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1
Valente, Ana I., Ana M. Ferreira, Mafalda R. Almeida, Aminou Mohamadou, Mara G. Freire, and Ana P. M. Tavares. "Efficient Extraction of the RuBisCO Enzyme from Spinach Leaves Using Aqueous Solutions of Biocompatible Ionic Liquids." Sustainable Chemistry 3, no. 1 (December 24, 2021): 1–18. http://dx.doi.org/10.3390/suschem3010001.
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Ribulose-1,5-biphosphate carboxylase/oxygenase (RuBisCO) is the most abundant protein on the planet, being present in plants, algae and various species of bacteria, with application in the pharmaceutical, chemical, cosmetic and food industries. However, current extraction methods of RuBisCO do not allow high yields of extraction. Therefore, the development of an efficient and selective RuBisCOs’ extraction method is required. In this work, aqueous solutions of biocompatible ionic liquids (ILs), i.e., ILs derived from choline and analogues of glycine-betaine, were applied in the RuBisCO’s extraction from spinach leaves. Three commercial imidazolium-based ILs were also investigated for comparison purposes. To optimize RuBisCO’s extraction conditions, response surface methodology was applied. Under optimum extraction conditions, extraction yields of 10.92 and 10.57 mg of RuBisCO/g of biomass were obtained with the ILs cholinium acetate ([Ch][Ac]) and cholinium chloride ([Ch]Cl), respectively. Circular dichroism (CD) spectroscopy results show that the secondary structure of RuBisCO is better preserved in the IL solutions when compared to the commonly used extraction solvent. The obtained results indicate that cholinium-based ILs are a promising and viable alternative for the extraction of RuBisCO from vegetable biomass.
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McNevin, Dennis B., Murray R. Badger, Spencer M. Whitney, Susanne von Caemmerer, Guillaume G. B. Tcherkez, and Graham D. Farquhar. "Differences in Carbon Isotope Discrimination of Three Variants of D-Ribulose-1,5-bisphosphate Carboxylase/Oxygenase Reflect Differences in Their Catalytic Mechanisms." Journal of Biological Chemistry 282, no. 49 (October 9, 2007): 36068–76. http://dx.doi.org/10.1074/jbc.m706274200.
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The carboxylation kinetic (stable carbon) isotope effect was measured for purified d-ribulose-1,5-bisphosphate carboxylases/oxygenases (Rubiscos) with aqueous CO2 as substrate by monitoring Rayleigh fractionation using membrane inlet mass spectrometry. This resulted in discriminations (Δ) of 27.4 ± 0.9‰ for wild-type tobacco Rubisco, 22.2 ± 2.1‰ for Rhodospirillum rubrum Rubisco, and 11.2 ± 1.6‰ for a large subunit mutant of tobacco Rubisco in which Leu335 is mutated to valine (L335V). These Δ values are consistent with the photosynthetic discrimination determined for wild-type tobacco and transplastomic tobacco lines that exclusively produce R. rubrum or L335V Rubisco. The Δ values are indicative of the potential evolutionary variability of Δ values for a range of Rubiscos from different species: Form I Rubisco from higher plants; prokaryotic Rubiscos, including Form II; and the L335V mutant. We explore the implications of these Δ values for the Rubisco catalytic mechanism and suggest that Rubiscos that are associated with a lower Δ value have a less product-like carboxylation transition state and/or allow a decarboxylation step that evolution has excluded in higher plants.
3
Whitney, Spencer M., and T. John Andrews. "The CO2/O2 specificity of single-subunit ribulose-bisphosphate carboxylase from the dinoflagellate, Amphidinium carterae." Functional Plant Biology 25, no. 2 (1998): 131. http://dx.doi.org/10.1071/pp97131.
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Some dinoflagellates have been shown recently to be unique among eukaryotes in having a ribulose-bisphosphate carboxylase-oxygenase (Rubisco, EC 4.1.1.39) composed of only one type of subunit, the 53-kDa large subunit [reviewed by Palmer, J.D. (1996) Plant Cell 8, 343–345]. Formerly, such homomeric Rubiscos had been found only in anaerobic bacteria and are characterised by such poor abilities to discriminate against the competitive alternate substrate, O2, that they would not be able to support net carbon gain if exposed to the current atmospheric CO2/O2 ratio. The capacity of Rubiscos from aerobic organisms to discriminate more effectively against O2 appeared to correlate with the presence of additional 12- to 18-kDa small subunits. Thus the CO2/O2 specificity of the homomeric dinoflagellate Rubisco is of considerable interest from the structural, physiological and evolutionary viewpoints. However, for unknown reasons, Rubiscos from dinoflagellates studied so far are so unstable after extraction from the cells that kinetic characterisation has not been possible. We redesigned two methods for measuring Rubisco’s CO2/O2 specificity to adapt them to rapid measurement at 10°C using unfractionated cell extracts. Both methods revealed that the CO2/O2 specificity of Rubisco from the dinoflagellate, Amphidinium carterae Hulburt, was approximately twice as great as that of other homomeric Rubiscos but unlikely to be sufficient to support dinoflagellate photosynthesis without assistance from an inorganic-carbon-concentrating mechanism.
4
Mueller-Cajar, Oliver, and Spencer M. Whitney. "Evolving improved Synechococcus Rubisco functional expression in Escherichia coli." Biochemical Journal 414, no. 2 (August 12, 2008): 205–14. http://dx.doi.org/10.1042/bj20080668.
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The photosynthetic CO2-fixing enzyme Rubisco [ribulose-P2 (D-ribulose-1,5-bisphosphate) carboxylase/oxygenase] has long been a target for engineering kinetic improvements. Towards this goal we used an RDE (Rubisco-dependent Escherichia coli) selection system to evolve Synechococcus PCC6301 Form I Rubisco under different selection pressures. In the fastest growing colonies, the Rubisco L (large) subunit substitutions I174V, Q212L, M262T, F345L or F345I were repeatedly selected and shown to increase functional Rubisco expression 4- to 7-fold in the RDE and 5- to 17-fold when expressed in XL1-Blue E. coli. Introducing the F345I L-subunit substitution into Synechococcus PCC7002 Rubisco improved its functional expression 11-fold in XL1-Blue cells but could not elicit functional Arabidopsis Rubisco expression in the bacterium. The L subunit substitutions L161M and M169L were complementary in improving Rubisco yield 11-fold, whereas individually they improved yield ∼5-fold. In XL1-Blue cells, additional GroE chaperonin enhanced expression of the I174V, Q212L and M262T mutant Rubiscos but engendered little change in the yield of the more assembly-competent F345I or F345L mutants. In contrast, the Rubisco chaperone RbcX stimulated functional assembly of wild-type and mutant Rubiscos. The kinetic properties of the mutated Rubiscos varied with noticeable reductions in carboxylation and oxygenation efficiency accompanying the Q212L mutation and a 2-fold increase in Kribulose-P2 (KM for the substrate ribulose-P2) for the F345L mutant, which was contrary to the ∼30% reductions in Kribulose-P2 for the other mutants. These results confirm the RDE systems versatility for identifying mutations that improve functional Rubisco expression in E. coli and provide an impetus for developing the system to screen for kinetic improvements.
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Iqbal, Wasim A., Isabel G. Miller, Rebecca L. Moore, Iain J. Hope, Daniel Cowan-Turner, and Maxim V. Kapralov. "Rubisco substitutions predicted to enhance crop performance through carbon uptake modelling." Journal of Experimental Botany 72, no. 17 (June 11, 2021): 6066–75. http://dx.doi.org/10.1093/jxb/erab278.
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Abstract Improving the performance of the CO2-fixing enzyme Rubisco is among the targets for increasing crop yields. Here, Earth system model (ESM) representations of canopy C3 and C4 photosynthesis were combined with species-specific Rubisco parameters to quantify the consequences of bioengineering foreign Rubiscos into C3 and C4 crops under field conditions. The ‘two big leaf’ (sunlit/shaded) model for canopy photosynthesis was used together with species-specific Rubisco kinetic parameters including maximum rate (Kcat), Michaelis–Menten constant for CO2 at ambient atmospheric O2 (Kc21%O2), specificity for CO2 to O2 (Sc/o), and associated heat activation (Ha) values. Canopy-scale consequences of replacing native Rubiscos in wheat, maize, and sugar beet with foreign enzymes from 27 species were modelled using data from Ameriflux and Fluxnet databases. Variation among the included Rubisco kinetics differentially affected modelled carbon uptake rates, and Rubiscos from several species of C4 grasses showed the greatest potential of >50% carbon uptake improvement in wheat, and >25% improvement in sugar beet and maize. This study also reaffirms the need for data on fully characterized Rubiscos from more species, and for better parameterization of ‘Vcmax’ and temperature response of ‘Jmax’ in ESMs.
6
Utåker, Janne B., Kjell Andersen, Ågot Aakra, Birgitte Moen, and Ingolf F. Nes. "Phylogeny and Functional Expression of Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase from the Autotrophic Ammonia-Oxidizing Bacterium Nitrosospira sp.Isolate 40KI." Journal of Bacteriology 184, no. 2 (January 15, 2002): 468–78. http://dx.doi.org/10.1128/jb.184.2.468-478.2002.
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ABSTRACT The autotrophic ammonia-oxidizing bacteria (AOB), which play an important role in the global nitrogen cycle, assimilate CO2 by using ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO). Here we describe the first detailed study of RubisCO (cbb) genes and proteins from the AOB. The cbbLS genes from Nitrosospira sp. isolate 40KI were cloned and sequenced. Partial sequences of the RubisCO large subunit (CbbL) from 13 other AOB belonging to the β and γ subgroups of the class Proteobacteria are also presented. All except one of the β-subgroup AOB possessed a red-like type I RubisCO with high sequence similarity to the Ralstonia eutropha enzyme. All of these new red-like RubisCOs had a unique six-amino-acid insert in CbbL. Two of the AOB, Nitrosococcus halophilus Nc4 and Nitrosomonas europaea Nm50, had a green-like RubisCO. With one exception, the phylogeny of the AOB CbbL was very similar to that of the 16S rRNA gene. The presence of a green-like RubisCO in N. europaea was surprising, as all of the other β-subgroup AOB had red-like RubisCOs. The green-like enzyme of N. europaea Nm50 was probably acquired by horizontal gene transfer. Functional expression of Nitrosospira sp. isolate 40KI RubisCO in the chemoautotrophic host R. eutropha was demonstrated. Use of an expression vector harboring the R. eutropha cbb control region allowed regulated expression of Nitrosospira sp. isolate 40KI RubisCO in an R. eutropha cbb deletion strain. The Nitrosospira RubisCO supported autotrophic growth of R. eutropha with a doubling time of 4.6 h. This expression system may allow further functional analysis of AOB cbb genes.
7
Ng, Jediael, Zhijun Guo, and Oliver Mueller-Cajar. "Rubisco activase requires residues in the large subunit N terminus to remodel inhibited plant Rubisco." Journal of Biological Chemistry 295, no. 48 (September 18, 2020): 16427–35. http://dx.doi.org/10.1074/jbc.ra120.015759.
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The photosynthetic CO2 fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) forms dead-end inhibited complexes while binding multiple sugar phosphates, including its substrate ribulose 1,5-bisphosphate. Rubisco can be rescued from this inhibited form by molecular chaperones belonging to the ATPases associated with diverse cellular activities (AAA+ proteins) termed Rubisco activases (Rcas). The mechanism of green-type Rca found in higher plants has proved elusive, in part because until recently higher-plant Rubiscos could not be expressed recombinantly. Identifying the interaction sites between Rubisco and Rca is critical to formulate mechanistic hypotheses. Toward that end here we purify and characterize a suite of 33 Arabidopsis Rubisco mutants for their ability to be activated by Rca. Mutation of 17 surface-exposed large subunit residues did not yield variants that were perturbed in their interaction with Rca. In contrast, we find that Rca activity is highly sensitive to truncations and mutations in the conserved N terminus of the Rubisco large subunit. Large subunits lacking residues 1–4 are functional Rubiscos but cannot be activated. Both T5A and T7A substitutions result in functional carboxylases that are poorly activated by Rca, indicating the side chains of these residues form a critical interaction with the chaperone. Many other AAA+ proteins function by threading macromolecules through a central pore of a disc-shaped hexamer. Our results are consistent with a model in which Rca transiently threads the Rubisco large subunit N terminus through the axial pore of the AAA+ hexamer.
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Wang, Renée Z., Albert K. Liu, Douglas M. Banda, Woodward W. Fischer, and Patrick M. Shih. "A Bacterial Form I’ Rubisco Has a Smaller Carbon Isotope Fractionation than Its Form I Counterpart." Biomolecules 13, no. 4 (March 26, 2023): 596. http://dx.doi.org/10.3390/biom13040596.
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Form I rubiscos evolved in Cyanobacteria ≥ 2.5 billion years ago and are enzymatically unique due to the presence of small subunits (RbcS) capping both ends of an octameric large subunit (RbcL) rubisco assembly to form a hexadecameric (L8S8) holoenzyme. Although RbcS was previously thought to be integral to Form I rubisco stability, the recent discovery of a closely related sister clade of octameric rubiscos (Form I’; L8) demonstrates that the L8 complex can assemble without small subunits (Banda et al. 2020). Rubisco also displays a kinetic isotope effect (KIE) where the 3PG product is depleted in 13C relative to 12C. In Cyanobacteria, only two Form I KIE measurements exist, making interpretation of bacterial carbon isotope data difficult. To aid comparison, we measured in vitro the KIEs of Form I’ (Candidatus Promineofilum breve) and Form I (Synechococcus elongatus PCC 6301) rubiscos and found the KIE to be smaller in the L8 rubisco (16.25 ± 1.36‰ vs. 22.42 ± 2.37‰, respectively). Therefore, while small subunits may not be necessary for protein stability, they may affect the KIE. Our findings may provide insight into the function of RbcS and allow more refined interpretation of environmental carbon isotope data.
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Loganathan, Nitin, Yi-Chin Candace Tsai, and Oliver Mueller-Cajar. "Characterization of the heterooligomeric red-type rubisco activase from red algae." Proceedings of the National Academy of Sciences 113, no. 49 (November 21, 2016): 14019–24. http://dx.doi.org/10.1073/pnas.1610758113.
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The photosynthetic CO2-fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco) is inhibited by nonproductive binding of its substrate ribulose-1,5-bisphosphate (RuBP) and other sugar phosphates. Reactivation requires ATP-hydrolysis–powered remodeling of the inhibited complexes by diverse molecular chaperones known as rubisco activases (Rcas). Eukaryotic phytoplankton of the red plastid lineage contain so-called red-type rubiscos, some of which have been shown to possess superior kinetic properties to green-type rubiscos found in higher plants. These organisms are known to encode multiple homologs of CbbX, the α-proteobacterial red-type activase. Here we show that the gene products of two cbbX genes encoded by the nuclear and plastid genomes of the red algae Cyanidioschyzon merolae are nonfunctional in isolation, but together form a thermostable heterooligomeric Rca that can use both α-proteobacterial and red algal-inhibited rubisco complexes as a substrate. The mechanism of rubisco activation appears conserved between the bacterial and the algal systems and involves threading of the rubisco large subunit C terminus. Whereas binding of the allosteric regulator RuBP induces oligomeric transitions to the bacterial activase, it merely enhances the kinetics of ATP hydrolysis in the algal enzyme. Mutational analysis of nuclear and plastid isoforms demonstrates strong coordination between the subunits and implicates the nuclear-encoded subunit as being functionally dominant. The plastid-encoded subunit may be catalytically inert. Efforts to enhance crop photosynthesis by transplanting red algal rubiscos with enhanced kinetics will need to take into account the requirement for a compatible Rca.
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Tabita, F. Robert, Thomas E. Hanson, Huiying Li, Sriram Satagopan, Jaya Singh, and Sum Chan. "Function, Structure, and Evolution of the RubisCO-Like Proteins and Their RubisCO Homologs." Microbiology and Molecular Biology Reviews 71, no. 4 (December 2007): 576–99. http://dx.doi.org/10.1128/mmbr.00015-07.
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SUMMARY About 30 years have now passed since it was discovered that microbes synthesize RubisCO molecules that differ from the typical plant paradigm. RubisCOs of forms I, II, and III catalyze CO2 fixation reactions, albeit for potentially different physiological purposes, while the RubisCO-like protein (RLP) (form IV RubisCO) has evolved, thus far at least, to catalyze reactions that are important for sulfur metabolism. RubisCO is the major global CO2 fixation catalyst, and RLP is a somewhat related protein, exemplified by the fact that some of the latter proteins, along with RubisCO, catalyze similar enolization reactions as a part of their respective catalytic mechanisms. RLP in some organisms catalyzes a key reaction of a methionine salvage pathway, while in green sulfur bacteria, RLP plays a role in oxidative thiosulfate metabolism. In many organisms, the function of RLP is unknown. Indeed, there now appear to be at least six different clades of RLP molecules found in nature. Consideration of the many RubisCO (forms I, II, and III) and RLP (form IV) sequences in the database has subsequently led to a coherent picture of how these proteins may have evolved, with a form III RubisCO arising from the Methanomicrobia as the most likely ultimate source of all RubisCO and RLP lineages. In addition, structure-function analyses of RLP and RubisCO have provided information as to how the active sites of these proteins have evolved for their specific functions.
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Whitney, Spencer M., Rosemary Birch, Celine Kelso, Jennifer L. Beck, and Maxim V. Kapralov. "Improving recombinant Rubisco biogenesis, plant photosynthesis and growth by coexpressing its ancillary RAF1 chaperone." Proceedings of the National Academy of Sciences 112, no. 11 (March 2, 2015): 3564–69. http://dx.doi.org/10.1073/pnas.1420536112.
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Enabling improvements to crop yield and resource use by enhancing the catalysis of the photosynthetic CO2-fixing enzyme Rubisco has been a longstanding challenge. Efforts toward realization of this goal have been greatly assisted by advances in understanding the complexities of Rubisco’s biogenesis in plastids and the development of tailored chloroplast transformation tools. Here we generate transplastomic tobacco genotypes expressing Arabidopsis Rubisco large subunits (AtL), both on their own (producing tobAtL plants) and with a cognate Rubisco accumulation factor 1 (AtRAF1) chaperone (producing tobAtL-R1 plants) that has undergone parallel functional coevolution with AtL. We show AtRAF1 assembles as a dimer and is produced in tobAtL-R1 and Arabidopsis leaves at 10–15 nmol AtRAF1 monomers per square meter. Consistent with a postchaperonin large (L)-subunit assembly role, the AtRAF1 facilitated two to threefold improvements in the amount and biogenesis rate of hybrid L8AS8t Rubisco [comprising AtL and tobacco small (S) subunits] in tobAtL-R1 leaves compared with tobAtL, despite >threefold lower steady-state Rubisco mRNA levels in tobAtL-R1. Accompanying twofold increases in photosynthetic CO2-assimilation rate and plant growth were measured for tobAtL-R1 lines. These findings highlight the importance of ancillary protein complementarity during Rubisco biogenesis in plastids, the possible constraints this has imposed on Rubisco adaptive evolution, and the likely need for such interaction specificity to be considered when optimizing recombinant Rubisco bioengineering in plants.
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Elsaied, Hosam, and Takeshi Naganuma. "Phylogenetic Diversity of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Large-Subunit Genes from Deep-Sea Microorganisms." Applied and Environmental Microbiology 67, no. 4 (April 1, 2001): 1751–65. http://dx.doi.org/10.1128/aem.67.4.1751-1765.2001.
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ABSTRACT The phylogenetic diversity of the ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO, E.C. 4.1.1.39) large-subunit genes of deep-sea microorganisms was analyzed. Bulk genomic DNA was isolated from seven samples, including samples from the Mid-Atlantic Ridge and various deep-sea habitats around Japan. The kinds of samples were hydrothermal vent water and chimney fragment; reducing sediments from a bathyal seep, a hadal seep, and a presumed seep; and symbiont-bearing tissues of the vent mussel, Bathymodiolus sp., and the seep vestimentiferan tubeworm, Lamellibrachia sp. The RuBisCO genes that encode both form I and form II large subunits (cbbL and cbbM) were amplified by PCR from the seven deep-sea sample DNA populations, cloned, and sequenced. From each sample, 50 cbbL clones and 50 cbbM clones, if amplified, were recovered and sequenced to group them into operational taxonomic units (OTUs). A total of 29 OTUs were recorded from the 300 total cbbL clones, and a total of 24 OTUs were recorded from the 250 total cbbM clones. All the current OTUs have the characteristic RuBisCO amino acid motif sequences that exist in other RuBisCOs. The recorded OTUs were related to different RuBisCO groups of proteobacteria, cyanobacteria, and eukarya. The diversity of the RuBisCO genes may be correlated with certain characteristics of the microbial habitats. The RuBisCO sequences from the symbiont-bearing tissues showed a phylogenetic relationship with those from the ambient bacteria. Also, the RuBisCO sequences of known species of thiobacilli and those from widely distributed marine habitats were closely related to each other. This suggests that theThiobacillus-related RuBisCO may be distributed globally and contribute to the primary production in the deep sea.
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Morell, MK, K. Paul, HJ Kane, and TJ Andrews. "Rubisco: Maladapted or Misunderstood." Australian Journal of Botany 40, no. 5 (1992): 431. http://dx.doi.org/10.1071/bt9920431.
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Life depends on a single enzyme, D-ribulose-1,5-bisphosphate carboxylase-oxygenase (Rubisco), for the acquisition of essentially all of its carbon. Applying Darwinian principles, one would expect this enzyme to have been rigorously selected for speed and accuracy, and it is a surprise to discover that, even in its most highly developed forms, it is both slow and confused. This review looks for clues about the causes of Rubisco's slow evolutionary refinement in its complex catalytic chemistry and in its tendency to catalyse abortive side reactions. We assess the possibilities for improving Rubisco artificially, either by random mutagenesis or by rational design, and imagine the consequences of an improved Rubisco for plant productivity and the global ecosystem.
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Rydzy, Małgorzata, Michał Tracz, Andrzej Szczepaniak, and Joanna Grzyb. "Insights into the Structure of Rubisco from Dinoflagellates-in Silico Studies." International Journal of Molecular Sciences 22, no. 16 (August 7, 2021): 8524. http://dx.doi.org/10.3390/ijms22168524.
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Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is one of the best studied enzymes. It is crucial for photosynthesis, and thus for all of biosphere’s productivity. There are four isoforms of this enzyme, differing by amino acid sequence composition and quaternary structure. However, there is still a group of organisms, dinoflagellates, single-cell eukaryotes, that are confirmed to possess Rubisco, but no successful purification of the enzyme of such origin, and hence a generation of a crystal structure was reported to date. Here, we are using in silico tools to generate the possible structure of Rubisco from a dinoflagellate representative, Symbiodinium sp. We selected two templates: Rubisco from Rhodospirillum rubrum and Rhodopseudomonas palustris. Both enzymes are the so-called form II Rubiscos, but the first is exclusively a homodimer, while the second one forms homo-hexamers. Obtained models show no differences in amino acids crucial for Rubisco activity. The variation was found at two closely located inserts in the C-terminal domain, of which one extends a helix and the other forms a loop. These inserts most probably do not play a direct role in the enzyme’s activity, but may be responsible for interaction with an unknown protein partner, possibly a regulator or a chaperone. Analysis of the possible oligomerization interface indicated that Symbiodinium sp. Rubisco most likely forms a trimer of homodimers, not just a homodimer. This hypothesis was empowered by calculation of binding energies. Additionally, we found that the protein of study is significantly richer in cysteine residues, which may be the cause for its activity loss shortly after cell lysis. Furthermore, we evaluated the influence of the loop insert, identified exclusively in the Symbiodinium sp. protein, on the functionality of the recombinantly expressed R. rubrum Rubisco. All these findings shed new light onto dinoflagellate Rubisco and may help in future obtainment of a native, active enzyme.
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Valegård, Karin, Dirk Hasse, Inger Andersson, and Laura H. Gunn. "Structure of Rubisco fromArabidopsis thalianain complex with 2-carboxyarabinitol-1,5-bisphosphate." Acta Crystallographica Section D Structural Biology 74, no. 1 (January 1, 2018): 1–9. http://dx.doi.org/10.1107/s2059798317017132.
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The crystal structure of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) fromArabidopsis thalianais reported at 1.5 Å resolution. In light of the importance ofA. thalianaas a model organism for understanding higher plant biology, and the pivotal role of Rubisco in photosynthetic carbon assimilation, there has been a notable absence of anA. thalianaRubisco crystal structure.A. thalianaRubisco is an L8S8hexadecamer comprising eight plastome-encoded catalytic large (L) subunits and eight nuclear-encoded small (S) subunits.A. thalianaproduces four distinct small-subunit isoforms (RbcS1A, RbcS1B, RbcS2B and RbcS3B), and this crystal structure provides a snapshot ofA. thalianaRubisco containing the low-abundance RbcS3B small-subunit isoform. Crystals were obtained in the presence of the transition-state analogue 2-carboxy-D-arabinitol-1,5-bisphosphate.A. thalianaRubisco shares the overall fold characteristic of higher plant Rubiscos, but exhibits an interesting disparity between sequence and structural relatedness to other Rubisco isoforms. These results provide the structural framework to understandA. thalianaRubisco and the potential catalytic differences that could be conferred by alternativeA. thalianaRubisco small-subunit isoforms.
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Wei, Xueming, Luis A. Sayavedra-Soto, and Daniel J. Arp. "The transcription of the cbb operon in Nitrosomonas europaea." Microbiology 150, no. 6 (June 1, 2004): 1869–79. http://dx.doi.org/10.1099/mic.0.26785-0.
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Nitrosomonas europaea is an aerobic ammonia-oxidizing bacterium that participates in the C and N cycles. N. europaea utilizes CO2 as its predominant carbon source, and is an obligate chemolithotroph, deriving all the reductant required for energy and biosynthesis from the oxidation of ammonia (NH3) to nitrite (). This bacterium fixes carbon via the Calvin–Benson–Bassham (CBB) cycle via a type I ribulose bisphosphate carboxylase/oxygenase (RubisCO). The RubisCO operon is composed of five genes, cbbLSQON. This gene organization is similar to that of the operon for ‘green-like’ type I RubisCOs in other organisms. The cbbR gene encoding the putative regulatory protein for RubisCO transcription was identified upstream of cbbL. This study showed that transcription of cbb genes was upregulated when the carbon source was limited, while amo, hao and other energy-harvesting-related genes were downregulated. N. europaea responds to carbon limitation by prioritizing resources towards key components for carbon assimilation. Unlike the situation for amo genes, NH3 was not required for the transcription of the cbb genes. All five cbb genes were only transcribed when an external energy source was provided. In actively growing cells, mRNAs from the five genes in the RubisCO operon were present at different levels, probably due to premature termination of transcription, rapid mRNA processing and mRNA degradation.
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Poudel, Saroj, Douglas H. Pike, Hagai Raanan, Joshua A. Mancini, Vikas Nanda, Rosalind E. M. Rickaby, and Paul G. Falkowski. "Biophysical analysis of the structural evolution of substrate specificity in RuBisCO." Proceedings of the National Academy of Sciences 117, no. 48 (November 16, 2020): 30451–57. http://dx.doi.org/10.1073/pnas.2018939117.
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Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the most abundant enzyme on Earth. However, its catalytic rate per molecule of protein is extremely slow and the binding of the primary substrate, CO2, is competitively displaced by O2.Hence, carbon fixation by RuBisCO is highly inefficient; indeed, in higher C3 plants, about 30% of the time the enzyme mistakes CO2for O2. Using genomic and structural analysis, we identify regions around the catalytic site that play key roles in discriminating between CO2and O2. Our analysis identified positively charged cavities directly around the active site, which are expanded as the enzyme evolved with higher substrate specificity. The residues that extend these cavities have recently been under selective pressure, indicating that larger charged pockets are a feature of modern RuBisCOs, enabling greater specificity for CO2. This paper identifies a key structural feature that enabled the enzyme to evolve improved CO2sequestration in an oxygen-rich atmosphere and may guide the engineering of more efficient RuBisCOs.
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Baker, Stefanie H., Songmu Jin, Henry C. Aldrich, Gary T. Howard, and Jessup M. Shively. "Insertion Mutation of the Form I cbbL Gene Encoding Ribulose Bisphosphate Carboxylase/Oxygenase (RuBisCO) in Thiobacillus neapolitanus Results in Expression of Form II RuBisCO, Loss of Carboxysomes, and an Increased CO2 Requirement for Growth." Journal of Bacteriology 180, no. 16 (August 15, 1998): 4133–39. http://dx.doi.org/10.1128/jb.180.16.4133-4139.1998.
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ABSTRACT It has been previously established that Thiobacillus neapolitanus fixes CO2 by using a form I ribulose bisphosphate carboxylase/oxygenase (RuBisCO), that much of the enzyme is sequestered into carboxysomes, and that the genes for the enzyme, cbbL and cbbS, are part of a putative carboxysome operon. In the present study, cbbL andcbbS were cloned and sequenced. Analysis of RNA showed thatcbbL and cbbS are cotranscribed on a message approximately 2,000 nucleotides in size. The insertion of a kanamycin resistance cartridge into cbbL resulted in a premature termination of transcription; a polar mutant was generated. The mutant is able to fix CO2, but requires a CO2supplement for growth. Separation of cellular proteins from both the wild type and the mutant on sucrose gradients and subsequent analysis of the RuBisCO activity in the collected fractions showed that the mutant assimilates CO2 by using a form II RuBisCO. This was confirmed by immunoblot analysis using antibodies raised against form I and form II RuBisCOs. The mutant does not possess carboxysomes. Smaller, empty inclusions are present, but biochemical analysis indicates that if they are carboxysome related, they are not functional, i.e., do not contain RuBisCO. Northern analysis showed that some of the shell components of the carboxysome are produced, which may explain the presence of these inclusions in the mutant.
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Young, J. N., R. E. M. Rickaby, M. V. Kapralov, and D. A. Filatov. "Adaptive signals in algal Rubisco reveal a history of ancient atmospheric carbon dioxide." Philosophical Transactions of the Royal Society B: Biological Sciences 367, no. 1588 (February 19, 2012): 483–92. http://dx.doi.org/10.1098/rstb.2011.0145.
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Rubisco, the most abundant enzyme on the Earth and responsible for all photosynthetic carbon fixation, is often thought of as a highly conserved and sluggish enzyme. Yet, different algal Rubiscos demonstrate a range of kinetic properties hinting at a history of evolution and adaptation. Here, we show that algal Rubisco has indeed evolved adaptively during ancient and distinct geological periods. Using DNA sequences of extant marine algae of the red and Chromista lineage, we define positive selection within the large subunit of Rubisco, encoded by rbcL , to occur basal to the radiation of modern marine groups. This signal of positive selection appears to be responding to changing intracellular concentrations of carbon dioxide (CO 2 ) triggered by physiological adaptations to declining atmospheric CO 2 . Within the ecologically important Haptophyta (including coccolithophores) and Bacillariophyta (diatoms), positive selection occurred consistently during periods of falling Phanerozoic CO 2 and suggests emergence of carbon-concentrating mechanisms. During the Proterozoic, a strong signal of positive selection after secondary endosymbiosis occurs at the origin of the Chromista lineage (approx. 1.1 Ga), with further positive selection events until 0.41 Ga, implying a significant and continuous decrease in atmospheric CO 2 encompassing the Cryogenian Snowball Earth events. We surmise that positive selection in Rubisco has been caused by declines in atmospheric CO 2 and hence acts as a proxy for ancient atmospheric CO 2 .
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Raven, John A., Mario Giordano, John Beardall, and Stephen C. Maberly. "Algal evolution in relation to atmospheric CO 2 : carboxylases, carbon-concentrating mechanisms and carbon oxidation cycles." Philosophical Transactions of the Royal Society B: Biological Sciences 367, no. 1588 (February 19, 2012): 493–507. http://dx.doi.org/10.1098/rstb.2011.0212.
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Oxygenic photosynthesis evolved at least 2.4 Ga; all oxygenic organisms use the ribulose bisphosphate carboxylase-oxygenase (Rubisco)–photosynthetic carbon reduction cycle (PCRC) rather than one of the five other known pathways of autotrophic CO 2 assimilation. The high CO 2 and (initially) O 2 -free conditions permitted the use of a Rubisco with a high maximum specific reaction rate. As CO 2 decreased and O 2 increased, Rubisco oxygenase activity increased and 2-phosphoglycolate was produced, with the evolution of pathways recycling this inhibitory product to sugar phosphates. Changed atmospheric composition also selected for Rubiscos with higher CO 2 affinity and CO 2 /O 2 selectivity correlated with decreased CO 2 -saturated catalytic capacity and/or for CO 2 -concentrating mechanisms (CCMs). These changes increase the energy, nitrogen, phosphorus, iron, zinc and manganese cost of producing and operating Rubisco–PCRC, while biosphere oxygenation decreased the availability of nitrogen, phosphorus and iron. The majority of algae today have CCMs; the timing of their origins is unclear. If CCMs evolved in a low-CO 2 episode followed by one or more lengthy high-CO 2 episodes, CCM retention could involve a combination of environmental factors known to favour CCM retention in extant organisms that also occur in a warmer high-CO 2 ocean. More investigations, including studies of genetic adaptation, are needed.
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Schulz, Luca, Zhijun Guo, Jan Zarzycki, Wieland Steinchen, Jan M. Schuller, Thomas Heimerl, Simone Prinz, Oliver Mueller-Cajar, Tobias J. Erb, and Georg K. A. Hochberg. "Evolution of increased complexity and specificity at the dawn of form I Rubiscos." Science 378, no. 6616 (October 14, 2022): 155–60. http://dx.doi.org/10.1126/science.abq1416.
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The evolution of ribulose-1,5-bisphosphate carboxylase/oxygenases (Rubiscos) that discriminate strongly between their substrate carbon dioxide and the undesired side substrate dioxygen was an important event for photosynthetic organisms adapting to an oxygenated environment. We use ancestral sequence reconstruction to recapitulate this event. We show that Rubisco increased its specificity and carboxylation efficiency through the gain of an accessory subunit before atmospheric oxygen was present. Using structural and biochemical approaches, we retrace how this subunit was gained and became essential. Our work illuminates the emergence of an adaptation to rising ambient oxygen levels, provides a template for investigating the function of interactions that have remained elusive because of their essentiality, and sheds light on the determinants of specificity in Rubisco.
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Waheeda, Kazi, and Po-Lin Chiu. "Complex formation of rubisco and rubisco activase." Biophysical Journal 121, no. 3 (February 2022): 452a. http://dx.doi.org/10.1016/j.bpj.2021.11.520.
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Sage, Rowan F., Danielle A. Way, and David S. Kubien. "Rubisco, Rubisco activase, and global climate change." Journal of Experimental Botany 59, no. 7 (April 23, 2008): 1581–95. http://dx.doi.org/10.1093/jxb/ern053.
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Portis, A. R. "The regulation of Rubisco by Rubisco activase." Journal of Experimental Botany 46, special (September 1, 1995): 1285–91. http://dx.doi.org/10.1093/jxb/46.special_issue.1285.
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Karthick, Palanivelu Vikram, Alagarswamy Senthil, Maduraimuthu Djanaguiraman, Kuppusamy Anitha, Ramalingam Kuttimani, Parasuraman Boominathan, Ramasamy Karthikeyan, and Muthurajan Raveendran. "Improving Crop Yield through Increasing Carbon Gain and Reducing Carbon Loss." Plants 13, no. 10 (May 10, 2024): 1317. http://dx.doi.org/10.3390/plants13101317.
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Photosynthesis is a process where solar energy is utilized to convert atmospheric CO2 into carbohydrates, which forms the basis for plant productivity. The increasing demand for food has created a global urge to enhance yield. Earlier, the plant breeding program was targeting the yield and yield-associated traits to enhance the crop yield. However, the yield cannot be further improved without improving the leaf photosynthetic rate. Hence, in this review, various strategies to enhance leaf photosynthesis were presented. The most promising strategies were the optimization of Rubisco carboxylation efficiency, the introduction of a CO2 concentrating mechanism in C3 plants, and the manipulation of photorespiratory bypasses in C3 plants, which are discussed in detail. Improving Rubisco’s carboxylation efficiency is possible by engineering targets such as Rubisco subunits, chaperones, and Rubisco activase enzyme activity. Carbon-concentrating mechanisms can be introduced in C3 plants by the adoption of pyrenoid and carboxysomes, which can increase the CO2 concentration around the Rubisco enzyme. Photorespiration is the process by which the fixed carbon is lost through an oxidative process. Different approaches to reduce carbon and nitrogen loss were discussed. Overall, the potential approaches to improve the photosynthetic process and the way forward were discussed in detail.
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Toyoda, Koichi, Yoichi Yoshizawa, Hiroyuki Arai, Masaharu Ishii, and Yasuo Igarashi. "The role of two CbbRs in the transcriptional regulation of three ribulose-1,5-bisphosphate carboxylase/oxygenase genes in Hydrogenovibrio marinus strain MH-110." Microbiology 151, no. 11 (November 1, 2005): 3615–25. http://dx.doi.org/10.1099/mic.0.28056-0.
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Hydrogenovibrio marinus MH-110 possesses three different sets of genes for ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO): two form I (cbbLS-1 and cbbLS-2) and one form II (cbbM). We have previously shown that the expression of these RubisCO genes is dependent on the ambient CO2 concentration. LysR-type transcriptional regulators, designated CbbR1 and CbbRm, are encoded upstream of the cbbLS-1 and cbbM genes, respectively. In this study, we revealed by gel shift assay that CbbR1 and CbbRm bind with higher affinity to the promoter regions of cbbLS-1 and cbbM, respectively, and with lower affinity to the other RubisCO gene promoters. The expression patterns of the three RubisCOs in the cbbR1 and the cbbRm gene mutants showed that CbbR1 and CbbRm were required to activate the expression of cbbLS-1 and cbbM, respectively, and that neither CbbR1 nor CbbRm was required for the expression of cbbLS-2. The expression of cbbLS-1 was significantly enhanced under high-CO2 conditions in the cbbRm mutant, in which the expression of cbbM was decreased. Although cbbLS-2 was not expressed under high-CO2 conditions in the wild-type strain or the single cbbR mutants, the expression of cbbLS-2 was observed in the cbbR1 cbbRm double mutant, in which the expression of both cbbLS-1 and cbbM was decreased. These results indicate that there is an interactive regulation among the three RubisCO genes.
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Yoshizawa, Yoichi, Koichi Toyoda, Hiroyuki Arai, Masaharu Ishii, and Yasuo Igarashi. "CO2-Responsive Expression and Gene Organization of Three Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Enzymes and Carboxysomes in Hydrogenovibrio marinus Strain MH-110." Journal of Bacteriology 186, no. 17 (September 1, 2004): 5685–91. http://dx.doi.org/10.1128/jb.186.17.5685-5691.2004.
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ABSTRACT Hydrogenovibrio marinus strain MH-110, an obligately lithoautotrophic hydrogen-oxidizing bacterium, fixes CO2 by the Calvin-Benson-Bassham cycle. Strain MH-110 possesses three different sets of genes for ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO): CbbLS-1 and CbbLS-2, which belong to form I (L8S8), and CbbM, which belongs to form II (Lx). In this paper, we report that the genes for CbbLS-1 (cbbLS-1) and CbbM (cbbM) are both followed by the cbbQO genes and preceded by the cbbR genes encoding LysR-type regulators. In contrast, the gene for CbbLS-2 (cbbLS-2) is followed by genes encoding carboxysome shell peptides. We also characterized the three RubisCOs in vivo by examining their expression profiles in environments with different CO2 availabilities. Immunoblot analyses revealed that when strain MH-110 was cultivated in 15% CO2, only the form II RubisCO, CbbM, was expressed. When strain MH-110 was cultivated in 2% CO2, CbbLS-1 was expressed in addition to CbbM. In the 0.15% CO2 culture, the expression of CbbM decreased and that of CbbLS-1 disappeared, and CbbLS-2 was expressed. In the atmospheric CO2 concentration of approximately 0.03%, all three RubisCOs were expressed. Transcriptional analyses of mRNA by reverse transcription-PCR showed that the regulation was at the transcriptional level. Electron microscopic observation of MH-110 cells revealed the formation of carboxysomes in the 0.15% CO2 concentration. The results obtained here indicate that strain MH-110 adapts well to various CO2 concentrations by using different types of RubisCO enzymes.
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Singh, Jaya, and F. Robert Tabita. "Roles of RubisCO and the RubisCO-Like Protein in 5-Methylthioadenosine Metabolism in the Nonsulfur Purple Bacterium Rhodospirillum rubrum." Journal of Bacteriology 192, no. 5 (December 28, 2009): 1324–31. http://dx.doi.org/10.1128/jb.01442-09.
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ABSTRACT Ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) catalyzes the assimilation of atmospheric CO2 into organic matter and is thus central to the existence of life on earth. The beginning of the 2000s was marked by the discovery of a new family of proteins, the RubisCO-like proteins (RLPs), which are structural homologs of RubisCO. RLPs are unable to catalyze CO2 fixation. The RLPs from Chlorobaculum tepidum, Bacillus subtilis, Geobacillus kaustophilus, and Microcystis aeruginosa have been shown to participate in sulfur metabolism. Whereas the precise function of C. tepidum RLP is unknown, the B. subtilis, G. kaustophilus, and M. aeruginosa RLPs function as tautomerases/enolases in a methionine salvage pathway (MSP). Here, we show that the form II RubisCO enzyme from the nonsulfur purple bacterium Rhodospirillum rubrum is also able to function as an enolase in vivo as part of an MSP, but only under anaerobic conditions. However, unlike B. subtilis RLP, R. rubrum RLP does not catalyze the enolization of 2,3-diketo-5-methylthiopentyl-1-phosphate. Instead, under aerobic growth conditions, R. rubrum RLP employs another intermediate of the MSP, 5-methylthioribulose-1-phosphate, as a substrate, resulting in the formation of different products. To further determine the interrelationship between RubisCOs and RLPs (and the potential integration of cellular carbon and sulfur metabolism), the functional roles of both RubisCO and RLP have been examined in vivo via the use of specific knockout strains and complementation studies of R. rubrum. The presence of functional, yet separate, MSPs in R. rubrum under both aerobic (chemoheterotrophic) and anaerobic (photoheterotrophic) growth conditions has not been observed previously in any organism. Moreover, the aerobic and anaerobic sulfur salvage pathways appear to be differentially controlled, with novel and previously undescribed steps apparent for sulfur salvage in this organism.
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Xiang, Fu, Yuanping Fang, and Jun Xiang. "Structural and evolutionary relationships among RuBisCOs inferred from their large and small subunits." Zeitschrift für Naturforschung C 71, no. 5-6 (May 1, 2016): 181–89. http://dx.doi.org/10.1515/znc-2016-0014.
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Abstract Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the key enzyme to assimilate CO2 into the biosphere. The nonredundant structural data sets for three RuBisCO domain superfamilies, i.e. large subunit C-terminal domain (LSC), large subunit N-terminal domain (LSN) and small subunit domain (SS), were selected using QR factorization based on the structural alignment with QH as the similarity measure. The structural phylogenies were then constructed to investigate a possible functional significance of the evolutionary diversification. The LSC could have occurred in both bacteria and archaea, and has evolved towards increased complexity in both bacteria and eukaryotes with a 4-helix–2-helix–2-helix bundle being extended into a 5-helix–3-helix–3-helix one at the LSC carboxyl-terminus. The structural variations of LSN could have originated not only in bacteria with a short coil, but also in eukaryotes with a long one. Meanwhile, the SS dendrogram can be contributed to the structural variations at the βA–βB-loop region. All the structural variations observed in the coil regions have influence on catalytic performance or CO2/O2 selectivities of RuBisCOs from different species. Such findings provide insights on RuBisCO improvements.
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Demirevska-Kepova, Klimentina, and Urs Feller. "Heat sensitivity of Rubisco, Rubisco activase and Rubisco binding protein in higher plants." Acta Physiologiae Plantarum 26, no. 1 (March 2004): 103–14. http://dx.doi.org/10.1007/s11738-004-0050-7.
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Hotto, Amber M., Coralie Salesse-Smith, Myat Lin, Florian A. Busch, Isabelle Simpson, and David B. Stern. "Rubisco production in maize mesophyll cells through ectopic expression of subunits and chaperones." Journal of Experimental Botany 72, no. 13 (April 30, 2021): 4930–37. http://dx.doi.org/10.1093/jxb/erab189.
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Abstract C4 plants, such as maize, strictly compartmentalize Rubisco to bundle sheath chloroplasts. The molecular basis for the restriction of Rubisco from the more abundant mesophyll chloroplasts is not fully understood. Mesophyll chloroplasts transcribe the Rubisco large subunit gene and, when normally quiescent transcription of the nuclear Rubisco small subunit gene family is overcome by ectopic expression, mesophyll chloroplasts still do not accumulate measurable Rubisco. Here we show that a combination of five ubiquitin promoter-driven nuclear transgenes expressed in maize leads to mesophyll accumulation of assembled Rubisco. These encode the Rubisco large and small subunits, Rubisco assembly factors 1 and 2, and the assembly factor Bundle sheath defective 2. In these plants, Rubisco large subunit accumulates in mesophyll cells, and appears to be assembled into a holoenzyme capable of binding the substrate analog CABP (carboxyarabinitol bisphosphate). Isotope discrimination assays suggest, however, that mesophyll Rubisco is not participating in carbon assimilation in these plants, most probably due to a lack of the substrate ribulose 1,5-bisphosphate and/or Rubisco activase. Overall, this work defines a minimal set of Rubisco assembly factors in planta and may help lead to methods of regulating the C4 pathway.
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Madhavan, S., M. S. Miller-Goodman, and K. W. Lee. "Immunolocalization of Rubisco Activase and Rubisco in C3 and C4 Plant Tissues." Microscopy and Microanalysis 6, S2 (August 2000): 472–73. http://dx.doi.org/10.1017/s1431927600034851.
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Ribulose bisphosphate carboxylase/oxygenase (Rubisco), an abundant enzyme in chloroplasts, must be activated by CO2 in order for it to catalyze the carboxylation of ribulose bisphosphate. Rubisco activase, a nuclear encoded chloroplast protein was first identified as a biochemical lesion in the rca mutant of Arabidopsis (1) which lacked this enzyme. Study of Rubisco in this mutant (2) and transgenic tobacco plants with reduced Rubisco activase levels showed that Rubisco could not achieve and maintain an adequate level of activity, in vivo, without an activase. Rubisco activase promotes ‘activation’ of Rubisco by overcoming the deleterious effects of tight binding sugar phosphates and low chloroplast CO2 levels on catalysis and carbamylation (1).Rubisco activase has been detected in higher plants (3), in unicellular green algae (4,5) and in cyanobacteria (6). Though the presence of Rubisco in guard cell chlroplasts was a subject of controversy, several immunolight and immunoelectron microscopic studies have demonstrated the presence of Rubisco in guard cells (7).
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Yokota, Akiho. "Revisiting RuBisCO." Bioscience, Biotechnology, and Biochemistry 81, no. 11 (September 27, 2017): 2039–49. http://dx.doi.org/10.1080/09168451.2017.1379350.
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Portis, Archie R. "Rubisco activase." Biochimica et Biophysica Acta (BBA) - Bioenergetics 1015, no. 1 (January 1990): 15–28. http://dx.doi.org/10.1016/0005-2728(90)90211-l.
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Feng, Yujiao, Hao Wu, Huanhuan Liu, Yonghui He, and Zhitong Yin. "Effects of OsRCA Overexpression on Rubisco Activation State and Photosynthesis in Maize." Plants 12, no. 8 (April 11, 2023): 1614. http://dx.doi.org/10.3390/plants12081614.
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Ribulose–1,5–bisphosphate carboxylase/oxygenase (Rubisco) is the rate–limiting enzyme for photosynthesis. Rubisco activase (RCA) can regulate the Rubisco activation state, influencing Rubisco activity and photosynthetic rate. We obtained transgenic maize plants that overproduced rice RCA (OsRCAOE) and evaluated photosynthesis in these plants by measuring gas exchange, energy conversion efficiencies in photosystem (PS) I and PSII, and Rubisco activity and activation state. The OsRCAOE lines showed significantly higher initial Rubisco activity and activation state, net photosynthetic rate, and PSII photochemical quantum yield than wild–type plants. These results suggest that OsRCA overexpression can promote maize photosynthesis by increasing the Rubisco activation state.
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Raunser, S., R. Magnani, Z. Huang, R. L. Houtz, R. C. Trievel, P. A. Penczek, and T. Walz. "Rubisco in complex with Rubisco large subunit methyltransferase." Proceedings of the National Academy of Sciences 106, no. 9 (February 10, 2009): 3160–65. http://dx.doi.org/10.1073/pnas.0810563106.
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SEVİNDİK, Emre. "Amino Acids Sequence Based in Silico Analysis of RuBisCO (Ribulose-1,5 Bisphosphate Carboxylase Oxygenase) Proteins in Some Carthamus L. ssp." Notulae Scientia Biologicae 9, no. 2 (June 30, 2017): 204–8. http://dx.doi.org/10.15835/nsb9210053.
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RuBisCO is an important enzyme for plants to photosynthesize and balance carbon dioxide in the atmosphere. This study aimed to perform sequence, physicochemical, phylogenetic and 3D (three-dimensional) comparative analyses of RuBisCO proteins in the Carthamus ssp. using various bioinformatics tools. The sequence lengths of the RuBisCO proteins were between 166 and 477 amino acids, with an average length of 411.8 amino acids. Their molecular weights (Mw) ranged from 18711.47 to 52843.09 Da; the most acidic and basic protein sequences were detected in C. tinctorius (pI = 5.99) and in C. tenuis (pI = 6.92), respectively. The extinction coefficients of RuBisCO proteins at 280 nm ranged from 17,670 to 69,830 M-1 cm-1, the instability index (II) values for RuBisCO proteins ranged from 33.31 to 39.39, while the GRAVY values of RuBisCO proteins ranged from -0.313 to -0.250. The most abundant amino acid in the RuBisCO protein was Gly (9.7%), while the least amino acid ratio was Trp (1.6 %). The putative phosphorylation sites of RuBisCO proteins were determined by NetPhos 2.0. Phylogenetic analysis revealed that RuBisCO proteins formed two main clades. A RAMPAGE analysis revealed that 96.3%-97.6% of residues were located in the favoured region of RuBisCO proteins. To predict the three dimensional (3D) structure of the RuBisCO proteins PyMOL was used. The results of the current study provide insights into fundamental characteristic of RuBisCO proteins in Carthamus ssp.
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Witte, Brian, David John, Boris Wawrik, John H. Paul, David Dayan, and F. Robert Tabita. "Functional Prokaryotic RubisCO from an Oceanic Metagenomic Library." Applied and Environmental Microbiology 76, no. 9 (March 12, 2010): 2997–3003. http://dx.doi.org/10.1128/aem.02661-09.
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ABSTRACT Culture-independent studies have indicated that there is significant diversity in the ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) enzymes used by marine, freshwater, and terrestrial autotrophic bacteria. Surprisingly, little is known about the catalytic properties of many environmentally significant RubisCO enzymes. Because one of the goals of RubisCO research is to somehow modify or select for RubisCO molecules with improved kinetic properties, a facile means to isolate functional and novel RubisCO molecules directly from the environment was developed. In this report, we describe the first example of functional RubisCO proteins obtained from genes cloned and characterized from metagenomic libraries derived from DNA isolated from environmental samples. Two form IA marine RubisCO genes were cloned, and each gene supported both photoheterotrophic and photoautotrophic growth of a RubisCO deletion strain of Rhodobacter capsulatus, strain SBI/II−, indicating that catalytically active recombinant RubisCO was synthesized. The catalytic properties of the metagenomic RubisCO molecules were further characterized. These experiments demonstrated the feasibility of studying the functional diversity and enzymatic properties of RubisCO enzymes without first cultivating the host organisms. Further, this “proof of concept” experiment opens the way for development of a simple functional screen to examine the properties of diverse RubisCO genes isolated from any environment, and subsequent further bioselection may be possible if the growth conditions of complemented R. capsulatus strain SBI/II− are varied.
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Suganami, Mao, Yuji Suzuki, Eri Kondo, Shinji Nishida, So Konno, and Amane Makino. "Effects of Overproduction of Rubisco Activase on Rubisco Content in Transgenic Rice Grown at Different N Levels." International Journal of Molecular Sciences 21, no. 5 (February 27, 2020): 1626. http://dx.doi.org/10.3390/ijms21051626.
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It has been reported that overproduction of Rubisco activase (RCA) in rice (Oryza sativa L.) decreased Rubisco content, resulting in declining photosynthesis. We examined the effects of RCA levels on Rubisco content using transgenic rice with overexpressed or suppressed RCA under the control of different promoters of the RCA and Rubisco small subunit (RBCS) genes. All plants were grown hydroponically with different N concentrations (0.5, 2.0 and 8.0 mM-N). In RCA overproduced plants with > 2-fold RCA content (RCA-HI lines), a 10%–20% decrease in Rubisco content was observed at 0.5 and 2.0 mM-N. In contrast, at 8.0 mM-N, Rubisco content did not change in RCA-HI lines. Conversely, in plants with 50%–60% increased RCA content (RCA-MI lines), Rubisco levels remained unchanged, regardless of N concentration. Such effects on Rubisco content were independent of the promoter that was used. In plants with RCA suppression to < 10% of the wild-type RCA content, Rubisco levels were increased at 0.5 mM-N, but were unchanged at 2.0 and 8.0 mM-N. Thus, the effects of the changes in RCA levels on Rubisco content depended on N supply. Moreover, RCA overproduction was feasible without a decrease in Rubisco content, depending on the degree of RCA production.
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Warren, Charles R., Mark A. Adams, and ZuLiang Chen. "Is photosynthesis related to concentrations of nitrogen and Rubisco in leaves of Australian native plants?" Functional Plant Biology 27, no. 5 (2000): 407. http://dx.doi.org/10.1071/pp98162.
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The relationships among light-saturated photosynthesis and concentrations of nitrogen and ribulose-1,5- bisphosphate carboxylase/oxygenase (Rubisco, EC 4.1.1.39) in Australian native plants are poorly known, primarily due to the difficulty of extracting and analysing Rubisco from such species. Rubisco may be rapidly quantified in crude extracts of plant tissue by capillary electrophoresis (CE); however, the presence of phenolic compounds in many Australian native plants limits the use of these methods. The addition of insoluble polyvinylpolypyrrolidone (PVPP) during leaf extractions effectively removed phenols permitting quantitation of Rubisco. Relationships among maximum rates of photosynthesis and concentrations of nitrogen and Rubisco were then investigated in ten species native to Australia. Total nitrogen and the major pools of N in foliage varied greatly between species. Equally, within species N-partitioning was highly plastic, as affected by different concentrations and forms of N applied in sand culture (0.5 or 8 mM, nitrate or ammonium). In Hakea prostrata, for example, the proportion of total N present as soluble proteins varied between 43 and 71%, while the proportion of total N present as Rubisco N ranged between 9.4 and 30.0%, and the contribution of Rubisco to soluble proteins varied between 21 and 42%. The measured concentration of Rubisco varied between 40% and 600% of that estimated from enzyme kinetics and measured rates of photosynthesis. Generally there was a large ‘excess’ of Rubisco, and in only two cases was the measured concentration of Rubisco significantly less than predicted. Total N, soluble protein and Rubisco concentrations were poorly related to maximum rates of photosynthesis, while the relationship between photosynthesis and Rubisco was worse than that with N, primarily due to the plants’ variable over-investment in Rubisco.
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Roh, Kwang-Soo. "Influence of Nitrate on Growth, Chlorophyll Content, Content and Activity of Rubisco and Rubisco Activase of Tobacco Plant Treated with Cadmium in vitro." Journal of Life Science 20, no. 11 (November 30, 2010): 1667–74. http://dx.doi.org/10.5352/jls.2010.20.11.1667.
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Cheng, Lailiang, and Leslie H. Fuchigami. "Photometric Measurements of Rubisco Activity in Leaves of Deciduous Fruit Crops." HortScience 32, no. 3 (June 1997): 531A—531. http://dx.doi.org/10.21273/hortsci.32.3.531a.
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Ribulose bisphosphate carboxylase/oxygenase (Rubisco) initiates the photosynthetic carbon metabolism;therefore, its activity has been measured in many physiological studies. However, information on in vitro Rubisco activity from leaves of deciduous fruit crops is very limited and the reported activities are suspiciously low. We measured Rubisco activity in crude extracts of leaves of apple, pear, peach, cherry, and grape by using a photometric method in which RuBP carboxylation was enzymically coupled to NADH oxidation. Replacing polyvinylpyrrolidone with polyvinylpolypyrrolidone in the extraction solution significantly increased extractable Rubisco activity. Depending on species, freezing leaf discs in liquid nitrogen followed by storage at –80°C for only 24 hr reduced both initial and total Rubisco activity to 5% to 50% of that obtained from fresh leaves. Initial Rubisco activity from fresh leaf tissues of all species was well correlated with maximum Rubisco activity (Vcmax) estimated from gas exchange; an exception was pear, where initial Rubisco activity was higher than Vcmax. In most cases, initial Rubisco activity was approximately two to three times higher than net photosynthesis.
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Watson, Gregory M. F., Jae-Pil Yu, and F. Robert Tabita. "Unusual Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase of Anoxic Archaea." Journal of Bacteriology 181, no. 5 (March 1, 1999): 1569–75. http://dx.doi.org/10.1128/jb.181.5.1569-1575.1999.
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ABSTRACT The predominant pool of organic matter on earth is derived from the biological reduction and assimilation of carbon dioxide gas, catalyzed primarily by the enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO). By virtue of its capacity to use molecular oxygen as an alternative and competing gaseous substrate, the catalytic efficiency of RubisCO and the enzyme’s ability to assimilate CO2 may be severely limited, with consequent environmental and agricultural effects. Recent genomic sequencing projects, however, have identified putative RubisCO genes from anoxic Archaea. In the present study, these potential RubisCO sequences, from Methanococcus jannaschiiand Archaeoglobus fulgidus, were analyzed in order to ascertain whether such sequences might encode functional proteins. We also report the isolation and properties of recombinant RubisCO using sequences obtained from the obligately anaerobic hyperthermophilic methanogen M. jannaschii. This is the first description of an archaeal RubisCO sequence; this study also represents the initial characterization of a RubisCO molecule that has evolved in the absence of molecular oxygen. The enzyme was shown to be a homodimer whose deduced sequence, along with other recently obtained archaeal RubisCO sequences, differs substantially from those of known RubisCO molecules. The recombinantM. jannaschii enzyme has a somewhat low, but reasonable k cat, however, unlike previously isolated RubisCO molecules, this enzyme is very oxygen sensitive yet it is stable to hyperthermal temperatures and catalyzes the formation of the expected carboxylation product. Despite inhibition by oxygen, this unusual RubisCO still catalyzes a weak yet demonstrable oxygenase activity, with perhaps the lowest capacity for CO2/O2 discrimination ever encountered for any RubisCO.
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MARTÍNEZ-BARAJAS, E., J. MOLINA-GALÁN, and E. SÁNCHEZ de JIMÉNEZ. "Regulation of Rubisco activity during grain-fill in maize: possible role of Rubisco activase." Journal of Agricultural Science 128, no. 2 (March 1997): 155–61. http://dx.doi.org/10.1017/s002185969600408x.
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Levels of ribulose bisphosphate carboxylase (Rubisco) and Rubisco activase were compared in leaves above the ear in two genetically related populations (Z0 and Z20) of maize (Zea mays L.). Z20 was obtained from Z0 after twenty agronomic selection cycles for grain yield improvement (c. 90% above Z0). Plants were cultivated in the highlands of Mexico and leaves were sampled weekly during the grain-filling period. Chlorophyll, soluble protein and Rubisco activity were measured. Chlorophyll and soluble protein content slowly decreased during this period, the former faster than the latter, with no significant differences between populations. During the first 40 days after anthesis, Rubisco activity was significantly greater in the high-yielding population (Z20), although Western blot analysis of Rubisco showed similar values for both populations within this period. However, the same analysis for Rubisco activase indicated a greater amount of this protein in the higher-yielding population (Z20) than the original one (Z0) during the early and middle part of the grain-filling period. The addition of Rubisco activase and an ATP-generating system to Z0 leaf extracts resulted in increased Rubisco activity. It was concluded that during grain-fill in maize, the level of Rubisco activase has a regulatory effect on Rubisco activity expression.
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Cheng, Lailiang, and Leslie H. Fuchigami. "The Relationship between Rubisco Activity and Photosynthesis in Apple Leaves with Different Nitrogen Content." HortScience 32, no. 3 (June 1997): 530E—531. http://dx.doi.org/10.21273/hortsci.32.3.530e.
Full textAbstract:
Based on the curvilinear relationship between carboxylation efficiency and leaf N in apple leaves, we hypothesized that deactivation of Rubisco accounts for the lack of response of photosynthesis to increasing leaf N under high N supply. A wide range of leaf N content (from 1.0 to 5.0 g·m–2) was achieved by fertigating bench-grafted Fuji/M26 apple trees for 6 weeks with different N concentrations using a modified Hoagland solution. Analysis of photosynthesis in response to intercellular CO2 under both 21% and 2% O2 indicated that photosynthesis at ambient CO2 was mainly determined by the activity of Rubisco. Measurements of Rubisco activity revealed that initial Rubisco activity increased with leaf N up to 3.0 g·m–2, then leveled off with further rise in leaf N, whereas total Rubisco activity increased linearly with increasing leaf N throughout the leaf N range. As a result, Rubisco activation state decreased with increasing leaf N. Photosynthesis at ambient CO2 and carboxylation efficiency were both linearly correlated with initial Rubisco activity, but showed curvilinear relationships with total Rubisco activity and leaf N. As leaf N increased, photosynthetic nitrogen use efficiency declined with decreasing Rubisco activation state.
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O'Leary, Brendan M., Andrew P. Scafaro, Ricarda Fenske, Owen Duncan, Elke Ströher, Jakob Petereit, and A. Harvey Millar. "Rubisco lysine acetylation occurs at very low stoichiometry in mature Arabidopsis leaves: implications for regulation of enzyme function." Biochemical Journal 477, no. 19 (October 12, 2020): 3885–96. http://dx.doi.org/10.1042/bcj20200413.
Full textAbstract:
Multiple studies have shown ribulose-1,5-bisphosphate carboxylase/oxygenase (E.C. 4.1.1.39; Rubisco) to be subject to Lys-acetylation at various residues; however, opposing reports exist about the biological significance of these post-translational modifications. One aspect of the Lys-acetylation that has not been addressed in plants generally, or with Rubisco specifically, is the stoichiometry at which these Lys-acetylation events occur. As a method to ascertain which Lys-acetylation sites on Arabidopsis Rubisco might be of regulatory importance to its catalytic function in the Calvin–Benson cycle, we purified Rubisco from leaves in both the day and night-time and performed independent mass spectrometry based methods to determine the stoichiometry of Rubisco Lys-acetylation events. The results indicate that Rubisco is acetylated at most Lys residues, but each acetylation event occurs at very low stoichiometry. Furthermore, in vitro treatments that increased the extent of Lys-acetylation on purified Rubisco had no effect on Rubisco maximal activity. Therefore, we are unable to confirm that Lys-acetylation at low stoichiometries can be a regulatory mechanism controlling Rubisco maximal activity. The results highlight the need for further use of stoichiometry measurements when determining the biological significance of reversible PTMs like acetylation.
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Tabita, F. Robert, Thomas E. Hanson, Sriram Satagopan, Brian H. Witte, and Nathan E. Kreel. "Phylogenetic and evolutionary relationships of RubisCO and the RubisCO-like proteins and the functional lessons provided by diverse molecular forms." Philosophical Transactions of the Royal Society B: Biological Sciences 363, no. 1504 (May 16, 2008): 2629–40. http://dx.doi.org/10.1098/rstb.2008.0023.
Full textAbstract:
Ribulose 1,5-bisphosphate (RuBP) carboxylase/oxygenase (RubisCO) catalyses the key reaction by which inorganic carbon may be assimilated into organic carbon. Phylogenetic analyses indicate that there are three classes of bona fide RubisCO proteins, forms I, II and III, which all catalyse the same reactions. In addition, there exists another form of RubisCO, form IV, which does not catalyse RuBP carboxylation or oxygenation. Form IV is actually a homologue of RubisCO and is called the RubisCO-like protein (RLP). Both RubisCO and RLP appear to have evolved from an ancestor protein in a methanogenic archaeon, and comprehensive analyses indicate that the different forms (I, II, III and IV) contain various subgroups, with individual sequences derived from representatives of all three kingdoms of life. The diversity of RubisCO molecules, many of which function in distinct milieus, has provided convenient model systems to study the ways in which the active site of this protein has evolved to accommodate necessary molecular adaptations. Such studies have proven useful to help provide a framework for understanding the molecular basis for many important aspects of RubisCO catalysis, including the elucidation of factors or functional groups that impinge on RubisCO carbon dioxide/oxygen substrate discrimination.
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Guo, Xue, Huaqun Yin, Jing Cong, Zhimin Dai, Yili Liang, and Xueduan Liu. "RubisCO Gene Clusters Found in a Metagenome Microarray from Acid Mine Drainage." Applied and Environmental Microbiology 79, no. 6 (January 18, 2013): 2019–26. http://dx.doi.org/10.1128/aem.03400-12.
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ABSTRACTThe enzyme responsible for carbon dioxide fixation in the Calvin cycle, ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), is always detected as a phylogenetic marker to analyze the distribution and activity of autotrophic bacteria. However, such an approach provides no indication as to the significance of genomic content and organization. Horizontal transfers of RubisCO genes occurring in eubacteria and plastids may seriously affect the credibility of this approach. Here, we presented a new method to analyze the diversity and genomic content of RubisCO genes in acid mine drainage (AMD). A metagenome microarray containing 7,776 large-insertion fosmids was constructed to quickly screen genome fragments containing RubisCO form I large-subunit genes (cbbL). Forty-sixcbbL-containing fosmids were detected, and six fosmids were fully sequenced. To evaluate the reliability of the metagenome microarray and understand the microbial community in AMD, the diversities ofcbbLand the 16S rRNA gene were analyzed. Fosmid sequences revealed that the form I RubisCO gene cluster could be subdivided into form IA and IB RubisCO gene clusters in AMD, because of significant divergences in molecular phylogenetics and conservative genomic organization. Interestingly, the form I RubisCO gene cluster coexisted with the form II RubisCO gene cluster in one fosmid genomic fragment. Phylogenetic analyses revealed that horizontal transfers of RubisCO genes may occur widely in AMD, which makes the evolutionary history of RubisCO difficult to reconcile with organismal phylogeny.
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Khaembah, Edith N., François Gastal, Serge Carre, Louis J. Irving, Philippe Barre, and Cory Matthew. "Morphology and Rubisco turnover characteristics of perennial ryegrass breeding populations after two and four cycles of divergent selection for long or short leaf length." Crop and Pasture Science 64, no. 7 (2013): 687. http://dx.doi.org/10.1071/cp13066.
Full textAbstract:
Perennial ryegrass populations previously subjected to two or four cycles of selection for short or long leaf length were studied to determine the response of morphological traits to selection and interaction to determine yield. Measured morphological traits were leaf length, leaf appearance interval, ligule appearance interval, leaf elongation duration, leaf elongation rate, tiller number, tiller dry weight, and herbage dry matter. Additionally, Rubisco concentration during leaf development was measured to determine the association of Rubisco turnover with morphological characteristics and yield. Rubisco was measured and modelled as a three-parameter (D, peak Rubisco concentration; G, time of D; and F, curve width measure), log-normal curve. Leaf length, leaf elongation rate, tiller weight, and plant dry matter diverged after two cycles of selection and further divergence occurred, with these traits being, respectively, 35, 28, 53, and 61% greater in the long- than the short-leaved plants after four cycles of selection. Opposite trends were displayed by Rubisco turnover, with selection for long leaves co-selecting for increased Rubisco turnover time and selection for short leaves resulting in increased leaf Rubisco concentration. There was indication of coupling of leaf appearance with Rubisco turnover. Across populations, multivariate analysis indicated that plant yield was associated with Rubisco concentration rather than Rubisco turnover. The association between higher yield and lower Rubisco concentration could be targeted in the breeding of high-yielding, nitrogen-efficient forage grasses. Plant yield was mainly associated with increased leaf area, indicating that yield could be improved by selecting for longer leaves and faster rates of leaf expansion.
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Woodrow, IE, ME Kelly, and KA Mott. "Limitation of the Rate of Ribulosebisphosphate Carboxylase Activation by Carbamylation and Ribulosebisphosphate Carboxylase Activase Activity: Development and Tests of a Mechanistic Model." Functional Plant Biology 23, no. 2 (1996): 141. http://dx.doi.org/10.1071/pp9960141.
Full textAbstract:
A mechanistically-based model of light-mediated activation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is developed. The model describes the kinetics of Rubisco activation following a relatively rapid increase in photon flux density (PPFD) from an initially low level. Underlying the model is the assumption that there are two slow processes that could potentially limit the rate of light-mediated Rubisco activation. These processes are the addition of the activator CO2 to the large subunit of Rubisco, which is accompanied by a conformational change in the enzyme (carbamylation), and activase-mediated removal of ribulose 1,5-bisphosphate from the inactive form of the enzyme. The contribution of these slow processes to the overall activation kinetics of Rubisco was resolved by measuring Rubisco activation in whole spinach leaves using non-steady-state CO2 exchange. It was found that when the change in PPFD was relatively small and a correspondingly small proportion of the Rubisco pool was activated, the kinetics of activation were highly sensitive to the intercellular CO2 concentration (ci). The apparent rate constant for activation under these conditions was found to be similar to that for the carbamylation of purified spinach Rubisco. When the change in PPFD and the proportion of Rubisco activated was relatively large, however, the kinetics of Rubisco activation were almost completely CO2 insensitive and were consistent with those of an enzyme-catalysed reaction. It is suggested that (1) CO2-insensitive activation reflects the operation of Rubisco activase and (2) the increasing CO2 sensitivity seen as the change in PPFD decreases reflects a transition to limitation by carbamylation.