ^
    PMID 9034362
    .
  24. PMID 16822231
    .
  25. S2CID 205052478
    .
  26. S2CID 2632
    .
  27. S2CID 1496584
    .
  28. PMID 7818481
    .
  29. PMID 10583377
    .
  30. PMID 11706186
    .
  31. PMID 11069297
    .
  32. PMID 11854454
    .
  33. PMID 10998060
    .
  34. S2CID 9387705
    .
  35. ^ Timmer J (7 December 2017). "We may now be able to engineer the most important lousy enzyme on the planet". Ars Technica. Retrieved 5 January 2019.
  36. ^ Timmer J (3 January 2019). "Fixing photosynthesis by engineering it to recycle a toxic mistake". Ars Technica. Retrieved 5 January 2019.
  37. ^
    PMID 30606819
    .
  38. ^
    doi:10.1016/j.fcr.2015.04.009
    .
  39. ^
    PMID 12709478
    .
  40. S2CID 4191791
    .
  41. PMID 21849620
    .
  42. PMID 21562335
    .
  43. S2CID 5568464
    .
  44. PMID 11724961
    .
  45. PMID 12781767
    .
  46. PMID 25231869
    .
  47. PMID 16641091
    .
  48. PMID 25767475
    .
  49. S2CID 10709679
    .
  50. PMID 28125284
    .
  51. PMID 28228773
    .
  52. PMID 29217567
    .
  53. ^
    ISBN 978-953-307-613-3
    .
  54. PMID 25820725
    .
  55. PMID 19766275
    .
  56. S2CID 38878805
    .
  57. PMID 16973185
    .
  58. PMID 18063427
    .
  59. S2CID 2455432
    .
  60. S2CID 23636617
    .
  61. JSTOR 2399846
    .
  62. PMID 18403380
    .
  63. S2CID 252897276
    .
  64. S2CID 24199852
    .
  65. ^
    PMID 24469821
    .
  66. S2CID 7622999
    .
  67. S2CID 39767233
    .
Figure 3. In this figure, each protein chain in the (LS)2 complex is given its own color for easy identification.

Further reading

External links

  • Gerritsen VB (September 2003). "The Plant Kingdom's sloth". Protein Spotlight. Swiss Institute of Bioinformatics (SIB). Rubisco plods along at a mere three molecules per second... To bypass such slothfulness, plants synthesize a gross amount of Rubisco, sometimes up to 50% of their total protein content!
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