1
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Liu AK, Kaeser B, Chen L, West-Roberts J, Taylor-Kearney LJ, Lavy A, Günzing D, Li WJ, Hammel M, Nogales E, Banfield JF, Shih PM. Deep-branching evolutionary intermediates reveal structural origins of form I rubisco. Curr Biol 2023; 33:5316-5325.e3. [PMID: 37979578 DOI: 10.1016/j.cub.2023.10.053] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/26/2023] [Accepted: 10/25/2023] [Indexed: 11/20/2023]
Abstract
The enzyme rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) catalyzes the majority of biological carbon fixation on Earth. Although the vast majority of rubiscos across the tree of life assemble as homo-oligomers, the globally predominant form I enzyme-found in plants, algae, and cyanobacteria-forms a unique hetero-oligomeric complex. The recent discovery of a homo-oligomeric sister group to form I rubisco (named form I') has filled a key gap in our understanding of the enigmatic origins of the form I clade. However, to elucidate the series of molecular events leading to the evolution of form I rubisco, we must examine more distantly related sibling clades to contextualize the molecular features distinguishing form I and form I' rubiscos. Here, we present a comparative structural study retracing the evolutionary history of rubisco that reveals a complex structural trajectory leading to the ultimate hetero-oligomerization of the form I clade. We structurally characterize the oligomeric states of deep-branching form Iα and I'' rubiscos recently discovered from metagenomes, which represent key evolutionary intermediates preceding the form I clade. We further solve the structure of form I'' rubisco, revealing the molecular determinants that likely primed the enzyme core for the transition from a homo-oligomer to a hetero-oligomer. Our findings yield new insight into the evolutionary trajectory underpinning the adoption and entrenchment of the prevalent assembly of form I rubisco, providing additional context when viewing the enzyme family through the broader lens of protein evolution.
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Affiliation(s)
- Albert K Liu
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA; Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California, Davis, Davis, CA 95616, USA
| | - Benjamin Kaeser
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - LinXing Chen
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jacob West-Roberts
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Leah J Taylor-Kearney
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
| | - Adi Lavy
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Damian Günzing
- Department of Physics, University of Duisburg-Essen, 47057 Duisburg, Germany
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, P.R. China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, P.R. China
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Eva Nogales
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, USA; School of Geography, Earth and Atmospheric Sciences, University of Melbourne, Melbourne, VIC 3053, Australia; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Patrick M Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA; Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, USA.
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2
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Nguyen ND, Pulsford SB, Hee WY, Rae BD, Rourke LM, Price GD, Long BM. Towards engineering a hybrid carboxysome. PHOTOSYNTHESIS RESEARCH 2023; 156:265-277. [PMID: 36892800 PMCID: PMC10154267 DOI: 10.1007/s11120-023-01009-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/17/2023] [Indexed: 05/03/2023]
Abstract
Carboxysomes are bacterial microcompartments, whose structural features enable the encapsulated Rubisco holoenzyme to operate in a high-CO2 environment. Consequently, Rubiscos housed within these compartments possess higher catalytic turnover rates relative to their plant counterparts. This particular enzymatic property has made the carboxysome, along with associated transporters, an attractive prospect to incorporate into plant chloroplasts to increase future crop yields. To date, two carboxysome types have been characterized, the α-type that has fewer shell components and the β-type that houses a faster Rubisco. While research is underway to construct a native carboxysome in planta, work investigating the internal arrangement of carboxysomes has identified conserved Rubisco amino acid residues between the two carboxysome types which could be engineered to produce a new, hybrid carboxysome. In theory, this hybrid carboxysome would benefit from the simpler α-carboxysome shell architecture while simultaneously exploiting the higher Rubisco turnover rates in β-carboxysomes. Here, we demonstrate in an Escherichia coli expression system, that the Thermosynechococcus elongatus Form IB Rubisco can be imperfectly incorporated into simplified Cyanobium α-carboxysome-like structures. While encapsulation of non-native cargo can be achieved, T. elongatus Form IB Rubisco does not interact with the Cyanobium carbonic anhydrase, a core requirement for proper carboxysome functionality. Together, these results suggest a way forward to hybrid carboxysome formation.
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Affiliation(s)
- Nghiem Dinh Nguyen
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Acton, ACT, 2601, Australia
| | - Sacha B Pulsford
- Australian Research Council Centre of Excellence in Synthetic Biology, Research School of Chemistry, The Australian National University, Building 46, Sullivan's Creek Road, Acton, ACT, 2601, Australia
| | - Wei Yi Hee
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
| | - Benjamin D Rae
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Acton, ACT, 2601, Australia
| | - Loraine M Rourke
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Acton, ACT, 2601, Australia
| | - G Dean Price
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Acton, ACT, 2601, Australia.
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia.
- Division of Plant Sciences, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Canberra, ACT, 2601, Australia.
| | - Benedict M Long
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Acton, ACT, 2601, Australia
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
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3
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Oh ZG, Askey B, Gunn LH. Red Rubiscos and opportunities for engineering green plants. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:520-542. [PMID: 36055563 PMCID: PMC9833100 DOI: 10.1093/jxb/erac349] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
Nature's vital, but notoriously inefficient, CO2-fixing enzyme Rubisco often limits the growth of photosynthetic organisms including crop species. Form I Rubiscos comprise eight catalytic large subunits and eight auxiliary small subunits and can be classified into two distinct lineages-'red' and 'green'. While red-type Rubiscos (Form IC and ID) are found in rhodophytes, their secondary symbionts, and certain proteobacteria, green-type Rubiscos (Form IA and IB) exist in terrestrial plants, chlorophytes, cyanobacteria, and other proteobacteria. Eukaryotic red-type Rubiscos exhibit desirable kinetic properties, namely high specificity and high catalytic efficiency, with certain isoforms outperforming green-type Rubiscos. However, it is not yet possible to functionally express a high-performing red-type Rubisco in chloroplasts to boost photosynthetic carbon assimilation in green plants. Understanding the molecular and evolutionary basis for divergence between red- and green-type Rubiscos could help us to harness the superior CO2-fixing power of red-type Rubiscos. Here we review our current understanding about red-type Rubisco distribution, biogenesis, and sequence-structure, and present opportunities and challenges for utilizing red-type Rubisco kinetics towards crop improvements.
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Affiliation(s)
- Zhen Guo Oh
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Bryce Askey
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
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4
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Mao Y, Catherall E, Díaz-Ramos A, Greiff GRL, Azinas S, Gunn L, McCormick AJ. The small subunit of Rubisco and its potential as an engineering target. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:543-561. [PMID: 35849331 PMCID: PMC9833052 DOI: 10.1093/jxb/erac309] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/07/2022] [Indexed: 05/06/2023]
Abstract
Rubisco catalyses the first rate-limiting step in CO2 fixation and is responsible for the vast majority of organic carbon present in the biosphere. The function and regulation of Rubisco remain an important research topic and a longstanding engineering target to enhance the efficiency of photosynthesis for agriculture and green biotechnology. The most abundant form of Rubisco (Form I) consists of eight large and eight small subunits, and is found in all plants, algae, cyanobacteria, and most phototrophic and chemolithoautotrophic proteobacteria. Although the active sites of Rubisco are located on the large subunits, expression of the small subunit regulates the size of the Rubisco pool in plants and can influence the overall catalytic efficiency of the Rubisco complex. The small subunit is now receiving increasing attention as a potential engineering target to improve the performance of Rubisco. Here we review our current understanding of the role of the small subunit and our growing capacity to explore its potential to modulate Rubisco catalysis using engineering biology approaches.
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Affiliation(s)
| | | | - Aranzazú Díaz-Ramos
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, King’s Buildings, University of Edinburgh, Edingburgh EH9 3BF, UK
| | - George R L Greiff
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Stavros Azinas
- Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden
| | - Laura Gunn
- Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
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5
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Bauwe H. Photorespiration - Rubisco's repair crew. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153899. [PMID: 36566670 DOI: 10.1016/j.jplph.2022.153899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/11/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
The photorespiratory repair pathway (photorespiration in short) was set up from ancient metabolic modules about three billion years ago in cyanobacteria, the later ancestors of chloroplasts. These prokaryotes developed the capacity for oxygenic photosynthesis, i.e. the use of water as a source of electrons and protons (with O2 as a by-product) for the sunlight-driven synthesis of ATP and NADPH for CO2 fixation in the Calvin cycle. However, the CO2-binding enzyme, ribulose 1,5-bisphosphate carboxylase (known under the acronym Rubisco), is not absolutely selective for CO2 and can also use O2 in a side reaction. It then produces 2-phosphoglycolate (2PG), the accumulation of which would inhibit and potentially stop the Calvin cycle and subsequently photosynthetic electron transport. Photorespiration removes the 2-PG and in this way prevents oxygenic photosynthesis from poisoning itself. In plants, the core of photorespiration consists of ten enzymes distributed over three different types of organelles, requiring interorganellar transport and interaction with several auxiliary enzymes. It goes together with the release and to some extent loss of freshly fixed CO2. This disadvantageous feature can be suppressed by CO2-concentrating mechanisms, such as those that evolved in C4 plants thirty million years ago, which enhance CO2 fixation and reduce 2PG synthesis. Photorespiration itself provided a pioneer variant of such mechanisms in the predecessors of C4 plants, C3-C4 intermediate plants. This article is a review and update particularly on the enzyme components of plant photorespiration and their catalytic mechanisms, on the interaction of photorespiration with other metabolism and on its impact on the evolution of photosynthesis. This focus was chosen because a better knowledge of the enzymes involved and how they are embedded in overall plant metabolism can facilitate the targeted use of the now highly advanced methods of metabolic network modelling and flux analysis. Understanding photorespiration more than before as a process that enables, rather than reduces, plant photosynthesis, will help develop rational strategies for crop improvement.
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Affiliation(s)
- Hermann Bauwe
- University of Rostock, Plant Physiology, Albert-Einstein-Straße 3, D-18051, Rostock, Germany.
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6
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Liu AK, Pereira JH, Kehl AJ, Rosenberg DJ, Orr DJ, Chu SKS, Banda DM, Hammel M, Adams PD, Siegel JB, Shih PM. Structural plasticity enables evolution and innovation of RuBisCO assemblies. SCIENCE ADVANCES 2022; 8:eadc9440. [PMID: 36026446 PMCID: PMC9417184 DOI: 10.1126/sciadv.adc9440] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Oligomerization is a core structural feature that defines the form and function of many proteins. Most proteins form molecular complexes; however, there remains a dearth of diversity-driven structural studies investigating the evolutionary trajectory of these assemblies. Ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO) is one such enzyme that adopts multiple assemblies, although the origins and distribution of its different oligomeric states remain cryptic. Here, we retrace the evolution of ancestral and extant form II RuBisCOs, revealing a complex and diverse history of oligomerization. We structurally characterize a newly discovered tetrameric RuBisCO, elucidating how solvent-exposed surfaces can readily adopt new interactions to interconvert or give rise to new oligomeric states. We further use these principles to engineer and demonstrate how changes in oligomerization can be mediated by relatively few mutations. Our findings yield insight into how structural plasticity may give rise to new oligomeric states.
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Affiliation(s)
- Albert K. Liu
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California, Davis, Davis, CA 95616, USA
| | - Jose H. Pereira
- Technology Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alexander J. Kehl
- Biophysics Graduate Group, University of California, Davis, Davis, CA, USA
| | - Daniel J. Rosenberg
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Douglas J. Orr
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Simon K. S. Chu
- Biophysics Graduate Group, University of California, Davis, Davis, CA, USA
| | - Douglas M. Banda
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Paul D. Adams
- Technology Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Justin B. Siegel
- Genome Center, University of California, Davis, Davis, CA 95616, USA
- Chemistry Department, University of California, Davis, Davis, CA 95616, USA
- Department of Biochemistry and Molecular Medicine, University of California, Sacramento, Sacramento, CA 95616, USA
| | - Patrick M. Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
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7
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Bathellier C, Tcherkez G. Experimental evidence for extra proton exchange in ribulose 1,5-bisphosphate carboxylase/oxygenase catalysis. Commun Integr Biol 2022; 15:68-74. [PMID: 35186179 PMCID: PMC8855871 DOI: 10.1080/19420889.2022.2039431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Despite considerable advances in the past 50 y, the mechanism of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalysis is still not well understood. In particular, the movement and exchange of protons within the active site is not well documented: typically, kinetics of H exchange during the first steps of catalysis, i.e. abstraction of the H3 atom of ribulose 1,5-bisphosphate (RuBP) and enolization, are not clearly established. Here, we took advantage of reaction assays run in heavy water (2H2O) to monitor the appearance of deuterated RuBP and deuterated products (3-phosphoglycerate and 2-phosphoglycolate) with exact mass LC-MS. Enolization was reversible such that de-enolization generated not only monodeuterated RuBP (2H-[H-3]-ribulose 1,5-bisphosphate) but also dideuterated RuBP (2H2-[H-3,O-3]-ribulose 1,5-bisphosphate). Carboxylation yielded about one half deuterated 3-phosphoglycerate (2H-[H-2]-3-phosphoglycerate) and also a small proportion of dideuterated 3-phosphoglycerate (2H2-[H-2,O-2]-3-phosphoglycerate). Oxygenation generated a small amount of monodeuterated, but no dideuterated, products. (Di)deuterated isotopologue abundance depended negatively on gas concentration. We conclude that in addition to the first step of proton exchange at H3 occurring before gas addition (and thus influenced by the competition between de-enolization and gas addition), there is another proton exchange step between solvent water, active site residues, and the 2,3-enediol(ate) leading to deuterated OH groups in products.
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Affiliation(s)
| | - Guillaume Tcherkez
- Research School of Biology, Australian National University, Canberra, Australia.,Institut de Recherche en Horticulture et Semences, Université d'Angers, INRAe, Beaucouzé, France
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8
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Füßl M, König AC, Eirich J, Hartl M, Kleinknecht L, Bohne AV, Harzen A, Kramer K, Leister D, Nickelsen J, Finkemeier I. Dynamic light- and acetate-dependent regulation of the proteome and lysine acetylome of Chlamydomonas. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:261-277. [PMID: 34709689 DOI: 10.1111/tpj.15555] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
The green alga Chlamydomonas reinhardtii is one of the most studied microorganisms in photosynthesis research and for biofuel production. A detailed understanding of the dynamic regulation of its carbon metabolism is therefore crucial for metabolic engineering. Post-translational modifications can act as molecular switches for the control of protein function. Acetylation of the ɛ-amino group of lysine residues is a dynamic modification on proteins across organisms from all kingdoms. Here, we performed mass spectrometry-based profiling of proteome and lysine acetylome dynamics in Chlamydomonas under varying growth conditions. Chlamydomonas liquid cultures were transferred from mixotrophic (light and acetate as carbon source) to heterotrophic (dark and acetate) or photoautotrophic (light only) growth conditions for 30 h before harvest. In total, 5863 protein groups and 1376 lysine acetylation sites were identified with a false discovery rate of <1%. As a major result of this study, our data show that dynamic changes in the abundance of lysine acetylation on various enzymes involved in photosynthesis, fatty acid metabolism, and the glyoxylate cycle are dependent on acetate and light. Exemplary determination of acetylation site stoichiometries revealed particularly high occupancy levels on K175 of the large subunit of RuBisCO and K99 and K340 of peroxisomal citrate synthase under heterotrophic conditions. The lysine acetylation stoichiometries correlated with increased activities of cellular citrate synthase and the known inactivation of the Calvin-Benson cycle under heterotrophic conditions. In conclusion, the newly identified dynamic lysine acetylation sites may be of great value for genetic engineering of metabolic pathways in Chlamydomonas.
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Affiliation(s)
- Magdalena Füßl
- Plant Proteomics, Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, Cologne, DE-50829, Germany
- Faculty of Biology, Ludwig-Maximilians-University, Grosshaderner Strasse 2-4, Munich, DE-82152, Germany
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Muenster, Schlossplatz 7, Muenster, DE-48149, Germany
| | - Ann-Christine König
- Plant Proteomics, Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, Cologne, DE-50829, Germany
- Faculty of Biology, Ludwig-Maximilians-University, Grosshaderner Strasse 2-4, Munich, DE-82152, Germany
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Protein Science, Heidemannstr. 1, Munich, DE-80939, Germany
| | - Jürgen Eirich
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Muenster, Schlossplatz 7, Muenster, DE-48149, Germany
| | - Markus Hartl
- Plant Proteomics, Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, Cologne, DE-50829, Germany
- Faculty of Biology, Ludwig-Maximilians-University, Grosshaderner Strasse 2-4, Munich, DE-82152, Germany
- Mass Spectrometry Facility, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, Vienna, AT-1030, Austria
| | - Laura Kleinknecht
- Faculty of Biology, Ludwig-Maximilians-University, Grosshaderner Strasse 2-4, Munich, DE-82152, Germany
| | - Alexandra-Viola Bohne
- Faculty of Biology, Ludwig-Maximilians-University, Grosshaderner Strasse 2-4, Munich, DE-82152, Germany
| | - Anne Harzen
- Plant Proteomics, Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, Cologne, DE-50829, Germany
| | - Katharina Kramer
- Plant Proteomics, Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, Cologne, DE-50829, Germany
| | - Dario Leister
- Faculty of Biology, Ludwig-Maximilians-University, Grosshaderner Strasse 2-4, Munich, DE-82152, Germany
| | - Jörg Nickelsen
- Faculty of Biology, Ludwig-Maximilians-University, Grosshaderner Strasse 2-4, Munich, DE-82152, Germany
| | - Iris Finkemeier
- Plant Proteomics, Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, Cologne, DE-50829, Germany
- Faculty of Biology, Ludwig-Maximilians-University, Grosshaderner Strasse 2-4, Munich, DE-82152, Germany
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Muenster, Schlossplatz 7, Muenster, DE-48149, Germany
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9
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The Mechanism of Rubisco Catalyzed Carboxylation Reaction: Chemical Aspects Involving Acid-Base Chemistry and Functioning of the Molecular Machine. Catalysts 2021. [DOI: 10.3390/catal11070813] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In recent years, a great deal of attention has been paid by the scientific community to improving the efficiency of photosynthetic carbon assimilation, plant growth and biomass production in order to achieve a higher crop productivity. Therefore, the primary carboxylase enzyme of the photosynthetic process Rubisco has received considerable attention focused on many aspects of the enzyme function including protein structure, protein engineering and assembly, enzyme activation and kinetics. Based on its fundamental role in carbon assimilation Rubisco is also targeted by the CO2-fertilization effect, which is the increased rate of photosynthesis due to increasing atmospheric CO2-concentration. The aim of this review is to provide a framework, as complete as possible, of the mechanism of the RuBP carboxylation/hydration reaction including description of chemical events occurring at the enzyme “activating” and “catalytic” sites (which involve Broensted acid-base reactions) and the functioning of the complex molecular machine. Important research results achieved over the last few years providing substantial advancement in understanding the enzyme functioning will be discussed.
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10
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Banda DM, Pereira JH, Liu AK, Orr DJ, Hammel M, He C, Parry MAJ, Carmo-Silva E, Adams PD, Banfield JF, Shih PM. Novel bacterial clade reveals origin of form I Rubisco. NATURE PLANTS 2020; 6:1158-1166. [PMID: 32868887 DOI: 10.1038/s41477-020-00762-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 07/28/2020] [Indexed: 05/12/2023]
Abstract
Rubisco sustains the biosphere through the fixation of CO2 into biomass. In plants and cyanobacteria, form I Rubisco is structurally comprised of large and small subunits, whereas all other Rubisco forms lack small subunits. The rise of the form I complex through the innovation of small subunits represents a key, yet poorly understood, transition in Rubisco's evolution. Through metagenomic analyses, we discovered a previously uncharacterized clade sister to form I Rubisco that evolved without small subunits. This clade diverged before the evolution of cyanobacteria and the origin of the small subunit; thus, it provides a unique reference point to advance our understanding of form I Rubisco evolution. Structural and kinetic data presented here reveal how a proto-form I Rubisco assembled and functioned without the structural stability imparted from small subunits. Our findings provide insight into a key evolutionary transition of the most abundant enzyme on Earth and the predominant entry point for nearly all global organic carbon.
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Affiliation(s)
- Douglas M Banda
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jose H Pereira
- Technology Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Albert K Liu
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Douglas J Orr
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christine He
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
| | - Martin A J Parry
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | | | - Paul D Adams
- Technology Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA.
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Patrick M Shih
- Department of Plant Biology, University of California, Davis, Davis, CA, USA.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA.
- Genome Center, University of California, Davis, Davis, CA, USA.
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11
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Gateau H, Blanckaert V, Veidl B, Burlet-Schiltz O, Pichereaux C, Gargaros A, Marchand J, Schoefs B. Application of pulsed electric fields for the biocompatible extraction of proteins from the microalga Haematococcus pluvialis. Bioelectrochemistry 2020; 137:107588. [PMID: 33147566 DOI: 10.1016/j.bioelechem.2020.107588] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 06/23/2020] [Accepted: 06/25/2020] [Indexed: 12/19/2022]
Abstract
This study aims to employ a pulsed electric field (PEF) treatment for the biocompatible (non-destructive) extraction of proteins from living cells of the green microalga Haematococcus pluvialis. Using a field strength of 1 kV cm-1, we achieved the extraction of 10.2 µg protein per mL of culture, which corresponded to 46% of the total amount of proteins that could be extracted by complete destructive extraction (i.e. the grinding of biomass with glass beads). We found that the extraction yield was not improved by stronger field strengths and was not dependent on the pulse frequency. A biocompatibility index (BI) was defined as the relative abundance of cells that remained alive after the PEF treatment. This index relied on measurements of several physiological parameters after a PEF treatment. It was found that at 1 kV cm-1 that cultures recovered after 72 h. Therefore, these PEF conditions constituted a good compromise between protein extraction efficiency and culture survival. To characterize the PEF treatment further at a molecular level, mass spectrometry-based proteomics analyses of PEF-prepared extracts was used. This led to the identification of 52 electro-extracted proteins. Of these, only 16 proteins were identified when proteins were extracted with PEF at 0.5 cm-1. They belong to core metabolism, stress response and cell movement. Unassigned proteins were also extracted. Their physiological implications and possible utilization in food as alimentary complements are discussed.
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Affiliation(s)
- Hélène Gateau
- Metabolism, Bioengineering of Molecules from Microalgae and Applications (MIMMA), Mer Molécules Santé, IUML - FR 3473 CNRS, Le Mans University, Le Mans, France
| | - Vincent Blanckaert
- Metabolism, Bioengineering of Molecules from Microalgae and Applications (MIMMA), Mer Molécules Santé, IUML - FR 3473 CNRS, IUT de Laval, Le Mans University, Le Mans, France
| | - Brigitte Veidl
- Metabolism, Bioengineering of Molecules from Microalgae and Applications (MIMMA), Mer Molécules Santé, IUML - FR 3473 CNRS, Le Mans University, Le Mans, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse UPS, CNRS, Toulouse, France
| | - Carole Pichereaux
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse UPS, CNRS, Toulouse, France; Fédération de Recherche (FR3450), Agrobiosciences, Interactions et Biodiversité (FRAIB), CNRS, Toulouse, France
| | | | - Justine Marchand
- Metabolism, Bioengineering of Molecules from Microalgae and Applications (MIMMA), Mer Molécules Santé, IUML - FR 3473 CNRS, Le Mans University, Le Mans, France
| | - Benoît Schoefs
- Metabolism, Bioengineering of Molecules from Microalgae and Applications (MIMMA), Mer Molécules Santé, IUML - FR 3473 CNRS, Le Mans University, Le Mans, France.
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12
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le Roux MSL, Burger NFV, Vlok M, Kunert KJ, Cullis CA, Botha AM. Wheat Line "RYNO3936" Is Associated With Delayed Water Stress-Induced Leaf Senescence and Rapid Water-Deficit Stress Recovery. FRONTIERS IN PLANT SCIENCE 2020; 11:1053. [PMID: 32760414 PMCID: PMC7372113 DOI: 10.3389/fpls.2020.01053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 06/25/2020] [Indexed: 06/11/2023]
Abstract
Random mutagenesis was applied to produce a new wheat mutant (RYNO3926) with superior characteristics regarding tolerance to water deficit stress induced at late booting stage. The mutant also displays rapid recovery from water stress conditions. Under water stress conditions mutant plants reached maturity faster and produced more seeds than its wild type wheat progenitor. Wild-type Tugela DN plants died within 7 days after induction of water stress induced at late booting stage, while mutant plants survived by maintaining a higher relative moisture content (RMC), increased total chlorophyll, and a higher photosynthesis rate and stomatal conductance. Analysis of the proteome of mutant plants revealed that they better regulate post-translational modification (SUMOylation) and have increased expression of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) proteins. Mutant plants also expressed unique proteins associated with dehydration tolerance including abscisic stress-ripening protein, cold induced protein, cold-responsive protein, dehydrin, Group 3 late embryogenesis, and a lipoprotein (LAlv9) belonging to the family of lipocalins. Overall, our results suggest that our new mutant RYNO3936 has a potential for inclusion in future breeding programs to improve drought tolerance under dryland conditions.
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Affiliation(s)
| | | | - Maré Vlok
- Proteomics Unit, Central Analytical Facilities, University of Stellenbosch, Stellenbosch, South Africa
| | - Karl J. Kunert
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Christopher A. Cullis
- Department of Biology, Case Western Reserve University, Cleveland, OH, United States
| | - Anna-Maria Botha
- Department of Genetics, University of Stellenbosch, Stellenbosch, South Africa
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13
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Yan Z, Shen Z, Gao ZF, Chao Q, Qian CR, Zheng H, Wang BC. A comprehensive analysis of the lysine acetylome reveals diverse functions of acetylated proteins during de-etiolation in Zea mays. JOURNAL OF PLANT PHYSIOLOGY 2020; 248:153158. [PMID: 32240968 DOI: 10.1016/j.jplph.2020.153158] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/02/2020] [Accepted: 02/02/2020] [Indexed: 06/11/2023]
Abstract
Lysine acetylation is one of the most important post-translational modifications and is involved in multiple cellular processes in plants. There is evidence that acetylation may play an important role in light-induced de-etiolation, a key developmental switch from skotomorphogenesis to photomorphogenesis. During this transition, establishment of photosynthesis is of great significance. However, studies on acetylome dynamics during de-etiolation are limited. Here, we performed the first global lysine acetylome analysis for Zea mays seedlings undergoing de-etiolation, using nano liquid chromatography coupled to tandem mass spectrometry, and identified 814 lysine-acetylated sites on 462 proteins. Bioinformatics analysis of this acetylome showed that most of the lysine-acetylated proteins are predicted to be located in the cytoplasm, nucleus, chloroplast, and mitochondria. In addition, we detected ten lysine acetylation motifs and found that the accumulation of 482 lysine-acetylated peptides corresponding to 289 proteins changed significantly during de-etiolation. These proteins include transcription factors, histones, and proteins involved in chlorophyll synthesis, photosynthesis light reaction, carbon assimilation, glycolysis, the TCA cycle, amino acid metabolism, lipid metabolism, and nucleotide metabolism. Our study provides an in-depth dataset that extends our knowledge of in vivo acetylome dynamics during de-etiolation in monocots. This dataset promotes our understanding of the functional consequences of lysine acetylation in diverse cellular metabolic regulatory processes, and will be a useful toolkit for further investigations of the lysine acetylome and de-etiolation in plants.
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Affiliation(s)
- Zhen Yan
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhuo Shen
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China.
| | - Zhi-Fang Gao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Qing Chao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China; The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100039, China.
| | - Chun-Rong Qian
- Institute of Crop Cultivation and Farming, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China.
| | - Haiyan Zheng
- Center for Advanced Biotechnology and Medicine, Biological Mass Spectrometry Facility, Rutgers University, Piscataway, New Jersey 08855, USA.
| | - Bai-Chen Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China; The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100039, China.
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14
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Evaluation of physiological and biochemical aberration linked to effect of sodium dodecyl sulphate on barley seedlings. SN APPLIED SCIENCES 2020. [DOI: 10.1007/s42452-020-2289-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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15
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Rohnke BA, Kerfeld CA, Montgomery BL. Binding Options for the Small Subunit-Like Domain of Cyanobacteria to Rubisco. Front Microbiol 2020; 11:187. [PMID: 32180764 PMCID: PMC7059596 DOI: 10.3389/fmicb.2020.00187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 01/27/2020] [Indexed: 01/13/2023] Open
Abstract
Two proteins found in cyanobacteria contain a C-terminal domain with homology to the small subunit of rubisco (RbcS). These small subunit-like domains (SSLDs) are important features of CcmM, a protein involved in the biogenesis of carboxysomes found in all β-cyanobacteria, and a rubisco activase homolog [activase-like protein of cyanobacteria (ALC)] found in over a third of sequenced cyanobacterial genomes. Interaction with rubisco is crucial to the function of CcmM and is believed to be important to ALC as well. In both cases, the SSLD aggregates rubisco, and this nucleation event may be important in regulating rubisco assembly and activity. Recently, two independent studies supported the conclusion that the SSLD of CcmM binds equatorially to L8S8 holoenzymes of rubisco rather than by displacing an RbcS, as its structural homology would suggest. We use sequence analysis and homology modeling to examine whether the SSLD from the ALC could bind the large subunit of rubisco either via an equatorial interaction or in an RbcS site, if available. We suggest that the SSLD from the ALC of Fremyella diplosiphon could bind either in a vacant RbcS site or equatorially. Our homology modeling takes into account N-terminal residues not represented in available cryo-electron microscopy structures that potentially contribute to the interface between the large subunit of rubisco (RbcL) and RbcS. Here, we suggest the perspective that binding site variability as a means of regulation is plausible and that the dynamic interaction between the RbcL, RbcS, and SSLDs may be important for carboxysome assembly and function.
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Affiliation(s)
- Brandon A Rohnke
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States.,Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Beronda L Montgomery
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States.,Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, United States
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16
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Yamada K, Davydov II, Besnard G, Salamin N. Duplication history and molecular evolution of the rbcS multigene family in angiosperms. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:6127-6139. [PMID: 31498865 PMCID: PMC6859733 DOI: 10.1093/jxb/erz363] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 08/12/2019] [Indexed: 05/22/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is considered to be the main enzyme determining the rate of photosynthesis. The small subunit of the protein, encoded by the rbcS gene, has been shown to influence the catalytic efficiency, CO2 specificity, assembly, activity, and stability of RuBisCO. However, the evolution of the rbcS gene remains poorly studied. We inferred the phylogenetic tree of the rbcS gene in angiosperms using the nucleotide sequences and found that it is composed of two lineages that may have existed before the divergence of land plants. Although almost all species sampled carry at least one copy of lineage 1, genes of lineage 2 were lost in most angiosperm species. We found the specific residues that have undergone positive selection during the evolution of the rbcS gene. We detected intensive coevolution between each rbcS gene copy and the rbcL gene encoding the large subunit of RuBisCO. We tested the role played by each rbcS gene copy on the stability of the RuBisCO protein through homology modelling. Our results showed that this evolutionary constraint could limit the level of divergence seen in the rbcS gene, which leads to the similarity among the rbcS gene copies of lineage 1 within species.
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Affiliation(s)
- Kana Yamada
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
| | - Iakov I Davydov
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
| | - Guillaume Besnard
- Laboratoire Evolution et Diversité Biologique (EDB UMR5174), CNRS-UPS-IRD, University of Toulouse III, Toulouse Cedex, France
| | - Nicolas Salamin
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
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17
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Zhou Y, Whitney S. Directed Evolution of an Improved Rubisco; In Vitro Analyses to Decipher Fact from Fiction. Int J Mol Sci 2019; 20:ijms20205019. [PMID: 31658746 PMCID: PMC6834295 DOI: 10.3390/ijms20205019] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/02/2019] [Accepted: 10/04/2019] [Indexed: 01/01/2023] Open
Abstract
Inaccuracies in biochemically characterizing the amount and CO2-fixing properties of the photosynthetic enzyme Ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase continue to hamper an accurate evaluation of Rubisco mutants selected by directed evolution. Here, we outline an analytical pipeline for accurately quantifying Rubisco content and kinetics that averts the misinterpretation of directed evolution outcomes. Our study utilizes a new T7-promoter regulated Rubisco Dependent Escherichia coli (RDE3) screen to successfully select for the first Rhodobacter sphaeroides Rubisco (RsRubisco) mutant with improved CO2-fixing properties. The RsRubisco contains four amino acid substitutions in the large subunit (RbcL) and an improved carboxylation rate (kcatC, up 27%), carboxylation efficiency (kcatC/Km for CO2, increased 17%), unchanged CO2/O2 specificity and a 40% lower holoenzyme biogenesis capacity. Biochemical analysis of RsRubisco chimers coding one to three of the altered amino acids showed Lys-83-Gln and Arg-252-Leu substitutions (plant RbcL numbering) together, but not independently, impaired holoenzyme (L8S8) assembly. An N-terminal Val-11-Ile substitution did not affect RsRubisco catalysis or assembly, while a Tyr-345-Phe mutation alone conferred the improved kinetics without an effect on RsRubisco production. This study confirms the feasibility of improving Rubisco by directed evolution using an analytical pipeline that can identify false positives and reliably discriminate carboxylation enhancing amino acids changes from those influencing Rubisco biogenesis (solubility).
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Affiliation(s)
- Yu Zhou
- Australian Research Council Center of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 0200, Australia.
| | - Spencer Whitney
- Australian Research Council Center of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 0200, Australia.
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18
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Satagopan S, North JA, Arbing MA, Varaljay VA, Haines SN, Wildenthal JA, Byerly KM, Shin A, Tabita FR. Structural Perturbations of Rhodopseudomonas palustris Form II RuBisCO Mutant Enzymes That Affect CO2 Fixation. Biochemistry 2019; 58:3880-3892. [DOI: 10.1021/acs.biochem.9b00617] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Sriram Satagopan
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Justin A. North
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mark A. Arbing
- UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Vanessa A. Varaljay
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sidney N. Haines
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - John A. Wildenthal
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Kathryn M. Byerly
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Annie Shin
- UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - F. Robert Tabita
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
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19
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Valegård K, Hasse D, Andersson I, Gunn LH. Structure of Rubisco from Arabidopsis thaliana in complex with 2-carboxyarabinitol-1,5-bisphosphate. Acta Crystallogr D Struct Biol 2018; 74:1-9. [PMID: 29372894 PMCID: PMC5786004 DOI: 10.1107/s2059798317017132] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/28/2017] [Indexed: 11/18/2022] Open
Abstract
The crystal structure of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from Arabidopsis thaliana is reported at 1.5 Å resolution. In light of the importance of A. thaliana as 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 an A. thaliana Rubisco crystal structure. A. thaliana Rubisco is an L8S8 hexadecamer comprising eight plastome-encoded catalytic large (L) subunits and eight nuclear-encoded small (S) subunits. A. thaliana produces four distinct small-subunit isoforms (RbcS1A, RbcS1B, RbcS2B and RbcS3B), and this crystal structure provides a snapshot of A. thaliana Rubisco 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. thaliana Rubisco 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 understand A. thaliana Rubisco and the potential catalytic differences that could be conferred by alternative A. thaliana Rubisco small-subunit isoforms.
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Affiliation(s)
- Karin Valegård
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-751 24 Uppsala, Sweden
| | - Dirk Hasse
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-751 24 Uppsala, Sweden
| | - Inger Andersson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-751 24 Uppsala, Sweden
| | - Laura H. Gunn
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-751 24 Uppsala, Sweden
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20
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Hermida-Carrera C, Fares MA, Fernández Á, Gil-Pelegrín E, Kapralov MV, Mir A, Molins A, Peguero-Pina JJ, Rocha J, Sancho-Knapik D, Galmés J. Positively selected amino acid replacements within the RuBisCO enzyme of oak trees are associated with ecological adaptations. PLoS One 2017; 12:e0183970. [PMID: 28859145 PMCID: PMC5578625 DOI: 10.1371/journal.pone.0183970] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 08/15/2017] [Indexed: 12/29/2022] Open
Abstract
Phylogenetic analysis by maximum likelihood (PAML) has become the standard approach to study positive selection at the molecular level, but other methods may provide complementary ways to identify amino acid replacements associated with particular conditions. Here, we compare results of the decision tree (DT) model method with ones of PAML using the key photosynthetic enzyme RuBisCO as a model system to study molecular adaptation to particular ecological conditions in oaks (Quercus). We sequenced the chloroplast rbcL gene encoding RuBisCO large subunit in 158 Quercus species, covering about a third of the global genus diversity. It has been hypothesized that RuBisCO has evolved differentially depending on the environmental conditions and leaf traits governing internal gas diffusion patterns. Here, we show, using PAML, that amino acid replacements at the residue positions 95, 145, 251, 262 and 328 of the RuBisCO large subunit have been the subject of positive selection along particular Quercus lineages associated with the leaf traits and climate characteristics. In parallel, the DT model identified amino acid replacements at sites 95, 219, 262 and 328 being associated with the leaf traits and climate characteristics, exhibiting partial overlap with the results obtained using PAML.
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Affiliation(s)
- Carmen Hermida-Carrera
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
| | - Mario A. Fares
- Integrative and Systems Biology Group, Department of Abiotic Stress, Instituto de Biología Molecular y Celular de Plantas (CSIC–UPV), Valencia, Spain
- Department of Genetics, University of Dublin, Trinity College Dublin, Dublin 2, Ireland
| | - Ángel Fernández
- Unidad de Recursos Forestales, C.I.T.A. de Aragón, Zaragoza, Spain
| | | | - Maxim V. Kapralov
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-Upon-Tyne, United Kingdom
| | - Arnau Mir
- Computational Biology and Bioinformatics Research Group, Department of Mathematics and Computer Science, Universitat de les Illes Balears, Palma, Balearic Islands, Spain
| | - Arántzazu Molins
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
| | | | - Jairo Rocha
- Computational Biology and Bioinformatics Research Group, Department of Mathematics and Computer Science, Universitat de les Illes Balears, Palma, Balearic Islands, Spain
| | | | - Jeroni Galmés
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
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21
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Turmo A, Gonzalez-Esquer CR, Kerfeld CA. Carboxysomes: metabolic modules for CO2 fixation. FEMS Microbiol Lett 2017; 364:4082729. [DOI: 10.1093/femsle/fnx176] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 08/12/2017] [Indexed: 11/13/2022] Open
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22
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Mueller-Cajar O. The Diverse AAA+ Machines that Repair Inhibited Rubisco Active Sites. Front Mol Biosci 2017; 4:31. [PMID: 28580359 PMCID: PMC5437159 DOI: 10.3389/fmolb.2017.00031] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 04/29/2017] [Indexed: 11/13/2022] Open
Abstract
Gaseous carbon dioxide enters the biosphere almost exclusively via the active site of the enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco). This highly conserved catalyst has an almost universal propensity to non-productively interact with its substrate ribulose 1,5-bisphosphate, leading to the formation of dead-end inhibited complexes. In diverse autotrophic organisms this tendency has been counteracted by the recruitment of dedicated AAA+ (ATPases associated with various cellular activities) proteins that all use the energy of ATP hydrolysis to remodel inhibited Rubisco active sites leading to release of the inhibitor. Three evolutionarily distinct classes of these Rubisco activases (Rcas) have been discovered so far. Green and red-type Rca are mostly found in photosynthetic eukaryotes of the green and red plastid lineage respectively, whereas CbbQO is associated with chemoautotrophic bacteria. Ongoing mechanistic studies are elucidating how the various motors are utilizing both similar and contrasting strategies to ultimately perform their common function of cracking the inhibited Rubisco active site. The best studied mechanism utilized by red-type Rca appears to involve transient threading of the Rubisco large subunit C-terminal peptide, reminiscent of the action performed by Clp proteases. As well as providing a fascinating example of convergent molecular evolution, Rca proteins can be considered promising crop-improvement targets. Approaches aiming to replace Rubisco in plants with improved enzymes will need to ensure the presence of a compatible Rca protein. The thermolability of the Rca protein found in crop plants provides an opportunity to fortify photosynthesis against high temperature stress. Photosynthesis also appears to be limited by Rca when light conditions are fluctuating. Synthetic biology strategies aiming to enhance the autotrophic CO2 fixation machinery will need to take into consideration the requirement for Rubisco activases as well as their properties.
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Affiliation(s)
- Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological UniversitySingapore, Singapore
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23
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Bracher A, Whitney SM, Hartl FU, Hayer-Hartl M. Biogenesis and Metabolic Maintenance of Rubisco. ANNUAL REVIEW OF PLANT BIOLOGY 2017; 68:29-60. [PMID: 28125284 DOI: 10.1146/annurev-arplant-043015-111633] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) mediates the fixation of atmospheric CO2 in photosynthesis by catalyzing the carboxylation of the 5-carbon sugar ribulose-1,5-bisphosphate (RuBP). Rubisco is a remarkably inefficient enzyme, fixing only 2-10 CO2 molecules per second. Efforts to increase crop yields by bioengineering Rubisco remain unsuccessful, owing in part to the complex cellular machinery required for Rubisco biogenesis and metabolic maintenance. The large subunit of Rubisco requires the chaperonin system for folding, and recent studies have shown that assembly of hexadecameric Rubisco is mediated by specific assembly chaperones. Moreover, Rubisco function can be inhibited by a range of sugar-phosphate ligands, including RuBP. Metabolic repair depends on remodeling of Rubisco by the ATP-dependent Rubisco activase and hydrolysis of inhibitory sugar phosphates by specific phosphatases. Here, we review our present understanding of the structure and function of these auxiliary factors and their utilization in efforts to engineer more catalytically efficient Rubisco enzymes.
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Affiliation(s)
- Andreas Bracher
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany ; , ,
| | - Spencer M Whitney
- Research School of Biology, Australian National University, Acton, Australian Capital Territory 2601, Australia;
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany ; , ,
| | - Manajit Hayer-Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany ; , ,
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24
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Grabsztunowicz M, Koskela MM, Mulo P. Post-translational Modifications in Regulation of Chloroplast Function: Recent Advances. FRONTIERS IN PLANT SCIENCE 2017; 8:240. [PMID: 28280500 PMCID: PMC5322211 DOI: 10.3389/fpls.2017.00240] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 02/08/2017] [Indexed: 05/08/2023]
Abstract
Post-translational modifications (PTMs) of proteins enable fast modulation of protein function in response to metabolic and environmental changes. Phosphorylation is known to play a major role in regulating distribution of light energy between the Photosystems (PS) I and II (state transitions) and in PSII repair cycle. In addition, thioredoxin-mediated redox regulation of Calvin cycle enzymes has been shown to determine the efficiency of carbon assimilation. Besides these well characterized modifications, recent methodological progress has enabled identification of numerous other types of PTMs in various plant compartments, including chloroplasts. To date, at least N-terminal and Lys acetylation, Lys methylation, Tyr nitration and S-nitrosylation, glutathionylation, sumoylation and glycosylation of chloroplast proteins have been described. These modifications impact DNA replication, control transcriptional efficiency, regulate translational machinery and affect metabolic activities within the chloroplast. Moreover, light reactions of photosynthesis as well as carbon assimilation are regulated at multiple levels by a number of PTMs. It is likely that future studies will reveal new metabolic pathways to be regulated by PTMs as well as detailed molecular mechanisms of PTM-mediated regulation.
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Affiliation(s)
| | | | - Paula Mulo
- Molecular Plant Biology, Department of Biochemistry, University of TurkuTurku, Finland
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25
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Rasineni GK, Loh PC, Lim BH. Characterization of Chlamydomonas Ribulose-1,5-bisphosphate carboxylase/oxygenase variants mutated at residues that are post-translationally modified. Biochim Biophys Acta Gen Subj 2017; 1861:79-85. [DOI: 10.1016/j.bbagen.2016.10.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 10/14/2016] [Accepted: 10/31/2016] [Indexed: 10/20/2022]
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26
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Gunn LH, Valegård K, Andersson I. A unique structural domain in Methanococcoides burtonii ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) acts as a small subunit mimic. J Biol Chem 2017; 292:6838-6850. [PMID: 28154188 PMCID: PMC5399129 DOI: 10.1074/jbc.m116.767145] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/18/2017] [Indexed: 01/16/2023] Open
Abstract
The catalytic inefficiencies of the CO2-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) often limit plant productivity. Strategies to engineer more efficient plant Rubiscos have been hampered by evolutionary constraints, prompting interest in Rubisco isoforms from non-photosynthetic organisms. The methanogenic archaeon Methanococcoides burtonii contains a Rubisco isoform that functions to scavenge the ribulose-1,5-bisphosphate (RuBP) by-product of purine/pyrimidine metabolism. The crystal structure of M. burtonii Rubisco (MbR) presented here at 2.6 Å resolution is composed of catalytic large subunits (LSu) assembled into pentamers of dimers, (L2)5, and differs from Rubiscos from higher plants where LSus are glued together by small subunits (SSu) into hexadecameric L8S8 enzymes. MbR contains a unique 29-amino acid insertion near the C terminus, which folds as a separate domain in the structure. This domain, which is visualized for the first time in this study, is located in a similar position to SSus in L8S8 enzymes between LSus of adjacent L2 dimers, where negatively charged residues coordinate around a Mg2+ ion in a fashion that suggests this domain may be important for the assembly process. The Rubisco assembly domain is thus an inbuilt SSu mimic that concentrates L2 dimers. MbR assembly is ligand-stimulated, and we show that only 6-carbon molecules with a particular stereochemistry at the C3 carbon can induce oligomerization. Based on MbR structure, subunit arrangement, sequence, phylogenetic distribution, and function, MbR and a subset of Rubiscos from the Methanosarcinales order are proposed to belong to a new Rubisco subgroup, named form IIIB.
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Affiliation(s)
- Laura H Gunn
- From the Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden
| | - Karin Valegård
- From the Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden
| | - Inger Andersson
- From the Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden
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27
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Gao X, Hong H, Li WC, Yang L, Huang J, Xiao YL, Chen XY, Chen GY. Downregulation of Rubisco Activity by Non-enzymatic Acetylation of RbcL. MOLECULAR PLANT 2016; 9:1018-27. [PMID: 27109602 DOI: 10.1016/j.molp.2016.03.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/08/2016] [Accepted: 03/29/2016] [Indexed: 05/24/2023]
Abstract
Atmospheric carbon dioxide (CO2) is assimilated by the most abundant but sluggish enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). Here we show that acetylation of lysine residues of the Rubisco large subunit (RbcL), including Lys201 and Lys334 in the active sites, may be an important mechanism in the regulation of Rubisco activities. It is well known that Lys201 reacts with CO2 for carbamylation, a prerequisite for both carboxylase and oxygenase activities of Rubisco, and Lys334 contacts with ribulose-1,5-bisphosphate (RuBP). The acetylation level of RbcL in plants is lower during the day and higher at night, inversely correlating with the Rubisco carboxylation activity. A search of the chloroplast proteome database did not reveal a canonical acetyltransferase; instead, we found that a plant-derived metabolite, 7-acetoxy-4-methylcoumarin (AMC), can non-enzymatically acetylate both native Rubisco and synthesized RbcL peptides spanning Lys334 or Lys201. Furthermore, lysine residues were modified by synthesized 4-methylumbelliferone esters with different electro- and stereo-substitutes, resulting in varied Rubisco activities. 1-Chloroethyl 4-methylcoumarin-7-yl carbonate (ClMC) could transfer the chloroethyl carbamate group to lysine residues of RbcL and completely inactivate Rubisco, whereas bis(4-methylcoumarin-7-yl) carbonate (BMC) improved Rubisco activity through increasing the level of Lys201 carbamylation. Our findings indicate that RbcL acetylation negatively regulates Rubisco activity, and metabolic derivatives can be designed to dissect and improve CO2 fixation efficiency of plants through lysine modification.
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Affiliation(s)
- Xiang Gao
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, 200032 Shanghai, China; University of Chinese Academy of Sciences, 200032 Shanghai, China
| | - Hui Hong
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, 200032 Shanghai, China; University of Chinese Academy of Sciences, 200032 Shanghai, China
| | - Wei-Chao Li
- CAS Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, 200032 Shanghai, China; University of Chinese Academy of Sciences, 200032 Shanghai, China
| | - Lili Yang
- Laboratory of Photosynthesis and Environmental Biology, Shanghai Institute for Biological Sciences, 200032 Shanghai, China; University of Chinese Academy of Sciences, 200032 Shanghai, China
| | - Jirong Huang
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, 200032 Shanghai, China; Laboratory of Photosynthesis and Environmental Biology, Shanghai Institute for Biological Sciences, 200032 Shanghai, China
| | - You-Li Xiao
- CAS Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, 200032 Shanghai, China
| | - Xiao-Ya Chen
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, 200032 Shanghai, China.
| | - Gen-Yun Chen
- Laboratory of Photosynthesis and Environmental Biology, Shanghai Institute for Biological Sciences, 200032 Shanghai, China.
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Fujihashi M, Nishitani Y, Kiriyama T, Aono R, Sato T, Takai T, Tagashira K, Fukuda W, Atomi H, Imanaka T, Miki K. Mutation design of a thermophilic Rubisco based on three-dimensional structure enhances its activity at ambient temperature. Proteins 2016; 84:1339-46. [PMID: 27273261 DOI: 10.1002/prot.25080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 04/24/2016] [Accepted: 05/30/2016] [Indexed: 11/09/2022]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) plays a central role in carbon dioxide fixation on our planet. Rubisco from a hyperthermophilic archaeon Thermococcus kodakarensis (Tk-Rubisco) shows approximately twenty times the activity of spinach Rubisco at high temperature, but only one-eighth the activity at ambient temperature. We have tried to improve the activity of Tk-Rubisco at ambient temperature, and have successfully constructed several mutants which showed higher activities than the wild-type enzyme both in vitro and in vivo. Here, we designed new Tk-Rubisco mutants based on its three-dimensional structure and a sequence comparison of thermophilic and mesophilic plant Rubiscos. Four mutations were introduced to generate new mutants based on this strategy, and one of the four mutants, T289D, showed significantly improved activity compared to that of the wild-type enzyme. The crystal structure of the Tk-Rubisco T289D mutant suggested that the increase in activity was due to mechanisms distinct from those involved in the improvement in activity of Tk-Rubisco SP8, a mutant protein previously reported to show the highest activity at ambient temperature. Combining the mutations of T289D and SP8 successfully generated a mutant protein (SP8-T289D) with the highest activity to date both in vitro and in vivo. The improvement was particularly pronounced for the in vivo activity of SP8-T289D when introduced into the mesophilic, photosynthetic bacterium Rhodopseudomonas palustris, which resulted in a strain with nearly two-fold higher specific growth rates compared to that of a strain harboring the wild-type enzyme at ambient temperature. Proteins 2016; 84:1339-1346. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Masahiro Fujihashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Yuichi Nishitani
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Tomohiro Kiriyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Riku Aono
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-Ku, Kyoto, 615-8510, Japan
| | - Takaaki Sato
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-Ku, Kyoto, 615-8510, Japan
| | - Tomoyuki Takai
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Kenta Tagashira
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Wakao Fukuda
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-Ku, Kyoto, 615-8510, Japan
| | - Tadayuki Imanaka
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto, 606-8502, Japan.
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29
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Koay TW, Wong HL, Lim BH. Engineering of chimeric eukaryotic/bacterial Rubisco large subunits in Escherichia coli. Genes Genet Syst 2016; 91:139-150. [PMID: 27301279 DOI: 10.1266/ggs.15-00054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is a rate-limiting photosynthetic enzyme that catalyzes carbon fixation in the Calvin cycle. Much interest has been devoted to engineering this ubiquitous enzyme with the goal of increasing plant growth. However, experiments that have successfully produced improved Rubisco variants, via directed evolution in Escherichia coli, are limited to bacterial Rubisco because the eukaryotic holoenzyme cannot be produced in E. coli. The present study attempts to determine the specific differences between bacterial and eukaryotic Rubisco large subunit primary structure that are responsible for preventing heterologous eukaryotic holoenzyme formation in E. coli. A series of chimeric Synechococcus Rubiscos were created in which different sections of the large subunit were swapped with those of the homologous Chlamydomonas Rubisco. Chimeric holoenzymes that can form in vivo would indicate that differences within the swapped sections do not disrupt holoenzyme formation. Large subunit residues 1-97, 198-247 and 448-472 were successfully swapped without inhibiting holoenzyme formation. In all ten chimeras, protein expression was observed for the separate subunits at a detectable level. As a first approximation, the regions that can tolerate swapping may be targets for future engineering.
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Affiliation(s)
- Teng Wei Koay
- Department of Chemical Science, Faculty of Science, Universiti Tunku Abdul Rahman
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30
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Tcherkez G. The mechanism of Rubisco-catalysed oxygenation. PLANT, CELL & ENVIRONMENT 2016; 39:983-997. [PMID: 26286702 DOI: 10.1111/pce.12629] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/28/2015] [Accepted: 08/09/2015] [Indexed: 06/04/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the cornerstone of photosynthetic carbon assimilation because it catalyses the fixation of CO2 onto ribulose-1,5-bisphosphate (RuBP). The enzyme also catalyses RuBP oxygenation, thereby evolving phosphoglycolate which is recycled along the photorespiratory pathway. Oxygenation is quantitatively important, because under ordinary gaseous conditions, more than one third of RuBP molecules are oxygenated rather than carboxylated. However, contrary to carboxylation, the chemical mechanism of oxygenation is not well known, and little progress has been made since the early 80s. Here, I review recent experimental data that provide some new insights into the reaction mechanism, and carry out simple calculations of kinetic parameters. Isotope effects suggest that oxygenation is less likely initiated by a redox phenomenon (such as superoxide production) and more likely involves concerted chemical events that imply interactions with protons. A possible energy profile of the reaction is drawn which suggests that the generation of the oxygenated reaction intermediate (peroxide) is irreversible. Possible changes in oxygenation-associated rate constants between Rubisco forms are discussed.
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Affiliation(s)
- Guillaume Tcherkez
- Research School of Biology, ANU College of Medicine, Biology and Environment, Australian National University, Canberra, 2601, ACT, Australia
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31
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Prins A, Orr DJ, Andralojc PJ, Reynolds MP, Carmo-Silva E, Parry MAJ. Rubisco catalytic properties of wild and domesticated relatives provide scope for improving wheat photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1827-38. [PMID: 26798025 PMCID: PMC4783365 DOI: 10.1093/jxb/erv574] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Rubisco is a major target for improving crop photosynthesis and yield, yet natural diversity in catalytic properties of this enzyme is poorly understood. Rubisco from 25 genotypes of the Triticeae tribe, including wild relatives of bread wheat (Triticum aestivum), were surveyed to identify superior enzymes for improving photosynthesis in this crop. In vitro Rubisco carboxylation velocity (V c), Michaelis-Menten constants for CO2 (K c) and O2 (K o) and specificity factor (S c/o) were measured at 25 and 35 °C. V c and K c correlated positively, while V c and S c/o were inversely related. Rubisco large subunit genes (rbcL) were sequenced, and predicted corresponding amino acid differences analysed in relation to the corresponding catalytic properties. The effect of replacing native wheat Rubisco with counterparts from closely related species was analysed by modelling the response of photosynthesis to varying CO2 concentrations. The model predicted that two Rubisco enzymes would increase photosynthetic performance at 25 °C while only one of these also increased photosynthesis at 35 °C. Thus, under otherwise identical conditions, catalytic variation in the Rubiscos analysed is predicted to improve photosynthetic rates at physiological CO2 concentrations. Naturally occurring Rubiscos with superior properties amongst the Triticeae tribe can be exploited to improve wheat photosynthesis and crop productivity.
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Affiliation(s)
- Anneke Prins
- Plant Biology and Crop Science Department, Rothamsted Research, Harpenden AL5 2JQ UK
| | - Douglas J Orr
- Plant Biology and Crop Science Department, Rothamsted Research, Harpenden AL5 2JQ UK
| | - P John Andralojc
- Plant Biology and Crop Science Department, Rothamsted Research, Harpenden AL5 2JQ UK
| | - Matthew P Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco CP 56130, Mexico
| | - Elizabete Carmo-Silva
- Plant Biology and Crop Science Department, Rothamsted Research, Harpenden AL5 2JQ UK
| | - Martin A J Parry
- Plant Biology and Crop Science Department, Rothamsted Research, Harpenden AL5 2JQ UK
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32
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33
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Cavanagh AP, Kubien DS. Can phenotypic plasticity in Rubisco performance contribute to photosynthetic acclimation? PHOTOSYNTHESIS RESEARCH 2014; 119:203-214. [PMID: 23543330 DOI: 10.1007/s11120-013-9816-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 03/19/2013] [Indexed: 06/02/2023]
Abstract
Photosynthetic acclimation varies among species, which likely reveals variations at the biochemical level in the pathways that constitute carbon assimilation and energy transfer. Local adaptation and phenotypic plasticity affect the environmental response of photosynthesis. Phenotypic plasticity allows for a wide array of responses from a single individual, encouraging fitness in a broad variety of environments. Rubisco catalyses the first enzymatic step of photosynthesis, and is thus central to life on Earth. The enzyme is well conserved, but there is habitat-dependent variation in kinetic parameters, indicating that local adaptation may occur. Here, we review evidence suggesting that land plants can adjust Rubisco's intrinsic biochemical characteristics during acclimation. We show that this plasticity can theoretically improve CO2 assimilation; the effect is non-trivial, but small relative to other acclimation responses. We conclude by discussing possible mechanisms that could account for biochemical plasticity in land plant Rubisco.
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Affiliation(s)
- Amanda P Cavanagh
- Department of Biology, University of New Brunswick, 10 Bailey Dr., Fredericton, NB, Canada
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34
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Sundberg M, Pfister B, Fulton D, Bischof S, Delatte T, Eicke S, Stettler M, Smith SM, Streb S, Zeeman SC. The heteromultimeric debranching enzyme involved in starch synthesis in Arabidopsis requires both isoamylase1 and isoamylase2 subunits for complex stability and activity. PLoS One 2013; 8:e75223. [PMID: 24098685 PMCID: PMC3787081 DOI: 10.1371/journal.pone.0075223] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 08/10/2013] [Indexed: 11/18/2022] Open
Abstract
Isoamylase-type debranching enzymes (ISAs) play an important role in determining starch structure. Amylopectin – a branched polymer of glucose – is the major component of starch granules and its architecture underlies the semi-crystalline nature of starch. Mutants of several species lacking the ISA1-subclass of isoamylase are impaired in amylopectin synthesis. Consequently, starch levels are decreased and an aberrant soluble glucan (phytoglycogen) with altered branch lengths and branching pattern accumulates. Here we use TAP (tandem affinity purification) tagging to provide direct evidence in Arabidopsis that ISA1 interacts with its homolog ISA2. No evidence for interaction with other starch biosynthetic enzymes was found. Analysis of the single mutants shows that each protein is destabilised in the absence of the other. Co-expression of both ISA1 and ISA2 Escherichia coli allowed the formation of the active recombinant enzyme and we show using site-directed mutagenesis that ISA1 is the catalytic subunit. The presence of the active isoamylase alters glycogen biosynthesis in E. coli, resulting in colonies that stain more starch-like with iodine. However, analysis of the glucans reveals that rather than producing an amylopectin like substance, cells expressing the active isoamylase still accumulate small amounts of glycogen together with a population of linear oligosaccharides that stain strongly with iodine. We conclude that for isoamylase to promote amylopectin synthesis it needs to act on a specific precursor (pre-amylopectin) generated by the combined actions of plant starch synthase and branching enzyme isoforms and when presented with an unsuitable substrate (i.e. E. coli glycogen) it simply degrades it.
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Affiliation(s)
| | | | - Daniel Fulton
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | | | | | - Simona Eicke
- Department of Biology, ETH Zurich, Zurich, Switzerland
| | | | - Steven M. Smith
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia, Australia
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35
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Sudhani HPK, García-Murria MJ, Moreno J. Reversible inhibition of CO2 fixation by ribulose 1,5-bisphosphate carboxylase/oxygenase through the synergic effect of arsenite and a monothiol. PLANT, CELL & ENVIRONMENT 2013; 36:1160-1170. [PMID: 23216059 DOI: 10.1111/pce.12050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 11/27/2012] [Accepted: 11/28/2012] [Indexed: 06/01/2023]
Abstract
The activity of the photosynthetic carbon-fixing enzyme, ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco), is partially inhibited by arsenite in the millimolar concentration range. However, micromolar arsenite can fully inhibit Rubisco in the presence of a potentiating monothiol such as cysteine, cysteamine, 2-mercaptoethanol or N-acetylcysteine, but not glutathione. Arsenite reacts specifically with the vicinal Cys172-Cys192 from the large subunit of Rubisco and with the monothiol to establish a ternary complex, which is suggested to be a trithioarsenical. The stability of the complex is strongly dependent on the nature of the monothiol. Enzyme activity is fully recovered through the disassembly of the complex after eliminating arsenite and/or the thiol from the medium. The synergic combination of arsenite and a monothiol acts also in vivo stopping carbon dioxide fixation in illuminated cultures of Chlamydomonas reinhardtii. Again, this effect may be reverted by washing the cells. However, in vivo inhibition does not result from the blocking of Rubisco since mutant strains carrying Rubiscos with Cys172 and/or Cys192 substitutions (which are insensitive to arsenite in vitro) are also arrested. This suggests the existence of a specific sensor controlling carbon fixation that is even more sensitive than Rubisco to the arsenite-thiol synergism.
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Affiliation(s)
- Hemanth P K Sudhani
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Valencia, Burjassot, E-46100, Spain
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36
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Miller EB, Murrett CS, Zhu K, Zhao S, Goldfeld DA, Bylund JH, Friesner RA. Prediction of Long Loops with Embedded Secondary Structure using the Protein Local Optimization Program. J Chem Theory Comput 2013; 9:1846-4864. [PMID: 23814507 DOI: 10.1021/ct301083q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Robust homology modeling to atomic-level accuracy requires in the general case successful prediction of protein loops containing small segments of secondary structure. Further, as loop prediction advances to success with larger loops, the exclusion of loops containing secondary structure becomes awkward. Here, we extend the applicability of the Protein Local Optimization Program (PLOP) to loops up to 17 residues in length that contain either helical or hairpin segments. In general, PLOP hierarchically samples conformational space and ranks candidate loops with a high-quality molecular mechanics force field. For loops identified to possess α-helical segments, we employ an alternative dihedral library composed of (ϕ,ψ) angles commonly found in helices. The alternative library is searched over a user-specified range of residues that define the helical bounds. The source of these helical bounds can be from popular secondary structure prediction software or from analysis of past loop predictions where a propensity to form a helix is observed. Due to the maturity of our energy model, the lowest energy loop across all experiments can be selected with an accuracy of sub-Ångström RMSD in 80% of cases, 1.0 to 1.5 Å RMSD in 14% of cases, and poorer than 1.5 Å RMSD in 6% of cases. The effectiveness of our current methods in predicting hairpin-containing loops is explored with hairpins up to 13 residues in length and again reaching an accuracy of sub-Ångström RMSD in 83% of cases, 1.0 to 1.5 Å RMSD in 10% of cases, and poorer than 1.5 Å RMSD in 7% of cases. Finally, we explore the effect of an imprecise surrounding environment, in which side chains, but not the backbone, are initially in perturbed geometries. In these cases, loops perturbed to 3Å RMSD from the native environment were restored to their native conformation with sub-Ångström RMSD.
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Affiliation(s)
- Edward B Miller
- Department of Chemistry, Columbia University, New York, New York
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37
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Tcherkez GGB, Bathellier C, Stuart-Williams H, Whitney S, Gout E, Bligny R, Badger M, Farquhar GD. D2O Solvent Isotope Effects Suggest Uniform Energy Barriers in Ribulose-1,5-bisphosphate Carboxylase/Oxygenase Catalysis. Biochemistry 2013; 52:869-77. [DOI: 10.1021/bi300933u] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Guillaume G. B. Tcherkez
- Institut de Biologie des Plantes,
CNRS UMR 8618, Université Paris-Sud 11, 91405 Orsay cedex, France
- Institut Universitaire de France, 103 boulevard Saint-Michel, 75005 Paris,
France
| | - Camille Bathellier
- Institut de Biologie des Plantes,
CNRS UMR 8618, Université Paris-Sud 11, 91405 Orsay cedex, France
- Research School of
Biology, Australian National University, Canberra ACT 0200,
Australia
| | - Hilary Stuart-Williams
- Research School of
Biology, Australian National University, Canberra ACT 0200,
Australia
| | - Spencer Whitney
- Research School of
Biology, Australian National University, Canberra ACT 0200,
Australia
| | - Elisabeth Gout
- Laboratoire de
Physiologie Cellulaire
Végétale, CEA-Grenoble, 17
rue des Martyrs, 38009 Grenoble cedex, France
| | - Richard Bligny
- Laboratoire de
Physiologie Cellulaire
Végétale, CEA-Grenoble, 17
rue des Martyrs, 38009 Grenoble cedex, France
| | - Murray Badger
- Research School of
Biology, Australian National University, Canberra ACT 0200,
Australia
| | - Graham D. Farquhar
- Research School of
Biology, Australian National University, Canberra ACT 0200,
Australia
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Miller SR, McGuirl MA, Carvey D. The Evolution of RuBisCO Stability at the Thermal Limit of Photoautotrophy. Mol Biol Evol 2013; 30:752-60. [DOI: 10.1093/molbev/mss327] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Parry MAJ, Andralojc PJ, Scales JC, Salvucci ME, Carmo-Silva AE, Alonso H, Whitney SM. Rubisco activity and regulation as targets for crop improvement. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:717-30. [PMID: 23162118 DOI: 10.1093/jxb/ers336] [Citation(s) in RCA: 232] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Rubisco (ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase) enables net carbon fixation through the carboxylation of RuBP. However, some characteristics of Rubisco make it surprisingly inefficient and compromise photosynthetic productivity. For example, Rubisco catalyses a wasteful reaction with oxygen that leads to the release of previously fixed CO(2) and NH(3) and the consumption of energy during photorespiration. Furthermore, Rubisco is slow and large amounts are needed to support adequate photosynthetic rates. Consequently, Rubisco has been studied intensively as a prime target for manipulations to 'supercharge' photosynthesis and improve both productivity and resource use efficiency. The catalytic properties of Rubiscos from diverse sources vary considerably, suggesting that changes in turnover rate, affinity, or specificity for CO(2) can be introduced to improve Rubisco performance in specific crops and environments. While attempts to manipulate plant Rubisco by nuclear transformation have had limited success, modifying its catalysis by targeted changes to its catalytic large subunit via chloroplast transformation have been much more successful. However, this technique is still in need of development for most major food crops including maize, wheat, and rice. Other bioengineering approaches for improving Rubisco performance include improving the activity of its ancillary protein, Rubisco activase, in addition to modulating the synthesis and degradation of Rubisco's inhibitory sugar phosphate ligands. As the rate-limiting step in carbon assimilation, even modest improvements in the overall performance of Rubisco pose a viable pathway for obtaining significant gains in plant yield, particularly under stressful environmental conditions.
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Affiliation(s)
- Martin A J Parry
- Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK.
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Kapralov MV, Smith JAC, Filatov DA. Rubisco evolution in C₄ eudicots: an analysis of Amaranthaceae sensu lato. PLoS One 2012; 7:e52974. [PMID: 23285238 PMCID: PMC3527620 DOI: 10.1371/journal.pone.0052974] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 11/26/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) catalyses the key reaction in the photosynthetic assimilation of CO₂. In C₄ plants CO₂ is supplied to Rubisco by an auxiliary CO₂-concentrating pathway that helps to maximize the carboxylase activity of the enzyme while suppressing its oxygenase activity. As a consequence, C₄ Rubisco exhibits a higher maximum velocity but lower substrate specificity compared with the C₃ enzyme. Specific amino-acids in Rubisco are associated with C₄ photosynthesis in monocots, but it is not known whether selection has acted on Rubisco in a similar way in eudicots. METHODOLOGY/PRINCIPAL FINDINGS We investigated Rubisco evolution in Amaranthaceae sensu lato (including Chenopodiaceae), the third-largest family of C₄ plants, using phylogeny-based maximum likelihood and Bayesian methods to detect Darwinian selection on the chloroplast rbcL gene in a sample of 179 species. Two Rubisco residues, 281 and 309, were found to be under positive selection in C₄ Amaranthaceae with multiple parallel replacements of alanine by serine at position 281 and methionine by isoleucine at position 309. Remarkably, both amino-acids have been detected in other C₄ plant groups, such as C₄ monocots, illustrating a striking parallelism in molecular evolution. CONCLUSIONS/SIGNIFICANCE Our findings illustrate how simple genetic changes can contribute to the evolution of photosynthesis and strengthen the hypothesis that parallel amino-acid replacements are associated with adaptive changes in Rubisco.
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Affiliation(s)
- Maxim V Kapralov
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, United Kingdom.
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Qian P, Marklew CJ, Viney J, Davison PA, Brindley AA, Söderberg C, Al-Karadaghi S, Bullough PA, Grossmann JG, Hunter CN. Structure of the cyanobacterial Magnesium Chelatase H subunit determined by single particle reconstruction and small-angle X-ray scattering. J Biol Chem 2012; 287:4946-56. [PMID: 22179610 PMCID: PMC3281664 DOI: 10.1074/jbc.m111.308239] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 12/07/2011] [Indexed: 02/02/2023] Open
Abstract
The biosynthesis of chlorophyll, an essential cofactor for photosynthesis, requires the ATP-dependent insertion of Mg(2+) into protoporphyrin IX catalyzed by the multisubunit enzyme magnesium chelatase. This enzyme complex consists of the I subunit, an ATPase that forms a complex with the D subunit, and an H subunit that binds both the protoporphyrin substrate and the magnesium protoporphyrin product. In this study we used electron microscopy and small-angle x-ray scattering to investigate the structure of the magnesium chelatase H subunit, ChlH, from the thermophilic cyanobacterium Thermosynechococcus elongatus. Single particle reconstruction of negatively stained apo-ChlH and Chl-porphyrin proteins was used to reconstitute three-dimensional structures to a resolution of ∼30 Å. ChlH is a large, 148-kDa protein of 1326 residues, forming a cage-like assembly comprising the majority of the structure, attached to a globular N-terminal domain of ∼16 kDa by a narrow linker region. This N-terminal domain is adjacent to a 5 nm-diameter opening in the structure that allows access to a cavity. Small-angle x-ray scattering analysis of ChlH, performed on soluble, catalytically active ChlH, verifies the presence of two domains and their relative sizes. Our results provide a basis for the multiple regulatory and catalytic functions of ChlH of oxygenic photosynthetic organisms and for a chaperoning function that sequesters the enzyme-bound magnesium protoporphyrin product prior to its delivery to the next enzyme in the chlorophyll biosynthetic pathway, magnesium protoporphyrin methyltransferase.
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Affiliation(s)
- Pu Qian
- From the Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Christopher J. Marklew
- From the Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Joanne Viney
- From the Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Paul A. Davison
- From the Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Amanda A. Brindley
- From the Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Christopher Söderberg
- the Department of Molecular Biophysics, Center for Molecular Protein Science, Lund University, 22100 Lund, Sweden, and
| | - Salam Al-Karadaghi
- the Department of Molecular Biophysics, Center for Molecular Protein Science, Lund University, 22100 Lund, Sweden, and
| | - Per A. Bullough
- From the Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - J. Günter Grossmann
- the Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - C. Neil Hunter
- From the Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
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Marcus Y, Altman-Gueta H, Wolff Y, Gurevitz M. Rubisco mutagenesis provides new insight into limitations on photosynthesis and growth in Synechocystis PCC6803. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:4173-82. [PMID: 21551078 PMCID: PMC3153676 DOI: 10.1093/jxb/err116] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Orthophosphate (Pi) stimulates the activation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) while paradoxically inhibiting its catalysis. Of three Pi-binding sites, the roles of the 5P- and latch sites have been documented, whereas that of the 1P-site remained unclear. Conserved residues at the 1P-site of Rubisco from the cyanobacterium Synechocystis PCC6803 were substituted and the kinetic properties of the enzyme derivatives and effects on cell photosynthesis and growth were examined. While Pi-stimulated Rubisco activation diminished for enzyme mutants T65A/S and G404A, inhibition of catalysis by Pi remained unchanged. Together with previous studies, the results suggest that all three Pi-binding sites are involved in stimulation of Rubisco activation, whereas only the 5P-site is involved in inhibition of catalysis. While all the mutations reduced the catalytic turnover of Rubisco (K(cat)) between 6- and 20-fold, the photosynthesis and growth rates under saturating irradiance and inorganic carbon (Ci) concentrations were only reduced 40-50% (in the T65A/S mutants) or not at all (G404A mutant). Analysis of the mutant cells revealed a 3-fold increase in Rubisco content that partially compensated for the reduced K(cat) so that the carboxylation rate per chlorophyll was one-third of that in the wild type. Correlation between the kinetic properties of Rubisco and the photosynthetic rate (P(max)) under saturating irradiance and Ci concentrations indicate that a >60% reduction in K(cat) can be tolerated before P(max) in Synechocystsis PCC6803 is affected. These results indicate that the limitation of Rubisco activity on the rate of photosynthesis in Synechocystis is low. Determination of Calvin cycle metabolites revealed that unlike in higher plants, cyanobacterial photosynthesis is constrained by phosphoglycerate reduction probably due to limitation of ATP or NADPH.
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Affiliation(s)
- Yehouda Marcus
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel.
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Subunit interface dynamics in hexadecameric rubisco. J Mol Biol 2011; 411:1083-98. [PMID: 21745478 DOI: 10.1016/j.jmb.2011.06.052] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Revised: 06/27/2011] [Accepted: 06/30/2011] [Indexed: 11/23/2022]
Abstract
Ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco) plays an important role in the global carbon cycle as a hub for biomass. Rubisco catalyzes not only the carboxylation of RuBP with carbon dioxide but also a competing oxygenation reaction of RuBP with a negative impact on photosynthetic yield. The functional active site is built from two large (L) subunits that form a dimer. The octameric core of four L(2) dimers is held at each end by a cluster of four small (S) subunits, forming a hexadecamer. Each large subunit contacts more than one S subunit. These interactions exploit the dynamic flexibility of Rubisco, which we address in this study. Here, we describe seven different types of interfaces of hexadecameric Rubisco. We have analyzed these interfaces with respect to the size of the interface area and the number of polar interactions, including salt bridges and hydrogen bonds in a variety of Rubisco enzymes from different organisms and different kingdoms of life, including the Rubisco-like proteins. We have also performed molecular dynamics simulations of Rubisco from Chlamydomonas reinhardtii and mutants thereof. From our computational analyses, we propose structural checkpoints of the S subunit to ensure the functionality and/or assembly of the Rubisco holoenzyme. These checkpoints appear to fine-tune the dynamics of the enzyme in a way that could influence enzyme performance.
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Ishikawa C, Hatanaka T, Misoo S, Miyake C, Fukayama H. Functional incorporation of sorghum small subunit increases the catalytic turnover rate of Rubisco in transgenic rice. PLANT PHYSIOLOGY 2011; 156:1603-11. [PMID: 21562335 PMCID: PMC3135941 DOI: 10.1104/pp.111.177030] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 05/06/2011] [Indexed: 05/17/2023]
Abstract
Rubisco limits photosynthetic CO(2) fixation because of its low catalytic turnover rate (k(cat)) and competing oxygenase reaction. Previous attempts to improve the catalytic efficiency of Rubisco by genetic engineering have gained little progress. Here we demonstrate that the introduction of the small subunit (RbcS) of high k(cat) Rubisco from the C(4) plant sorghum (Sorghum bicolor) significantly enhances k(cat) of Rubisco in transgenic rice (Oryza sativa). Three independent transgenic lines expressed sorghum RbcS at a high level, accounting for 30%, 44%, and 79% of the total RbcS. Rubisco was likely present as a chimera of sorghum and rice RbcS, and showed 1.32- to 1.50-fold higher k(cat) than in nontransgenic rice. Rubisco from transgenic lines showed a higher K(m) for CO(2) and slightly lower specificity for CO(2) than nontransgenic controls. These results suggest that Rubisco in rice transformed with sorghum RbcS partially acquires the catalytic properties of sorghum Rubisco. Rubisco content in transgenic lines was significantly increased over wild-type levels but Rubisco activation was slightly decreased. The expression of sorghum RbcS did not affect CO(2) assimilation rates under a range of CO(2) partial pressures. The J(max)/V(cmax) ratio was significantly lower in transgenic line compared to the nontransgenic plants. These observations suggest that the capacity of electron transport is not sufficient to support the increased Rubisco capacity in transgenic rice. Although the photosynthetic rate was not enhanced, the strategy presented here opens the way to engineering Rubisco for improvement of photosynthesis and productivity in the future.
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Wu X, Oh MH, Schwarz EM, Larue CT, Sivaguru M, Imai BS, Yau PM, Ort DR, Huber SC. Lysine acetylation is a widespread protein modification for diverse proteins in Arabidopsis. PLANT PHYSIOLOGY 2011; 155:1769-78. [PMID: 21311030 PMCID: PMC3091122 DOI: 10.1104/pp.110.165852] [Citation(s) in RCA: 163] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 02/04/2011] [Indexed: 05/20/2023]
Abstract
Lysine acetylation (LysAc), a form of reversible protein posttranslational modification previously known only for histone regulation in plants, is shown to be widespread in Arabidopsis (Arabidopsis thaliana). Sixty-four Lys modification sites were identified on 57 proteins, which operate in a wide variety of pathways/processes and are located in various cellular compartments. A number of photosynthesis-related proteins are among this group of LysAc proteins, including photosystem II (PSII) subunits, light-harvesting chlorophyll a/b-binding proteins (LHCb), Rubisco large and small subunits, and chloroplastic ATP synthase (β-subunit). Using two-dimensional native green/sodium dodecyl sulfate gels, the loosely PSII-bound LHCb was separated from the LHCb that is tightly bound to PSII and shown to have substantially higher level of LysAc, implying that LysAc may play a role in distributing the LHCb complexes. Several potential LysAc sites were identified on eukaryotic elongation factor-1A (eEF-1A) by liquid chromatography/mass spectrometry and using sequence- and modification-specific antibodies the acetylation of Lys-227 and Lys-306 was established. Lys-306 is contained within a predicted calmodulin-binding sequence and acetylation of Lys-306 strongly inhibited the interactions of eEF-1A synthetic peptides with calmodulin recombinant proteins in vitro. These results suggest that LysAc of eEF-1A may directly affect regulatory properties and localization of the protein within the cell. Overall, these findings reveal the possibility that reversible LysAc may be an important and previously unknown regulatory mechanism of a large number of nonhistone proteins affecting a wide range of pathways and processes in Arabidopsis and likely in all plants.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Steven C. Huber
- Program in Physiological and Molecular Plant Biology (X.W., E.M.S.), United States Department of Agriculture-Agricultural Research Service and Department of Plant Biology (M.-H.O., C.T.L., D.R.O., S.C.H.), Microscopy Facility, Institute for Genomic Biology (M.S.), and Protein Sciences Facility, Carver Biotechnology Center (B.S.I., P.M.Y.), University of Illinois, Urbana, Illinois 61801
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Finkemeier I, Laxa M, Miguet L, Howden AJM, Sweetlove LJ. Proteins of diverse function and subcellular location are lysine acetylated in Arabidopsis. PLANT PHYSIOLOGY 2011; 155:1779-90. [PMID: 21311031 PMCID: PMC3091095 DOI: 10.1104/pp.110.171595] [Citation(s) in RCA: 195] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 02/04/2011] [Indexed: 05/20/2023]
Abstract
Acetylation of the ε-amino group of lysine (Lys) is a reversible posttranslational modification recently discovered to be widespread, occurring on proteins outside the nucleus, in most subcellular locations in mammalian cells. Almost nothing is known about this modification in plants beyond the well-studied acetylation of histone proteins in the nucleus. Here, we report that Lys acetylation in plants also occurs on organellar and cytosolic proteins. We identified 91 Lys-acetylated sites on 74 proteins of diverse functional classes. Furthermore, our study suggests that Lys acetylation may be an important posttranslational modification in the chloroplast, since four Calvin cycle enzymes were acetylated. The plastid-encoded large subunit of Rubisco stands out because of the large number of acetylated sites occurring at important Lys residues that are involved in Rubisco tertiary structure formation and catalytic function. Using the human recombinant deacetylase sirtuin 3, it was demonstrated that Lys deacetylation significantly affects Rubisco activity as well as the activities of other central metabolic enzymes, such as the Calvin cycle enzyme phosphoglycerate kinase, the glycolytic enzyme glyceraldehyde 3-phosphate dehydrogenase, and the tricarboxylic acid cycle enzyme malate dehydrogenase. Our results demonstrate that Lys acetylation also occurs on proteins outside the nucleus in Arabidopsis (Arabidopsis thaliana) and that Lys acetylation could be important in the regulation of key metabolic enzymes.
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Zhang XH, Webb J, Huang YH, Lin L, Tang RS, Liu A. Hybrid Rubisco of tomato large subunits and tobacco small subunits is functional in tobacco plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 180:480-8. [PMID: 21421395 DOI: 10.1016/j.plantsci.2010.11.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Revised: 11/07/2010] [Accepted: 11/09/2010] [Indexed: 05/08/2023]
Abstract
Biogenesis of functional ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) in plants requires specific assembly in the chloroplast of the imported, cytosol-synthesized small subunits (SS) with the chloroplast-made large subunits (LS). Accumulating evidence indicates that chloroplasts (plastids) generally have a low tolerance for assembling foreign or modified Rubisco. To explore Rubisco engineering, we created two lines of transplastomic tobacco plants whose rbcL gene was replaced by tomato-derived rbcL: plant LLS2 with Rubisco composed of tobacco SS and Q437R LS and plant LLS4 with a hybrid Rubisco of tobacco SS and tomato LS (representing four substitutions of Y226F, A230T, S279T and Q437R from tobacco LS). Plant LLS2 exhibited similar phenotypes as the wild type. Plant LLS4 showed lower chlorophyll and Rubisco levels particularly in young emerging leaves, lower photosynthesis rates and biomass during early stages of development, but was able to reach reproductive maturity and somewhat wild type-like phenotype under ambient CO₂ condition. In vitro assays detected similar carboxylase activity and RuBP affinity in LLS2 and LLS4 plants as in wild type. Our studies demonstrated that tomato LS was sufficiently assembled with tobacco SS into functional Rubisco. The hybrid Rubisco of tomato LS and tobacco SS can drive photosynthesis that supports photoautotrophic growth and reproduction of tobacco plants under ambient CO₂ and light conditions. We discuss the effect of these residue substitutions on Rubisco activity and the possible attribution of chlorophyll deficiency to the in planta photosynthesis performance in the hybrid Rubisco plants.
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Affiliation(s)
- Xing-Hai Zhang
- Department of Biological Sciences, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431, USA.
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Kapralov MV, Kubien DS, Andersson I, Filatov DA. Changes in Rubisco kinetics during the evolution of C4 photosynthesis in Flaveria (Asteraceae) are associated with positive selection on genes encoding the enzyme. Mol Biol Evol 2010; 28:1491-503. [PMID: 21172830 DOI: 10.1093/molbev/msq335] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Rubisco, the primary photosynthetic carboxylase, evolved 3-4 billion years ago in an anaerobic, high CO(2) atmosphere. The combined effect of low CO(2) and high O(2) levels in the modern atmosphere, and the inability of Rubisco to distinguish completely between CO(2) and O(2), leads to the occurrence of an oxygenation reaction that reduces the efficiency of photosynthesis. Among land plants, C(4) photosynthesis largely solves this problem by facilitating a high CO(2)/O(2) ratio at the site of Rubisco that resembles the atmosphere in which the ancestral enzyme evolved. The prediction that such conditions favor Rubiscos with higher kcat(CO2) and lower CO(2)/O(2) specificity (S(C/O)) is well supported, but the structural basis for the differences between C(3) and C(4) Rubiscos is not clear. Flaveria (Asteraceae) includes C(3), C(3)-C(4) intermediate, and C(4) species with kinetically distinct Rubiscos, providing a powerful system in which to study the biochemical transition of Rubisco during the evolution from C(3) to C(4) photosynthesis. We analyzed the molecular evolution of chloroplast rbcL and nuclear rbcS genes encoding the large subunit (LSu) and small subunit (SSu) of Rubisco from 15 Flaveria species. We demonstrate positive selection on both subunits, although selection is much stronger on the LSu. In Flaveria, two positively selected LSu amino acid substitutions, M309I and D149A, distinguish C(4) Rubiscos from the ancestral C(3) species and statistically account for much of the kinetic difference between the two groups. However, although Flaveria lacks a characteristic "C(4)" SSu, our data suggest that specific residue substitutions in the SSu are correlated with the kinetic properties of Rubisco in this genus.
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Affiliation(s)
- Maxim V Kapralov
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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Nishitani Y, Yoshida S, Fujihashi M, Kitagawa K, Doi T, Atomi H, Imanaka T, Miki K. Structure-based catalytic optimization of a type III Rubisco from a hyperthermophile. J Biol Chem 2010; 285:39339-47. [PMID: 20926376 PMCID: PMC2998091 DOI: 10.1074/jbc.m110.147587] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Revised: 09/21/2010] [Indexed: 11/06/2022] Open
Abstract
The Calvin-Benson-Bassham cycle is responsible for carbon dioxide fixation in all plants, algae, and cyanobacteria. The enzyme that catalyzes the carbon dioxide-fixing reaction is ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). Rubisco from a hyperthermophilic archaeon Thermococcus kodakarensis (Tk-Rubisco) belongs to the type III group, and shows high activity at high temperatures. We have previously found that replacement of the entire α-helix 6 of Tk-Rubisco with the corresponding region of the spinach enzyme (SP6 mutant) results in an improvement of catalytic performance at mesophilic temperatures, both in vivo and in vitro, whereas the former and latter half-replacements of the α-helix 6 (SP4 and SP5 mutants) do not yield such improvement. We report here the crystal structures of the wild-type Tk-Rubisco and the mutants SP4 and SP6, and discuss the relationships between their structures and enzymatic activities. A comparison among these structures shows the movement and the increase of temperature factors of α-helix 6 induced by four essential factors. We thus supposed that an increase in the flexibility of the α-helix 6 and loop 6 regions was important to increase the catalytic activity of Tk-Rubisco at ambient temperatures. Based on this structural information, we constructed a new mutant, SP5-V330T, which was designed to have significantly greater flexibility in the above region, and it proved to exhibit the highest activity among all mutants examined to date. The thermostability of the SP5-V330T mutant was lower than that of wild-type Tk-Rubisco, providing further support on the relationship between flexibility and activity at ambient temperatures.
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Affiliation(s)
- Yuichi Nishitani
- From the Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502 and
| | - Shosuke Yoshida
- the Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Masahiro Fujihashi
- From the Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502 and
| | - Kazuya Kitagawa
- From the Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502 and
| | - Takashi Doi
- From the Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502 and
| | - Haruyuki Atomi
- the Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tadayuki Imanaka
- the Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kunio Miki
- From the Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502 and
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