Rubisco: still the most abundant protein of Earth?
Ribulose bisphosphate carboxylase‐oxygenase (Rubisco) is the core autotrophic carboxylase in all oxygenic photosynthetic organisms, and > 99.5% of the inorganic carbon (C) assimilated in primary producers (chemolithotrophs as well as photolithotrophs) involves Rubisco (Raven, 2009). The global gross primary productivity of at least 100 Pmol CO2 handled by Rubisco (Field et al., 1998; Raven, 2009) requires a very large global catalytic capacity and hence a large quantity of the enzyme, as a result of its low substrate‐saturated specific catalytic rate on a protein mass basis, low CO2 affinity and expression of oxygenase as well as carboxylase activities, with major constraints on how these properties can vary among Rubiscos (Losh et al., pp. 52–58 in this issue of New Phytologist).
‘How can leaf Rubisco N values for vascular plants best be compared with whole organism (whole cell) Rubisco protein values for cyanobacteria and algae?’
Ellis (1979) suggested that Rubisco was the most globally abundant protein in land biota, based on the enzyme from C3 land plants. However, work on organisms with Rubiscos with different kinetics and CO2 supply mechanisms, specifically CO2 concentrating mechanisms (CCMs), suggests that less Rubisco is needed in some organisms to catalyse a given rate of CO2 assimilation. In this issue of New Phytologist, Losh et al. provide a very important data set which measures the Rubisco content in cultures of eight species of microalgae, and also in natural populations of marine phytoplankton. A very important finding is that the protein content of the algal cells, as a fraction of total cell protein, is only about a fifth of that in the leaves of C3 plants, and is the minimum Rubisco content needed to support the observed maximum growth rate of the algae.
Rubisco content of algae and plants
The highest values of Rubisco per unit nitrogen (N) among the flowering plants (Table 1) are found in C3 plants relying on diffusive entry of CO2 to Rubisco from the bulk atmosphere. All the other organisms listed have CCMs; for the terrestrial vascular plants these are all C4 plants, and they have lower Rubisco values on a leaf blade N basis (Table 1), based on the measurements on seven NADme (using NAD malic enzyme as the C4 decarboxylase) grasses, as well as for seven NADPme (using NADP malic enzyme as the C4 decarboxylase) grasses. There seem to be no comparable values for Rubisco N as a fraction of total leaf protein in plants with the PEPck (PEP carboxykians as the C4 decarboxylase) variants of C4 metabolism, or those with the other kind of CCM, that is, Crassulacean Acid Metabolism (CAM), although Niewiadomska et al. (2011) examined the CAM and C3 phenotypes of a facultative CAM plant and found that the CAM phenotype had a lower Rubisco content than did the C3 phenotype.
| Organisms, C assimilation pathway | Rubisco N :total leaf N | Rubisco protein :total protein | Comments | References |
|---|---|---|---|---|
| C3 physiology flowering plants | 0.095–0.28 | Lowest value is for a shade‐adapted plant | Evans (1989) | |
| 5 species of C3 flowering plants | 0.158–0.259 | CO2 300 ppm | Sage et al. (1989) | |
| 7 C4‐NADme monocotyledons | 0.042–0.084 | N‐replete values | Ghannoum et al. (2005) | |
| 7 C4‐NADPme monocotyledons | 0.044–0.074 | N‐replete values | Ghannoum et al. (2005) | |
| Cyanobacteria and microalgae, apparently all with CCMs | 0.024–0.120 (0.16, 0.23) | Range is for 15 values, many for high and low CO2 cultures of the same organism, with two higher values Some values involve an assumed chla : total protein ratio | Raven (1991) | |
| Microalgae (8 species): 5 marine diatoms, 2 marine prymnesiophytes, 1 freshwater green, all with CCMs | 0.02–0.06 | Nutrient‐replete laboratory cultures; values for field material and nutrient‐limited laboratory cultures are all below 0.025 | Losh et al. (pp. 52–58) |
- CCM, CO2 concentrating mechanism.
The other category of oxygenic phototrophs with CCMs in Table 1 is that found in the cyanobacteria and microalgae. The values in Table 1 are Rubisco as a fraction of total protein in the cells. The very careful work of Losh et al. is all based on Rubisco protein as a fraction of total protein, and the values for nutrient‐replete culture show much less variation than those cited in Raven (1991). Losh et al. also give values for phytoplankton from the marine environment; the values are near or below the values found for nutrient‐replete cultures.
How can the leaf Rubisco N as a fraction of the total leaf N values for the vascular plants in Table 1 best be compared with whole organism (whole cell) Rubisco protein as a fraction of total protein values for cyanobacteria and algae? Rubisco N on a leaf‐blade‐N basis is less than Rubisco N as a fraction of leaf protein N since some leaf N is in nucleic acids, free amino acids and other intermediary metabolites, and stored N; possibly outweighing this is the protein occurring in the rest of the plant where the fraction contributed to Rubisco is much less than in leaf blades. However, a more detailed analysis is needed before it can be concluded that the Rubisco N : leaf N ratios needs downward correction for comparison with the Rubisco : total organism protein ratios in Table 1.
Global aspects of Rubisco content
Returning to the global quantitative significance of Rubisco relative to other proteins, the lower fraction of Rubisco in algae and vascular plants with CCMs can be considered in relation to the contribution of these organisms to global primary productivity. The contributions of marine and continental primary productivity are given by Field et al. (1998) and Raven (2009). Essentially all of the marine planktonic net primary productivity (47.5 Pg C yr−1; Field et al., 1998) involved organisms with CCMs, and CCMs also occur in many of the organisms contributing to coastal benthic net primary productivity (c. 1 Pg C yr−1: Field et al., 1998). It is important to note that CCMs seem to be as prevalent in polar as in warmer waters (Tortell et al., 2006); even though the arguments as to the smaller, or absent, competitive advantage of CCMs at low temperatures used for terrestrial C4 plants (Long, 1999) also apply to marine primary producers (Raven et al., 2002). On land, Field et al. (1998) suggest a global net primary productivity of 56 Pg C yr−1; from global values for natural abundance stable C isotope discrimination, 21% of this is due to C4 plants (Lloyd & Farquhar, 1994).
These values suggest that at least half of global primary productivity involves CCMs, and the organisms with CCMs have less Rubisco per unit biomass, and a smaller fraction of total protein allocated to Rubisco, than in C3 terrestrial plants. The values in Table 1 suggest that the organisms with CCMs have less than half of the Rubisco content of terrestrial C3 plants. The global quantity of Rubisco is, then, less than three quarters, and possibly less than five‐eighths, of what would be the case if all primary producers using Rubisco had the quantity of Rubisco found in C3 terrestrial plants. The smaller quantity of Rubisco in photolithotrophs using CCMs is often reflected in a greater N use efficiency (NUE; rate of biomass gain per unit N in the organism), in C4 plants (Long, 1999), and predicted for algae with CCMs (Raven, 1991; Raven et al., 2012). This greater NUE means that the decreased content of Rubisco, and of the machinery used in the photorespiratory C oxidation cycle(s) in organisms with CCMs than in C3 terrestrial plants, is not quantitatively offset by the need for additional N in the catalysts and structures required by CCMs.
Are there any other autotrophic CO2 assimilation pathways which could function in oxygenic photosynthetic organisms in the present atmosphere with a lower requirement for protein in the CO2 assimilation pathway per unit CO2 fixation rate than for Rubisco‐based systems? Of the five well‐characterized alternatives to Rubisco and the Benson–Calvin cycle, all have a lower running cost (mol ATP and mol NADPH per mol CO2 assimilated) than the Rubisco‐based systems in the present atmosphere, but some are ruled out by irreversible inhibition by O2 or low inorganic C affinity (Raven, 2009; Bar‐Even et al., 2012; Raven et al., 2012). However, lower energy inputs mean that the overall reaction sequence is closer to thermodynamic equilibrium, with a greater extent of back‐reactions and so a requirement for enzyme protein than for a reaction sequence further from equilibrium (Bar‐Even et al., 2012). Bar‐Even et al. (2012) also point out that the enzymes with the lowest specific reaction sequence in the pathway are typically carboxylases, so non‐Rubisco‐based pathways can also have a high protein allocation to carboxylases. The most plausible alternative to the Rubisco‐based systems is the 3‐hydroxypropionate bi‐cycle (Bar‐Even et al., 2012), although even this pathway only represents a protein saving, for a given rate of CO2 assimilation, of 0.33 relative to a Rubisco‐based system with the PCOC (Bar‐Even et al., 2012) and a smaller factor for Rubisco‐based systems with CCMs (Raven, 1991; Long, 1999).
What now of the suggestion by Ellis (1979) that Rubisco is the commonest protein in the (terrestrial) world? The allocation of 20% of terrestrial primary productivity to C4 plants decreases the quantity of Rubisco on land to 85–90% of the value calculated by Ellis (1979); this would probably still allow Rubisco to be the most abundant protein on land, with actin (quantity unspecified) suggested by Ellis as the next most abundant protein. Even with the global quantity of Rubisco in the ocean suggested by the work of Losh et al., it could be the most abundant protein in marine biota.
References
Number of times cited according to CrossRef: 58
- Yuri Pinheiro Alves de Souza and Alexandre Soares Rosado, Opening the Black Box of Thermophilic Autotrophic Bacterial Diversity, Microbial Diversity in the Genomic Era, 10.1016/B978-0-12-814849-5.00019-8, (333-343), (2019).
- Dan Binkley and Richard F. Fisher, References, Ecology and Management of Forest Soils, (393-433), (2019).
- Lewis M. Ward and Patrick M. Shih, The evolution and productivity of carbon fixation pathways in response to changes in oxygen concentration over geological time, Free Radical Biology and Medicine, 10.1016/j.freeradbiomed.2019.01.049, (2019).
- Yang Li, Zhaojun Wu, Xingchen Dong, Zhongjun Jia and Qingye Sun, Variance in bacterial communities, potential bacterial carbon sequestration and nitrogen fixation between light and dark conditions under elevated CO2 in mine tailings, Science of The Total Environment, 10.1016/j.scitotenv.2018.10.253, 652, (234-242), (2019).
- Arnold J Bloom, Metal regulation of metabolism, Current Opinion in Chemical Biology, 10.1016/j.cbpa.2018.09.017, 49, (33-38), (2019).
- David J. Des Marais and Linda L. Jahnke, Biosignatures of Cellular Components and Metabolic Activity, Biosignatures for Astrobiology, 10.1007/978-3-319-96175-0_3, (51-85), (2018).
- Albin Alfreider and Teresa Bogensperger, Specific detection of form IA RubisCO genes in chemoautotrophic bacteria, Journal of Basic Microbiology, 58, 8, (712-716), (2018).
- Alessio Cherubini‐Celli, Javier Mateos, Marcella Bonchio, Luca Dell'Amico and Xavier Companyó, Transition Metal‐Free CO2 Fixation into New Carbon–Carbon Bonds, ChemSusChem, 11, 18, (3056-3070), (2018).
- Chaofan Ji, Jing Han, Jingbo Zhang, Jing Hu, Yinghuan Fu, Hang Qi, Yue Sun and Chenxu Yu, Omics‐prediction of bioactive peptides from the edible cyanobacterium Arthrospira platensis proteome, Journal of the Science of Food and Agriculture, 98, 3, (984-990), (2017).
- Saura R. Silva, Robert Gibson, Lubomír Adamec, Yoannis Domínguez and Vitor F.O. Miranda, Molecular phylogeny of bladderworts: A wide approach of Utricularia (Lentibulariaceae) species relationships based on six plastidial and nuclear DNA sequences, Molecular Phylogenetics and Evolution, 118, (244), (2018).
- Oliver Ebenhöh and Stephanie Spelberg, The importance of the photosynthetic Gibbs effect in the elucidation of the Calvin–Benson–Bassham cycle, Biochemical Society Transactions, 10.1042/BST20170245, 46, 1, (131-140), (2018).
- Paola Branduardi and Michael Sauer, Microbial carbon dioxide fixation: new tricks for an old game, FEMS Microbiology Letters, 365, 3, (2018).
- Robert E. Sharwood, Engineering chloroplasts to improve Rubisco catalysis: prospects for translating improvements into food and fiber crops, New Phytologist, 213, 2, (494-510), (2016).
- Ireneusz Ślesak, Halina Ślesak and Jerzy Kruk, RubisCO Early Oxygenase Activity: A Kinetic and Evolutionary Perspective, BioEssays, 39, 11, (2017).
- Mattia Pierangelini, John A. Raven and Mario Giordano, The relative availability of inorganic carbon and inorganic nitrogen influences the response of the dinoflagellate Protoceratium reticulatum to elevated CO2, Journal of Phycology, 53, 2, (298-307), (2016).
- Xiao Yi, Experimental evolution and proximate mechanisms in biology, Synthetic and Systems Biotechnology, 2, 4, (253), (2017).
- Di Liu, Ramaswamy Chettiyan Seetharaman Ramya and Oliver Mueller-Cajar, Surveying the expanding prokaryotic Rubisco multiverse, FEMS Microbiology Letters, 10.1093/femsle/fnx156, 364, 16, (2017).
- John A Raven, John Beardall and Patricia Sánchez-Baracaldo, The possible evolution and future of CO2-concentrating mechanisms, Journal of Experimental Botany, 10.1093/jxb/erx110, 68, 14, (3701-3716), (2017).
- Piotr Kolesinski, Malgorzata Rydzy and Andrzej Szczepaniak, Is RAF1 protein from Synechocystis sp. PCC 6803 really needed in the cyanobacterial Rubisco assembly process?, Photosynthesis Research, 132, 2, (135), (2017).
- Kevin J. Flynn and John A. Raven, What is the limit for photoautotrophic plankton growth rates?, Journal of Plankton Research, 10.1093/plankt/fbw067, 39, 1, (13-22), (2016).
- , Bibliography, Microbial Symbioses, 10.1016/B978-1-78548-220-5.50013-1, (135-149), (2017).
- Li Jiao, Yali Zhang and Jiang Lu, Overexpression of a stress-responsive U-box protein gene VaPUB affects the accumulation of resistance related proteins in Vitis vinifera ‘Thompson Seedless’, Plant Physiology and Biochemistry, 112, (53), (2017).
- Erik Jensen, Romain Clément, Stephen C. Maberly and Brigitte Gontero, Regulation of the Calvin–Benson–Bassham cycle in the enigmatic diatoms: biochemical and evolutionary variations on an original theme, Philosophical Transactions of the Royal Society B: Biological Sciences, 10.1098/rstb.2016.0401, 372, 1728, (20160401), (2017).
- Gleb Dotsenko and Lene Lange, Enzyme Enhanced Protein Recovery from Green Biomass Pulp, Waste and Biomass Valorization, 8, 4, (1257), (2017).
- Sabrine Kobbi, Ali Bougatef, Guillaume Le flem, Rafik Balti, Chevalier Mickael, Bertrand Fertin, Semia Chaabouni, Pascal Dhulster and Naima Nedjar, Purification and Recovery of RuBisCO Protein from Alfalfa Green Juice: Antioxidative Properties of Generated Protein Hydrolysate, Waste and Biomass Valorization, 8, 2, (493), (2017).
- Stefanie Böhnke and Mirjam Perner, Unraveling RubisCO Form I and Form II Regulation in an Uncultured Organism from a Deep-Sea Hydrothermal Vent via Metagenomic and Mutagenesis Studies, Frontiers in Microbiology, 8, (2017).
- Alejandra A. Covarrubias, Cesar L. Cuevas-Velazquez, Paulette S. Romero-Pérez, David F. Rendón-Luna and Caspar C. C. Chater, Structural disorder in plant proteins: where plasticity meets sessility, Cellular and Molecular Life Sciences, 10.1007/s00018-017-2557-2, 74, 17, (3119-3147), (2017).
- Andrew K. Ringsmuth, Michael J. Landsberg and Ben Hankamer, Can photosynthesis enable a global transition from fossil fuels to solar fuels, to mitigate climate change and fuel-supply limitations?, Renewable and Sustainable Energy Reviews, 10.1016/j.rser.2016.04.016, 62, (134-163), (2016).
- Robert E. Sharwood, Oula Ghannoum, Maxim V. Kapralov, Laura H. Gunn and Spencer M. Whitney, Temperature responses of Rubisco from Paniceae grasses provide opportunities for improving C3 photosynthesis, Nature Plants, 2, 12, (16186), (2016).
- Iqbal Saeed, Daoura Goudia Bachir, Liang Chen, Yin-Gang Hu and Genlou Sun, The Expression of TaRca2-α Gene Associated with Net Photosynthesis Rate, Biomass and Grain Yield in Bread Wheat (Triticum aestivum L.) under Field Conditions, PLOS ONE, 11, 8, (e0161308), (2016).
- Yuansheng Zhang, Yongtao Liu, Xupeng Cao, Peng Gao, Xinyu Liu, Xiyue Wang, Junjie Zhang, Jiannan Zhou, Song Xue, Guowang Xu and Jing Tian, Free amino acids and small molecular acids profiling of marine microalga Isochrysis zhangjiangensis under nitrogen deficiency, Algal Research, 10.1016/j.algal.2015.12.001, 13, (207-217), (2016).
- Claudia Durall, Nita Rukminasari and Peter Lindblad, Enhanced growth at low light intensity in the cyanobacterium Synechocystis PCC 6803 by overexpressing phosphoenolpyruvate carboxylase, Algal Research, 16, (275), (2016).
- Daniel Sebastian Goll, Coupled Cycling of Carbon, Nitrogen, and Phosphorus, Soil Phosphorus, 10.1201/9781315372327-4, (43-63), (2016).
- Aykut Sağlam, Fuat Yetişsin, Mehmet Demiralay and Rabiye Terzi, Copper Stress and Responses in Plants, Plant Metal Interaction, 10.1016/B978-0-12-803158-2.00002-3, (21-40), (2016).
- P.-A. Christin and D. Wood, C4 and CAM Photosynthesis in Land Plants, Evolution and Diversification of, Encyclopedia of Evolutionary Biology, 10.1016/B978-0-12-800049-6.00260-2, (254-259), (2016).
- ELIZABETE CARMO‐SILVA, JOANNA C. SCALES, PIPPA J. MADGWICK and MARTIN A. J. PARRY, Optimizing Rubisco and its regulation for greater resource use efficiency, Plant, Cell & Environment, 38, 9, (1817-1832), (2014).
- John A. Raven and Peter J. Ralph, Enhanced biofuel production using optimality, pathway modification and waste minimization, Journal of Applied Phycology, 10.1007/s10811-014-0323-5, 27, 1, (1-31), (2014).
- Howard Thomas and Helen Ougham, Senescence and crop performance, Crop Physiology, 10.1016/B978-0-12-417104-6.00010-8, (223-249), (2015).
- Stefanie Böhnke and Mirjam Perner, A function-based screen for seeking RubisCO active clones from metagenomes: novel enzymes influencing RubisCO activity, The ISME Journal, 10.1038/ismej.2014.163, 9, 3, (735-745), (2014).
- Shu-Bin Wang, Shi-Lin Tian, Syed N. M. Shah, Bao-Gui Pan, Wei-Ping Diao and Zhen-Hui Gong, Cloning and characterization of the CarbcL gene related to chlorophyll in pepper (Capsicum annuum L.) under fruit shade stress, Frontiers in Plant Science, 6, (2015).
- John A. Raven, John Beardall and Mario Giordano, Energy costs of carbon dioxide concentrating mechanisms in aquatic organisms, Photosynthesis Research, 121, 2-3, (111), (2014).
- J.A. Raven and J. Beardall, CO 2 concentrating mechanisms and environmental change, Aquatic Botany, 118, (24), (2014).
- Xiaohong Wu, Tida Ge, Hongzhao Yuan, Ping Zhou, Xiangbi Chen, Shan Chen, Phil Brookes and Jinshui Wu, Evaluation of an optimal extraction method for measuring d-ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) in agricultural soils and its association with soil microbial CO2 assimilation, Pedobiologia, 57, 4-6, (277), (2014).
- Lin Zhou, Hui Xu, Sue Mischke, Lyndel W Meinhardt, Dapeng Zhang, Xujun Zhu, Xinghui Li and Wanping Fang, Exogenous abscisic acid significantly affects proteome in tea plant (Camellia sinensis) exposed to drought stress, Horticulture Research, 1, 1, (2014).
- John Beardall and John A. Raven, Calcification and ocean acidification: new insights from the coccolithophore Emiliania huxleyi, New Phytologist, 199, 1, (1-3), (2013).
- , Erratum, New Phytologist, 198, 3, (970-970), (2013).
- J. A. Raven, The evolution of autotrophy in relation to phosphorus requirement, Journal of Experimental Botany, 10.1093/jxb/ert306, 64, 13, (4023-4046), (2013).
- Chibuike C. Udenigwe, Min Gong and Sihong Wu, In silico analysis of the large and small subunits of cereal RuBisCO as precursors of cryptic bioactive peptides, Process Biochemistry, 10.1016/j.procbio.2013.08.013, 48, 11, (1794-1799), (2013).
- Pascal-Antoine Christin and Colin P. Osborne, The recurrent assembly of C4 photosynthesis, an evolutionary tale, Photosynthesis Research, 117, 1-3, (163), (2013).
- Ulrich Kutschera and Karl J. Niklas, Metabolic scaling theory in plant biology and the three oxygen paradoxa of aerobic life, Theory in Biosciences, 10.1007/s12064-013-0194-3, 132, 4, (277-288), (2013).
- Armin Kubis and Arren Bar-Even, Synthetic biology approaches for improving photosynthesis, Journal of Experimental Botany, 10.1093/jxb/erz029, (2019).
- Stéphanie Arrivault, Thiago Alexandre Moraes, Toshihiro Obata, David B Medeiros, Alisdair R Fernie, Alix Boulouis, Martha Ludwig, John E Lunn, Gian Luca Borghi, Armin Schlereth, Manuela Guenther and Mark Stitt, Metabolite profiles reveal interspecific variation in operation of the Calvin–Benson cycle in both C4 and C3 plants, Journal of Experimental Botany, 10.1093/jxb/erz051, (2019).
- Robert W. Read, David C. Vuono, Iva Neveux, Carl Staub and Joseph J. Grzymski, Coordinated downregulation of the photosynthetic apparatus as a protective mechanism against UV exposure in the diatom Corethron hystrix, Applied Microbiology and Biotechnology, 10.1007/s00253-018-9544-x, (2019).
- Aurélie Bichot, Jean-Philippe Delgenès, Valérie Méchin, Hélène Carrère, Nicolas Bernet and Diana García-Bernet, Understanding biomass recalcitrance in grasses for their efficient utilization as biorefinery feedstock, Reviews in Environmental Science and Bio/Technology, 10.1007/s11157-018-9485-y, (2018).
- Babu Kannappan, Peter L. Cummins and Jill E. Gready, Mechanism of Oxygenase Pathway Reactions Catalysed by Rubisco from Large Scale Kohn-Sham Density Functional Calculations, The Journal of Physical Chemistry B, 10.1021/acs.jpcb.9b00518, (2019).
- Gabriel Thieulin-Pardo, Luisana Avilan, Mila Kojadinovic and Brigitte Gontero, Fairy “tailsâ€: flexibility and function of intrinsically disordered extensions in the photosynthetic world, Frontiers in Molecular Biosciences, 10.3389/fmolb.2015.00023, 2, (2015).
- Eva Johansson, Thomas Prade, Irini Angelidaki, Sven-Erik Svensson, William Newson, Ingólfur Gunnarsson and Helena Hovmalm, Economically Viable Components from Jerusalem Artichoke (Helianthus tuberosus L.) in a Biorefinery Concept, International Journal of Molecular Sciences, 10.3390/ijms16048997, 16, 4, (8997-9016), (2015).
- Yaping Wu, Jennifer Jeans, David J. Suggett, Zoe V. Finkel and Douglas A. Campbell, Large centric diatoms allocate more cellular nitrogen to photosynthesis to counter slower RUBISCO turnover rates, Frontiers in Marine Science, 10.3389/fmars.2014.00068, 1, (2014).
