51
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Claassens NJ. A warm welcome for alternative CO 2 fixation pathways in microbial biotechnology. Microb Biotechnol 2017; 10:31-34. [PMID: 27873465 PMCID: PMC5270723 DOI: 10.1111/1751-7915.12456] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 10/19/2016] [Indexed: 12/31/2022] Open
Affiliation(s)
- Nico J. Claassens
- Laboratory of MicrobiologyWageningen UniversityStippeneng 46708 WEWageningenThe Netherlands
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52
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Evolutionary trend toward kinetic stability in the folding trajectory of RNases H. Proc Natl Acad Sci U S A 2016; 113:13045-13050. [PMID: 27799545 DOI: 10.1073/pnas.1611781113] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proper folding of proteins is critical to producing the biological machinery essential for cellular function. The rates and energetics of a protein's folding process, which is described by its energy landscape, are encoded in the amino acid sequence. Over the course of evolution, this landscape must be maintained such that the protein folds and remains folded over a biologically relevant time scale. How exactly a protein's energy landscape is maintained or altered throughout evolution is unclear. To study how a protein's energy landscape changed over time, we characterized the folding trajectories of ancestral proteins of the ribonuclease H (RNase H) family using ancestral sequence reconstruction to access the evolutionary history between RNases H from mesophilic and thermophilic bacteria. We found that despite large sequence divergence, the overall folding pathway is conserved over billions of years of evolution. There are robust trends in the rates of protein folding and unfolding; both modern RNases H evolved to be more kinetically stable than their most recent common ancestor. Finally, our study demonstrates how a partially folded intermediate provides a readily adaptable folding landscape by allowing the independent tuning of kinetics and thermodynamics.
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53
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Claassens NJ, Sousa DZ, dos Santos VAPM, de Vos WM, van der Oost J. Harnessing the power of microbial autotrophy. Nat Rev Microbiol 2016; 14:692-706. [DOI: 10.1038/nrmicro.2016.130] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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54
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Shih PM, Liang Y, Loqué D. Biotechnology and synthetic biology approaches for metabolic engineering of bioenergy crops. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:103-17. [PMID: 27030440 DOI: 10.1111/tpj.13176] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 03/18/2016] [Accepted: 03/22/2016] [Indexed: 05/26/2023]
Abstract
The Green Revolution has fuelled an exponential growth in human population since the mid-20th century. Due to population growth, food and energy demands will soon surpass supply capabilities. To overcome these impending problems, significant improvements in genetic engineering will be needed to complement breeding efforts in order to accelerate the improvement of agronomical traits. The new field of plant synthetic biology has emerged in recent years and is expected to support rapid, precise, and robust engineering of plants. In this review, we present recent advances made in the field of plant synthetic biology, specifically in genome editing, transgene expression regulation, and bioenergy crop engineering, with a focus on traits related to lignocellulose, oil, and soluble sugars. Ultimately, progress and innovation in these fields may facilitate the development of beneficial traits in crop plants to meet society's bioenergy needs.
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Affiliation(s)
- Patrick M Shih
- Joint BioEnergy Institute, Emery Station East, 5885 Hollis St, 4th Floor, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Yan Liang
- Joint BioEnergy Institute, Emery Station East, 5885 Hollis St, 4th Floor, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Dominique Loqué
- Joint BioEnergy Institute, Emery Station East, 5885 Hollis St, 4th Floor, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Université Lyon 1, INSA de Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 rue Raphaël Dubois, F-69622, Villeurbanne, France
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55
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Satagopan S, Tabita FR. RubisCO selection using the vigorously aerobic and metabolically versatile bacterium Ralstonia eutropha. FEBS J 2016; 283:2869-80. [PMID: 27261087 DOI: 10.1111/febs.13774] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/06/2016] [Accepted: 06/03/2016] [Indexed: 11/29/2022]
Abstract
UNLABELLED Recapturing atmospheric CO2 is key to reducing global warming and increasing biological carbon availability. Ralstonia eutropha is a biotechnologically useful aerobic bacterium that uses the Calvin-Benson-Bassham (CBB) cycle and the enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) for CO2 utilization, suggesting that it may be a useful host to bioselect RubisCO molecules with improved CO2 -capture capabilities. A host strain of R. eutropha was constructed for this purpose after deleting endogenous genes encoding two related RubisCOs. This strain could be complemented for CO2 -dependent growth by introducing native or heterologous RubisCO genes. Mutagenesis and suppressor selection identified amino acid substitutions in a hydrophobic region that specifically influences RubisCO's interaction with its substrates, particularly O2 , which competes with CO2 at the active site. Unlike most RubisCOs, the R. eutropha enzyme has evolved to retain optimal CO2 -fixation rates in a fast-growing host, despite the presence of high levels of competing O2 . Yet its structure-function properties resemble those of several commonly found RubisCOs, including the higher plant enzymes, allowing strategies to engineer analogous enzymes. Because R. eutropha can be cultured rapidly under harsh environmental conditions (e.g., with toxic industrial flue gas), in the presence of near saturation levels of oxygen, artificial selection and directed evolution studies in this organism could potentially impact efforts toward improving RubisCO-dependent biological CO2 utilization in aerobic environments. ENZYMES d-ribulose 1,5-bisphosphate carboxylase/oxygenase, EC 4.1.1.39; phosphoribulokinase, EC 2.7.1.19.
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Affiliation(s)
- Sriram Satagopan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - F Robert Tabita
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
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56
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Antonovsky N, Gleizer S, Noor E, Zohar Y, Herz E, Barenholz U, Zelcbuch L, Amram S, Wides A, Tepper N, Davidi D, Bar-On Y, Bareia T, Wernick DG, Shani I, Malitsky S, Jona G, Bar-Even A, Milo R. Sugar Synthesis from CO2 in Escherichia coli. Cell 2016; 166:115-25. [PMID: 27345370 PMCID: PMC4930481 DOI: 10.1016/j.cell.2016.05.064] [Citation(s) in RCA: 212] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 03/02/2016] [Accepted: 05/17/2016] [Indexed: 11/29/2022]
Abstract
Can a heterotrophic organism be evolved to synthesize biomass from CO2 directly? So far, non-native carbon fixation in which biomass precursors are synthesized solely from CO2 has remained an elusive grand challenge. Here, we demonstrate how a combination of rational metabolic rewiring, recombinant expression, and laboratory evolution has led to the biosynthesis of sugars and other major biomass constituents by a fully functional Calvin-Benson-Bassham (CBB) cycle in E. coli. In the evolved bacteria, carbon fixation is performed via a non-native CBB cycle, while reducing power and energy are obtained by oxidizing a supplied organic compound (e.g., pyruvate). Genome sequencing reveals that mutations in flux branchpoints, connecting the non-native CBB cycle to biosynthetic pathways, are essential for this phenotype. The successful evolution of a non-native carbon fixation pathway, though not yet resulting in net carbon gain, strikingly demonstrates the capacity for rapid trophic-mode evolution of metabolism applicable to biotechnology. PaperClip
Non-native Calvin-Benson cycle allows for sugar synthesis from CO2 in E. coli Metabolic cutoff allows for the decoupling of energy harvesting from biomass synthesis Chemostat-based directed evolution led to the emergence of sugar synthesis from CO2 Mutations in flux branchpoints are essential for the CBB cycle stable operation
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Affiliation(s)
- Niv Antonovsky
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shmuel Gleizer
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yehudit Zohar
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elad Herz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Uri Barenholz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Lior Zelcbuch
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shira Amram
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Aryeh Wides
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Naama Tepper
- Department of Computer Science, Technion, Israel Institute of Technology, Haifa 3200003, Israel
| | - Dan Davidi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yinon Bar-On
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tasneem Bareia
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David G Wernick
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ido Shani
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sergey Malitsky
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ghil Jona
- Department of Biological Services, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Arren Bar-Even
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
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57
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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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58
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Wilson RH, Alonso H, Whitney SM. Evolving Methanococcoides burtonii archaeal Rubisco for improved photosynthesis and plant growth. Sci Rep 2016; 6:22284. [PMID: 26926260 PMCID: PMC4772096 DOI: 10.1038/srep22284] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 02/10/2016] [Indexed: 11/28/2022] Open
Abstract
In photosynthesis Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyses the often rate limiting CO2-fixation step in the Calvin cycle. This makes Rubisco both the gatekeeper for carbon entry into the biosphere and a target for functional improvement to enhance photosynthesis and plant growth. Encumbering the catalytic performance of Rubisco is its highly conserved, complex catalytic chemistry. Accordingly, traditional efforts to enhance Rubisco catalysis using protracted "trial and error" protein engineering approaches have met with limited success. Here we demonstrate the versatility of high throughput directed (laboratory) protein evolution for improving the carboxylation properties of a non-photosynthetic Rubisco from the archaea Methanococcoides burtonii. Using chloroplast transformation in the model plant Nicotiana tabacum (tobacco) we confirm the improved forms of M. burtonii Rubisco increased photosynthesis and growth relative to tobacco controls producing wild-type M. burtonii Rubisco. Our findings indicate continued directed evolution of archaeal Rubisco offers new potential for enhancing leaf photosynthesis and plant growth.
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Affiliation(s)
- Robert H. Wilson
- Research School of Biology, The Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Hernan Alonso
- Research School of Biology, The Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Spencer M. Whitney
- Research School of Biology, The Australian National University, Acton, Australian Capital Territory 2601, Australia
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59
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Zhou J, Zhu T, Cai Z, Li Y. From cyanochemicals to cyanofactories: a review and perspective. Microb Cell Fact 2016; 15:2. [PMID: 26743222 PMCID: PMC4705643 DOI: 10.1186/s12934-015-0405-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 12/25/2015] [Indexed: 11/18/2022] Open
Abstract
Engineering cyanobacteria for production of chemicals from solar energy, CO2 and water is a potential approach to address global energy and environment issues such as greenhouse effect. To date, more than 20 chemicals have been synthesized by engineered cyanobacteria using CO2 as raw materials, and these studies have been well reviewed. However, unlike heterotrophic microorganisms, the low CO2 fixation rate makes it a long way to go from cyanochemicals to cyanofactories. Here we review recent progresses on improvement of carbon fixation and redistribution of intercellular carbon flux, and discuss the challenges for developing cyanofactories in the future.
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Affiliation(s)
- Jie Zhou
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, No 1, West Beichen Road, Chaoyang District, 100101, Beijing, China.
| | - Taicheng Zhu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, No 1, West Beichen Road, Chaoyang District, 100101, Beijing, China.
| | - Zhen Cai
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, No 1, West Beichen Road, Chaoyang District, 100101, Beijing, China.
| | - Yin Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, No 1, West Beichen Road, Chaoyang District, 100101, Beijing, China.
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60
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Wobbe L, Bassi R, Kruse O. Multi-Level Light Capture Control in Plants and Green Algae. TRENDS IN PLANT SCIENCE 2016; 21:55-68. [PMID: 26545578 DOI: 10.1016/j.tplants.2015.10.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 09/16/2015] [Accepted: 10/05/2015] [Indexed: 05/02/2023]
Abstract
Life on Earth relies on photosynthesis, and the ongoing depletion of fossil carbon fuels has renewed interest in phototrophic light-energy conversion processes as a blueprint for the conversion of atmospheric CO2 into various organic compounds. Light-harvesting systems have evolved in plants and green algae, which are adapted to the light intensity and spectral composition encountered in their habitats. These organisms are constantly challenged by a fluctuating light supply and other environmental cues affecting photosynthetic performance. Excess light can be especially harmful, but plants and microalgae are equipped with different acclimation mechanisms to control the processing of sunlight absorbed at both photosystems. We summarize the current knowledge and discuss the potential for optimization of phototrophic light-energy conversion.
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Affiliation(s)
- Lutz Wobbe
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Roberto Bassi
- Universita degli Studi di Verona, Department of Biotechnology, Strada Le Grazie 15, 37134 Verona, Italy
| | - Olaf Kruse
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615, Bielefeld, Germany.
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61
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Hazra S, Henderson JN, Liles K, Hilton MT, Wachter RM. Regulation of ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) activase: product inhibition, cooperativity, and magnesium activation. J Biol Chem 2015; 290:24222-36. [PMID: 26283786 PMCID: PMC4591810 DOI: 10.1074/jbc.m115.651745] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 08/04/2015] [Indexed: 12/24/2022] Open
Abstract
In many photosynthetic organisms, tight-binding Rubisco inhibitors are released by the motor protein Rubisco activase (Rca). In higher plants, Rca plays a pivotal role in regulating CO2 fixation. Here, the ATPase activity of 0.005 mm tobacco Rca was monitored under steady-state conditions, and global curve fitting was utilized to extract kinetic constants. The kcat was best fit by 22.3 ± 4.9 min(-1), the Km for ATP by 0.104 ± 0.024 mm, and the Ki for ADP by 0.037 ± 0.007 mm. Without ADP, the Hill coefficient for ATP hydrolysis was extracted to be 1.0 ± 0.1, indicating noncooperative behavior of homo-oligomeric Rca assemblies. However, the addition of ADP was shown to introduce positive cooperativity between two or more subunits (Hill coefficient 1.9 ± 0.2), allowing for regulation via the prevailing ATP/ADP ratio. ADP-mediated activation was not observed, although larger amounts led to competitive product inhibition of hydrolytic activity. The catalytic efficiency increased 8.4-fold upon cooperative binding of a second magnesium ion (Hill coefficient 2.5 ± 0.5), suggesting at least three conformational states (ATP-bound, ADP-bound, and empty) within assemblies containing an average of about six subunits. The addition of excess Rubisco (24:1, L8S8/Rca6) and crowding agents did not modify catalytic rates. However, high magnesium provided for thermal Rca stabilization. We propose that magnesium mediates the formation of closed hexameric toroids capable of high turnover rates and amenable to allosteric regulation. We suggest that in vivo, the Rca hydrolytic activity is tuned by fluctuating [Mg(2+)] in response to changes in available light.
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Affiliation(s)
- Suratna Hazra
- From the Department of Chemistry and Biochemistry and Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, Arizona 85287
| | - J Nathan Henderson
- From the Department of Chemistry and Biochemistry and Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, Arizona 85287
| | - Kevin Liles
- From the Department of Chemistry and Biochemistry and Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, Arizona 85287
| | - Matthew T Hilton
- From the Department of Chemistry and Biochemistry and Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, Arizona 85287
| | - Rebekka M Wachter
- From the Department of Chemistry and Biochemistry and Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, Arizona 85287
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62
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The GroEL-GroES Chaperonin Machine: A Nano-Cage for Protein Folding. Trends Biochem Sci 2015; 41:62-76. [PMID: 26422689 DOI: 10.1016/j.tibs.2015.07.009] [Citation(s) in RCA: 249] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 07/21/2015] [Accepted: 07/31/2015] [Indexed: 01/12/2023]
Abstract
The bacterial chaperonin GroEL and its cofactor GroES constitute the paradigmatic molecular machine of protein folding. GroEL is a large double-ring cylinder with ATPase activity that binds non-native substrate protein (SP) via hydrophobic residues exposed towards the ring center. Binding of the lid-shaped GroES to GroEL displaces the bound protein into an enlarged chamber, allowing folding to occur unimpaired by aggregation. GroES and SP undergo cycles of binding and release, regulated allosterically by the GroEL ATPase. Recent structural and functional studies are providing insights into how the physical environment of the chaperonin cage actively promotes protein folding, in addition to preventing aggregation. Here, we review different models of chaperonin action and discuss issues of current debate.
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63
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Wilson R, Whitney S. Photosynthesis: Getting it together for CO2 fixation. NATURE PLANTS 2015; 1:15130. [PMID: 27250683 DOI: 10.1038/nplants.2015.130] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Affiliation(s)
- Robert Wilson
- Research School of Biology at the Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Spencer Whitney
- Research School of Biology at the Australian National University, Canberra, Australian Capital Territory 2601, Australia
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64
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Hauser T, Bhat JY, Miličić G, Wendler P, Hartl FU, Bracher A, Hayer-Hartl M. Structure and mechanism of the Rubisco-assembly chaperone Raf1. Nat Struct Mol Biol 2015; 22:720-8. [PMID: 26237510 DOI: 10.1038/nsmb.3062] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 07/01/2015] [Indexed: 01/31/2023]
Abstract
Biogenesis of the photosynthetic enzyme Rubisco, a complex of eight large (RbcL) and eight small (RbcS) subunits, requires assembly chaperones. Here we analyzed the role of Rubisco accumulation factor1 (Raf1), a dimer of ∼40-kDa subunits. We find that Raf1 from Synechococcus elongatus acts downstream of chaperonin-assisted RbcL folding by stabilizing RbcL antiparallel dimers for assembly into RbcL8 complexes with four Raf1 dimers bound. Raf1 displacement by RbcS results in holoenzyme formation. Crystal structures show that Raf1 from Arabidopsis thaliana consists of a β-sheet dimerization domain and a flexibly linked α-helical domain. Chemical cross-linking and EM reconstruction indicate that the β-domains bind along the equator of each RbcL2 unit, and the α-helical domains embrace the top and bottom edges of RbcL2. Raf1 fulfills a role similar to that of the assembly chaperone RbcX, thus suggesting that functionally redundant factors ensure efficient Rubisco biogenesis.
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Affiliation(s)
- Thomas Hauser
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Javaid Y Bhat
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Goran Miličić
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Petra Wendler
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Andreas Bracher
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Manajit Hayer-Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
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65
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Hauser T, Popilka L, Hartl FU, Hayer-Hartl M. Role of auxiliary proteins in Rubisco biogenesis and function. NATURE PLANTS 2015; 1:15065. [PMID: 27250005 DOI: 10.1038/nplants.2015.65] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 04/20/2015] [Indexed: 05/05/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyses the conversion of atmospheric CO2 into organic compounds during photosynthesis. Despite its pivotal role in plant metabolism, Rubisco is an inefficient enzyme and has therefore been a key target in bioengineering efforts to improve crop yields. Much has been learnt about the complex cellular machinery involved in Rubisco assembly and metabolic repair over recent years. The simple form of Rubisco found in certain bacteria and dinoflagellates comprises two large subunits, and generally requires the chaperonin system for folding. However, the evolution of hexadecameric Rubisco, which comprises eight large and eight small subunits, from its dimeric precursor has rendered Rubisco in most plants, algae, cyanobacteria and proteobacteria dependent on an array of additional factors. These auxiliary factors include several chaperones for assembly as well as ATPases of the AAA+ family for functional maintenance. An integrated view of the pathways underlying Rubisco biogenesis and repair will pave the way for efforts to improve the enzyme with the goal of increasing crop yields.
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Affiliation(s)
- Thomas Hauser
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Leonhard Popilka
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Manajit Hayer-Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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66
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Cotton CAR, Douglass JS, De Causmaecker S, Brinkert K, Cardona T, Fantuzzi A, Rutherford AW, Murray JW. Photosynthetic constraints on fuel from microbes. Front Bioeng Biotechnol 2015; 3:36. [PMID: 25853129 PMCID: PMC4364286 DOI: 10.3389/fbioe.2015.00036] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 03/04/2015] [Indexed: 01/12/2023] Open
Affiliation(s)
| | | | | | | | - Tanai Cardona
- Department of Life Sciences, Imperial College London , London , UK
| | - Andrea Fantuzzi
- Department of Life Sciences, Imperial College London , London , UK
| | | | - James W Murray
- Department of Life Sciences, Imperial College London , London , UK
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