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Nguyen ND, Pulsford SB, Förster B, Rottet S, Rourke L, Long BM, Price GD. A carboxysome-based CO 2 concentrating mechanism for C 3 crop chloroplasts: advances and the road ahead. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:940-952. [PMID: 38321620 DOI: 10.1111/tpj.16667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/17/2024] [Accepted: 01/24/2024] [Indexed: 02/08/2024]
Abstract
The introduction of the carboxysome-based CO2 concentrating mechanism (CCM) into crop plants has been modelled to significantly increase crop yields. This projection serves as motivation for pursuing this strategy to contribute to global food security. The successful implementation of this engineering challenge is reliant upon the transfer of a microcompartment that encapsulates cyanobacterial Rubisco, known as the carboxysome, alongside active bicarbonate transporters. To date, significant progress has been achieved with respect to understanding various aspects of the cyanobacterial CCM, and more recently, different components of the carboxysome have been successfully introduced into plant chloroplasts. In this Perspective piece, we summarise recent findings and offer new research avenues that will accelerate research in this field to ultimately and successfully introduce the carboxysome into crop plants for increased crop yields.
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Affiliation(s)
- Nghiem D Nguyen
- Plant Science Division, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory, 2601, Australia
| | - Sacha B Pulsford
- Research School of Chemistry, Australian National University, 137 Sullivan's Ck Rd, Acton, Australian Capital Territory, 2601, Australia
| | - Britta Förster
- Plant Science Division, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory, 2601, Australia
| | - Sarah Rottet
- Plant Science Division, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory, 2601, Australia
| | - Loraine Rourke
- Plant Science Division, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory, 2601, Australia
| | - Benedict M Long
- Discipline of Biological Sciences, School of Environmental and Life Sciences, ARC Centre of Excellence in Synthetic Biology, The University of Newcastle, University Drive, Callaghan, New South Wales, 2308, Australia
| | - G Dean Price
- Plant Science Division, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory, 2601, Australia
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2
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Trettel DS, Pacheco SL, Laskie AK, Gonzalez-Esquer CR. Modeling bacterial microcompartment architectures for enhanced cyanobacterial carbon fixation. FRONTIERS IN PLANT SCIENCE 2024; 15:1346759. [PMID: 38425792 PMCID: PMC10902431 DOI: 10.3389/fpls.2024.1346759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024]
Abstract
The carboxysome is a bacterial microcompartment (BMC) which plays a central role in the cyanobacterial CO2-concentrating mechanism. These proteinaceous structures consist of an outer protein shell that partitions Rubisco and carbonic anhydrase from the rest of the cytosol, thereby providing a favorable microenvironment that enhances carbon fixation. The modular nature of carboxysomal architectures makes them attractive for a variety of biotechnological applications such as carbon capture and utilization. In silico approaches, such as molecular dynamics (MD) simulations, can support future carboxysome redesign efforts by providing new spatio-temporal insights on their structure and function beyond in vivo experimental limitations. However, specific computational studies on carboxysomes are limited. Fortunately, all BMC (including the carboxysome) are highly structurally conserved which allows for practical inferences to be made between classes. Here, we review simulations on BMC architectures which shed light on (1) permeation events through the shell and (2) assembly pathways. These models predict the biophysical properties surrounding the central pore in BMC-H shell subunits, which in turn dictate the efficiency of substrate diffusion. Meanwhile, simulations on BMC assembly demonstrate that assembly pathway is largely dictated kinetically by cargo interactions while final morphology is dependent on shell factors. Overall, these findings are contextualized within the wider experimental BMC literature and framed within the opportunities for carboxysome redesign for biomanufacturing and enhanced carbon fixation.
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Affiliation(s)
- Daniel S. Trettel
- Los Alamos National Laboratory, Bioscience Division, Microbial and Biome Sciences Group, Los Alamos, NM, United States
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3
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Toward a glycyl radical enzyme containing synthetic bacterial microcompartment to produce pyruvate from formate and acetate. Proc Natl Acad Sci U S A 2022; 119:2116871119. [PMID: 35193962 PMCID: PMC8872734 DOI: 10.1073/pnas.2116871119] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2022] [Indexed: 12/15/2022] Open
Abstract
The enormous complexity of metabolic pathways, in both their regulation and propensity for metabolite cross-talk, represents a major obstacle for metabolic engineering. Self-assembling, catalytically programmable and genetically transferable bacterial microcompartments (BMCs) offer solutions to decrease this complexity through compartmentalization of enzymes within a selectively permeable protein shell. Synthetic BMCs can operate as autonomous metabolic modules decoupled from the cell’s regulatory network, only interfacing with the cell’s metabolism via the highly engineerable proteinaceous shell. Here, we build a synthetic, modular, multienzyme BMC. It functions not only as a proof-of-concept for next-generation metabolic engineering, but also provides the foundation for subsequent tuning, with the goal to create a microanaerobic environment protecting an oxygen-sensitive reaction in aerobic growth conditions that could be deployed. Formate has great potential to function as a feedstock for biorefineries because it can be sustainably produced by a variety of processes that don’t compete with agricultural production. However, naturally formatotrophic organisms are unsuitable for large-scale cultivation, difficult to engineer, or have inefficient native formate assimilation pathways. Thus, metabolic engineering needs to be developed for model industrial organisms to enable efficient formatotrophic growth. Here, we build a prototype synthetic formate utilizing bacterial microcompartment (sFUT) encapsulating the oxygen-sensitive glycyl radical enzyme pyruvate formate lyase and a phosphate acyltransferase to convert formate and acetyl-phosphate into the central biosynthetic intermediate pyruvate. This metabolic module offers a defined environment with a private cofactor coenzyme A that can cycle efficiently between the encapsulated enzymes. To facilitate initial design-build-test-refine cycles to construct an active metabolic core, we used a “wiffleball” architecture, defined as an icosahedral bacterial microcompartment (BMC) shell with unoccupied pentameric vertices to freely permit substrate and product exchange. The resulting sFUT prototype wiffleball is an active multi enzyme synthetic BMC functioning as platform technology.
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Khan MJ, Singh N, Mishra S, Ahirwar A, Bast F, Varjani S, Schoefs B, Marchand J, Rajendran K, Banu JR, Saratale GD, Saratale RG, Vinayak V. Impact of light on microalgal photosynthetic microbial fuel cells and removal of pollutants by nanoadsorbent biopolymers: Updates, challenges and innovations. CHEMOSPHERE 2022; 288:132589. [PMID: 34678344 DOI: 10.1016/j.chemosphere.2021.132589] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/09/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
Photosynthetic microbial fuel cells (PMFCs) with microalgae have huge potential for treating wastewater while simultaneously converting light energy into electrical energy. The efficiency of such cells directly depends on algal growth, which depends on light intensity. Higher light intensity results in increased potential as well as enhancement in generation of biomass rich in biopolymers. Such biopolymers are produced either by microbes at anode and algae at cathode or vice versa. The biopolymers recovered from these biological sources can be added in wastewater alone or in combination with nanomaterials to act as nanoadsorbents. These nanoadsorbents further increase the efficiency of PMFC by removing the pollutants like metals and dyes. In this review firstly the effect of different light intensities on the growth of microalgae, importance of diatoms in a PMFC and their impact on PMFCs efficiencies have been narrated. Secondly recovery of biopolymers from different biological sources and their role in removal of metals, dyes along with their impact on circular bioeconomy have been discussed. Thereafter bottlenecks and future perspectives in this field of research have been narrated.
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Affiliation(s)
- Mohd Jahir Khan
- Diatom Nanoengineering and Metabolism Laboratory (DNM), School of Applied Science, Dr. HarisinghGour Central University, Sagar, MP, 470003, India
| | - Nikhil Singh
- Diatom Nanoengineering and Metabolism Laboratory (DNM), School of Applied Science, Dr. HarisinghGour Central University, Sagar, MP, 470003, India
| | - Sudhanshu Mishra
- Diatom Nanoengineering and Metabolism Laboratory (DNM), School of Applied Science, Dr. HarisinghGour Central University, Sagar, MP, 470003, India
| | - Ankesh Ahirwar
- Diatom Nanoengineering and Metabolism Laboratory (DNM), School of Applied Science, Dr. HarisinghGour Central University, Sagar, MP, 470003, India
| | - Felix Bast
- Department of Botany, Central University of Punjab, Ghudda-VPO, Bathinda, 151401, Punjab, 151001, India
| | - Sunita Varjani
- Gujarat Pollution Control Board, Gandhinagar, Gujarat, 382010, India.
| | - Benoit Schoefs
- Metabolism, Bioengineering of Microalgal Metabolism and Applications (MIMMA), Mer Molecules Santé, Le Mans University, IUML - FR 3473 CNRS, Le Mans, France
| | - Justine Marchand
- Metabolism, Bioengineering of Microalgal Metabolism and Applications (MIMMA), Mer Molecules Santé, Le Mans University, IUML - FR 3473 CNRS, Le Mans, France
| | - Karthik Rajendran
- Department of Environmental Science, SRM University-AP, Neerukonda, Andhra Pradesh, India
| | - J Rajesh Banu
- Department of Life Science, Central University of Tamilnadu, Thiruvar, 610005, India
| | - Ganesh Dattatraya Saratale
- Department of Food Science and Biotechnology, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggido, 10326, Republic of Korea
| | - Rijuta Ganesh Saratale
- Research Institute of Biotechnology and Medical Converged Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggido, 10326, Republic of Korea
| | - Vandana Vinayak
- Diatom Nanoengineering and Metabolism Laboratory (DNM), School of Applied Science, Dr. HarisinghGour Central University, Sagar, MP, 470003, India.
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5
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Liu LN. Advances in the bacterial organelles for CO 2 fixation. Trends Microbiol 2021; 30:567-580. [PMID: 34802870 DOI: 10.1016/j.tim.2021.10.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 02/08/2023]
Abstract
Carboxysomes are a family of bacterial microcompartments (BMCs), present in all cyanobacteria and some proteobacteria, which encapsulate the primary CO2-fixing enzyme, Rubisco, within a virus-like polyhedral protein shell. Carboxysomes provide significantly elevated levels of CO2 around Rubisco to maximize carboxylation and reduce wasteful photorespiration, thus functioning as the central CO2-fixation organelles of bacterial CO2-concentration mechanisms. Their intriguing architectural features allow carboxysomes to make a vast contribution to carbon assimilation on a global scale. In this review, we discuss recent research progress that provides new insights into the mechanisms of how carboxysomes are assembled and functionally maintained in bacteria and recent advances in synthetic biology to repurpose the metabolic module in diverse applications.
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Affiliation(s)
- Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK; College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 266003 Qingdao, China.
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6
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Borden JS, Savage DF. New discoveries expand possibilities for carboxysome engineering. Curr Opin Microbiol 2021; 61:58-66. [PMID: 33798818 DOI: 10.1016/j.mib.2021.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/06/2021] [Accepted: 03/11/2021] [Indexed: 12/19/2022]
Abstract
Carboxysomes are CO2-fixing protein compartments present in all cyanobacteria and some proteobacteria. These structures are attractive candidates for carbon assimilation bioengineering because they concentrate carbon, allowing the fixation reaction to occur near its maximum rate, and because they self-assemble in diverse organisms with a set of standard biological parts. Recent discoveries have expanded our understanding of how the carboxysome assembles, distributes itself, and sustains its metabolism. These studies have already led to substantial advances in engineering the carboxysome and carbon concentrating mechanism into recombinant organisms, with an eye towards establishing the system in industrial microbes and plants. Future studies may also consider the potential of in vitro carboxysomes for both discovery and applied science.
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Affiliation(s)
- Julia S Borden
- Department of Molecular & Cellular Biology, UC Berkeley, Berkeley, CA 94720, USA
| | - David F Savage
- Department of Molecular & Cellular Biology, UC Berkeley, Berkeley, CA 94720, USA.
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7
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Scaffolding protein CcmM directs multiprotein phase separation in β-carboxysome biogenesis. Nat Struct Mol Biol 2021; 28:909-922. [PMID: 34759380 PMCID: PMC8580825 DOI: 10.1038/s41594-021-00676-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/28/2021] [Indexed: 12/01/2022]
Abstract
Carboxysomes in cyanobacteria enclose the enzymes Rubisco and carbonic anhydrase to optimize photosynthetic carbon fixation. Understanding carboxysome assembly has implications in agricultural biotechnology. Here we analyzed the role of the scaffolding protein CcmM of the β-cyanobacterium Synechococcus elongatus PCC 7942 in sequestrating the hexadecameric Rubisco and the tetrameric carbonic anhydrase, CcaA. We find that the trimeric CcmM, consisting of γCAL oligomerization domains and linked small subunit-like (SSUL) modules, plays a central role in mediation of pre-carboxysome condensate formation through multivalent, cooperative interactions. The γCAL domains interact with the C-terminal tails of the CcaA subunits and additionally mediate a head-to-head association of CcmM trimers. Interestingly, SSUL modules, besides their known function in recruiting Rubisco, also participate in intermolecular interactions with the γCAL domains, providing further valency for network formation. Our findings reveal the mechanism by which CcmM functions as a central organizer of the pre-carboxysome multiprotein matrix, concentrating the core components Rubisco and CcaA before β-carboxysome shell formation.
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8
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Kerfeld CA, Sutter M. Engineered bacterial microcompartments: apps for programming metabolism. Curr Opin Biotechnol 2020; 65:225-232. [PMID: 32554213 PMCID: PMC7719235 DOI: 10.1016/j.copbio.2020.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 12/12/2022]
Abstract
Bacterial Microcompartments (BMCs) are used by diverse bacteria to compartmentalize enzymatic reactions, functioning analogously to the organelles of eukaryotes. The bounding membrane and encapsulated components are composed entirely of protein, which makes them ideal targets for modification by genetic engineering. In contrast to viruses, in which generally only one protein forms the capsid, the shells of BMCs consist of a variety of shell proteins, each a potential unit of selection. Despite their differences in permeability, the shell proteins are surprisingly interchangeable. Recent developments have shown that they are also highly amenable to engineered modifications which poise them for a variety of biotechnological applications. Given their modular structure, with a module defined as a semi-autonomous functional unit, BMCs can be considered apps for programming metabolism that can be de-bugged by adaptive evolution.
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Affiliation(s)
- Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory and Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA; Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory and Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA; Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
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9
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Demchuk AM, Patel TR. The biomedical and bioengineering potential of protein nanocompartments. Biotechnol Adv 2020; 41:107547. [PMID: 32294494 DOI: 10.1016/j.biotechadv.2020.107547] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 03/21/2020] [Accepted: 04/03/2020] [Indexed: 12/18/2022]
Abstract
Protein nanocompartments (PNCs) are self-assembling biological nanocages that can be harnessed as platforms for a wide range of nanobiotechnology applications. The most widely studied examples of PNCs include virus-like particles, bacterial microcompartments, encapsulin nanocompartments, enzyme-derived nanocages (such as lumazine synthase and the E2 component of the pyruvate dehydrogenase complex), ferritins and ferritin homologues, small heat shock proteins, and vault ribonucleoproteins. Structural PNC shell proteins are stable, biocompatible, and tolerant of both interior and exterior chemical or genetic functionalization for use as vaccines, therapeutic delivery vehicles, medical imaging aids, bioreactors, biological control agents, emulsion stabilizers, or scaffolds for biomimetic materials synthesis. This review provides an overview of the recent biomedical and bioengineering advances achieved with PNCs with a particular focus on recombinant PNC derivatives.
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Affiliation(s)
- Aubrey M Demchuk
- Department of Neuroscience, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, Canada.
| | - Trushar R Patel
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, Canada; Department of Microbiology, Immunology and Infectious Diseases, Cumming, School of Medicine, University of Calgary, 2500 University Dr. N.W., Calgary, AB T2N 1N4, Canada; Li Ka Shing Institute of Virology and Discovery Lab, Faculty of Medicine & Dentistry, University of Alberta, 6-010 Katz Center for Health Research, Edmonton, AB T6G 2E1, Canada.
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10
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Lv X, Cui S, Gu Y, Li J, Du G, Liu L. Enzyme Assembly for Compartmentalized Metabolic Flux Control. Metabolites 2020; 10:E125. [PMID: 32224973 PMCID: PMC7241084 DOI: 10.3390/metabo10040125] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/25/2020] [Accepted: 03/25/2020] [Indexed: 11/16/2022] Open
Abstract
Enzyme assembly by ligand binding or physically sequestrating enzymes, substrates, or metabolites into isolated compartments can bring key molecules closer to enhance the flux of a metabolic pathway. The emergence of enzyme assembly has provided both opportunities and challenges for metabolic engineering. At present, with the development of synthetic biology and systems biology, a variety of enzyme assembly strategies have been proposed, from the initial direct enzyme fusion to scaffold-free assembly, as well as artificial scaffolds, such as nucleic acid/protein scaffolds, and even some more complex physical compartments. These assembly strategies have been explored and applied to the synthesis of various important bio-based products, and have achieved different degrees of success. Despite some achievements, enzyme assembly, especially in vivo, still has many problems that have attracted significant attention from researchers. Here, we focus on some selected examples to review recent research on scaffold-free strategies, synthetic artificial scaffolds, and physical compartments for enzyme assembly or pathway sequestration, and we discuss their notable advances. In addition, the potential applications and challenges in the applications are highlighted.
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Affiliation(s)
- Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Shixiu Cui
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yang Gu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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11
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Baers LL, Breckels LM, Mills LA, Gatto L, Deery MJ, Stevens TJ, Howe CJ, Lilley KS, Lea-Smith DJ. Proteome Mapping of a Cyanobacterium Reveals Distinct Compartment Organization and Cell-Dispersed Metabolism. PLANT PHYSIOLOGY 2019; 181:1721-1738. [PMID: 31578229 PMCID: PMC6878006 DOI: 10.1104/pp.19.00897] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 09/11/2019] [Indexed: 05/23/2023]
Abstract
Cyanobacteria are complex prokaryotes, incorporating a Gram-negative cell wall and internal thylakoid membranes (TMs). However, localization of proteins within cyanobacterial cells is poorly understood. Using subcellular fractionation and quantitative proteomics, we produced an extensive subcellular proteome map of an entire cyanobacterial cell, identifying ∼67% of proteins in Synechocystis sp. PCC 6803, ∼1000 more than previous studies. Assigned to six specific subcellular regions were 1,712 proteins. Proteins involved in energy conversion localized to TMs. The majority of transporters, with the exception of a TM-localized copper importer, resided in the plasma membrane (PM). Most metabolic enzymes were soluble, although numerous pathways terminated in the TM (notably those involved in peptidoglycan monomer, NADP+, heme, lipid, and carotenoid biosynthesis) or PM (specifically, those catalyzing lipopolysaccharide, molybdopterin, FAD, and phylloquinol biosynthesis). We also identified the proteins involved in the TM and PM electron transport chains. The majority of ribosomal proteins and enzymes synthesizing the storage compound polyhydroxybuyrate formed distinct clusters within the data, suggesting similar subcellular distributions to one another, as expected for proteins operating within multicomponent structures. Moreover, heterogeneity within membrane regions was observed, indicating further cellular complexity. Cyanobacterial TM protein localization was conserved in Arabidopsis (Arabidopsis thaliana) chloroplasts, suggesting similar proteome organization in more developed photosynthetic organisms. Successful application of this technique in Synechocystis suggests it could be applied to mapping the proteomes of other cyanobacteria and single-celled organisms. The organization of the cyanobacterial cell revealed here substantially aids our understanding of these environmentally and biotechnologically important organisms.
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Affiliation(s)
- Laura L Baers
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Lisa M Breckels
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
- Computational Proteomics Unit, Cambridge Centre for Proteomics, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Lauren A Mills
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Laurent Gatto
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
- Computational Proteomics Unit, Cambridge Centre for Proteomics, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Michael J Deery
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Tim J Stevens
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH United Kingdom
| | - Christopher J Howe
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Kathryn S Lilley
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - David J Lea-Smith
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
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12
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Synthetic biology applied in the agrifood sector: Public perceptions, attitudes and implications for future studies. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.07.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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13
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Long BM, Hee WY, Sharwood RE, Rae BD, Kaines S, Lim YL, Nguyen ND, Massey B, Bala S, von Caemmerer S, Badger MR, Price GD. Carboxysome encapsulation of the CO 2-fixing enzyme Rubisco in tobacco chloroplasts. Nat Commun 2018; 9:3570. [PMID: 30177711 PMCID: PMC6120970 DOI: 10.1038/s41467-018-06044-0] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 08/12/2018] [Indexed: 12/30/2022] Open
Abstract
A long-term strategy to enhance global crop photosynthesis and yield involves the introduction of cyanobacterial CO2-concentrating mechanisms (CCMs) into plant chloroplasts. Cyanobacterial CCMs enable relatively rapid CO2 fixation by elevating intracellular inorganic carbon as bicarbonate, then concentrating it as CO2 around the enzyme Rubisco in specialized protein micro-compartments called carboxysomes. To date, chloroplastic expression of carboxysomes has been elusive, requiring coordinated expression of almost a dozen proteins. Here we successfully produce simplified carboxysomes, isometric with those of the source organism Cyanobium, within tobacco chloroplasts. We replace the endogenous Rubisco large subunit gene with cyanobacterial Form-1A Rubisco large and small subunit genes, along with genes for two key α-carboxysome structural proteins. This minimal gene set produces carboxysomes, which encapsulate the introduced Rubisco and enable autotrophic growth at elevated CO2. This result demonstrates the formation of α-carboxysomes from a reduced gene set, informing the step-wise construction of fully functional α-carboxysomes in chloroplasts.
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Affiliation(s)
- Benedict M Long
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia.
| | - Wei Yih Hee
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
| | - Robert E Sharwood
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, 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, 134 Linnaeus Way, Acton, ACT, 2601, Australia
| | - Sarah Kaines
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
| | - Yi-Leen Lim
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
| | - Nghiem D Nguyen
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
| | - Baxter Massey
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
| | - Soumi Bala
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
| | - Susanne von Caemmerer
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
| | - Murray R Badger
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
| | - G Dean Price
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
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14
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Pouvreau B, Vanhercke T, Singh S. From plant metabolic engineering to plant synthetic biology: The evolution of the design/build/test/learn cycle. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:3-12. [PMID: 29907306 DOI: 10.1016/j.plantsci.2018.03.035] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/19/2018] [Accepted: 03/28/2018] [Indexed: 05/21/2023]
Abstract
Genetic improvement of crops started since the dawn of agriculture and has continuously evolved in parallel with emerging technological innovations. The use of genome engineering in crop improvement has already revolutionised modern agriculture in less than thirty years. Plant metabolic engineering is still at a development stage and faces several challenges, in particular with the time necessary to develop plant based solutions to bio-industrial demands. However the recent success of several metabolic engineering approaches applied to major crops are encouraging and the emerging field of plant synthetic biology offers new opportunities. Some pioneering studies have demonstrated that synthetic genetic circuits or orthogonal metabolic pathways can be introduced into plants to achieve a desired function. The combination of metabolic engineering and synthetic biology is expected to significantly accelerate crop improvement. A defining aspect of both fields is the design/build/test/learn cycle, or the use of iterative rounds of testing modifications to refine hypotheses and develop best solutions. Several technological and technical improvements are now available to make a better use of each design, build, test, and learn components of the cycle. All these advances should facilitate the rapid development of a wide variety of bio-products for a world in need of sustainable solutions.
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Affiliation(s)
- Benjamin Pouvreau
- CSIRO Agriculture and Food, PO Box 1600, Canberra, ACT 2601, Australia.
| | - Thomas Vanhercke
- CSIRO Agriculture and Food, PO Box 1600, Canberra, ACT 2601, Australia
| | - Surinder Singh
- CSIRO Agriculture and Food, PO Box 1600, Canberra, ACT 2601, Australia
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15
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Plegaria JS, Kerfeld CA. Engineering nanoreactors using bacterial microcompartment architectures. Curr Opin Biotechnol 2018; 51:1-7. [PMID: 29035760 PMCID: PMC5899066 DOI: 10.1016/j.copbio.2017.09.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/19/2017] [Indexed: 12/30/2022]
Abstract
Bacterial microcompartments (BMCs) are organelles that encapsulate enzymes involved in CO2 fixation or carbon catabolism in a selectively permeable protein shell. Here, we highlight recent advances in the bioengineering of these protein-based nanoreactors in heterologous systems, including transfer and expression of BMC gene clusters, the production of template empty shells, and the encapsulation of non-native enzymes.
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Affiliation(s)
- Jefferson S Plegaria
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Berkeley Synthetic Biology Institute, Berkeley, CA 94720, USA.
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16
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Jakobson CM, Tullman-Ercek D, Mangan NM. Spatially organizing biochemistry: choosing a strategy to translate synthetic biology to the factory. Sci Rep 2018; 8:8196. [PMID: 29844460 PMCID: PMC5974357 DOI: 10.1038/s41598-018-26399-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 05/09/2018] [Indexed: 12/20/2022] Open
Abstract
Natural biochemical systems are ubiquitously organized both in space and time. Engineering the spatial organization of biochemistry has emerged as a key theme of synthetic biology, with numerous technologies promising improved biosynthetic pathway performance. One strategy, however, may produce disparate results for different biosynthetic pathways. We use a spatially resolved kinetic model to explore this fundamental design choice in systems and synthetic biology. We predict that two example biosynthetic pathways have distinct optimal organization strategies that vary based on pathway-dependent and cell-extrinsic factors. Moreover, we demonstrate that the optimal design varies as a function of kinetic and biophysical properties, as well as culture conditions. Our results suggest that organizing biosynthesis has the potential to substantially improve performance, but that choosing the appropriate strategy is key. The flexible design-space analysis we propose can be adapted to diverse biosynthetic pathways, and lays a foundation to rationally choose organization strategies for biosynthesis.
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Affiliation(s)
- Christopher M Jakobson
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Niall M Mangan
- Department of Engineering Science and Applied Mathematics, Northwestern University, Evanston, IL, 60208, USA.
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17
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Abstract
Bacterial microcompartments (BMCs) are self-assembling organelles that consist of an enzymatic core that is encapsulated by a selectively permeable protein shell. The potential to form BMCs is widespread and found across the kingdom Bacteria. BMCs have crucial roles in carbon dioxide fixation in autotrophs and the catabolism of organic substrates in heterotrophs. They contribute to the metabolic versatility of bacteria, providing a competitive advantage in specific environmental niches. Although BMCs were first visualized more than 60 years ago, it is mainly in the past decade that progress has been made in understanding their metabolic diversity and the structural basis of their assembly and function. This progress has not only heightened our understanding of their role in microbial metabolism but is also beginning to enable their use in a variety of applications in synthetic biology. In this Review, we focus on recent insights into the structure, assembly, diversity and function of BMCs.
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Affiliation(s)
- Cheryl A. Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Clement Aussignargues
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Jan Zarzycki
- Max-Planck-Institute for Terrestrial Microbiology, D-35043, Marburg, Germany
| | - Fei Cai
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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18
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Kerfeld CA. A bioarchitectonic approach to the modular engineering of metabolism. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0387. [PMID: 28808103 DOI: 10.1098/rstb.2016.0387] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2017] [Indexed: 01/13/2023] Open
Abstract
Dissociating the complexity of metabolic processes into modules is a shift in focus from the single gene/gene product to functional and evolutionary units spanning the scale of biological organization. When viewing the levels of biological organization through this conceptual lens, modules are found across the continuum: domains within proteins, co-regulated groups of functionally associated genes, operons, metabolic pathways and (sub)cellular compartments. Combining modules as components or subsystems of a larger system typically leads to increased complexity and the emergence of new functions. By virtue of their potential for 'plug and play' into new contexts, modules can be viewed as units of both evolution and engineering. Through consideration of lessons learned from recent efforts to install new metabolic modules into cells and the emerging understanding of the structure, function and assembly of protein-based organelles, bacterial microcompartments, a structural bioengineering approach is described: one that builds from an architectural vocabulary of protein domains. This bioarchitectonic approach to engineering cellular metabolism can be applied to microbial cell factories, used in the programming of members of synthetic microbial communities or used to attain additional levels of metabolic organization in eukaryotic cells for increasing primary productivity and as the foundation of a green economy.This article is part of the themed issue 'Enhancing photosynthesis in crop plants: targets for improvement'.
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Affiliation(s)
- Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA .,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.,Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA.,Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA 94720, USA
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19
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Fang Y, Huang F, Faulkner M, Jiang Q, Dykes GF, Yang M, Liu LN. Engineering and Modulating Functional Cyanobacterial CO 2-Fixing Organelles. FRONTIERS IN PLANT SCIENCE 2018; 9:739. [PMID: 29922315 PMCID: PMC5996877 DOI: 10.3389/fpls.2018.00739] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/15/2018] [Indexed: 05/12/2023]
Abstract
Bacterial microcompartments (BMCs) are proteinaceous organelles widespread among bacterial phyla and provide a means for compartmentalizing specific metabolic pathways. They sequester catalytic enzymes from the cytoplasm, using an icosahedral proteinaceous shell with selective permeability to metabolic molecules and substrates, to enhance metabolic efficiency. Carboxysomes were the first BMCs discovered and their unprecedented capacity of CO2 fixation allows cyanobacteria to make a significant contribution to global carbon fixation. There is an increasing interest in utilizing synthetic biology to construct synthetic carboxysomes in new hosts, i.e., higher plants, to enhance carbon fixation and productivity. Here, we report the construction of a synthetic operon of the β-carboxysome from the cyanobacterium Synechococcus elongatus PCC7942 to generate functional β-carboxysome-like structures in Escherichia coli. The protein expression, structure, assembly, and activity of synthetic β-carboxysomes were characterized in depth using confocal, electron and atomic force microscopy, proteomics, immunoblot analysis, and enzymatic assays. Furthermore, we examined the in vivo interchangeability of β-carboxysome building blocks with other BMC components. To our knowledge, this is the first production of functional β-carboxysome-like structures in heterologous organisms. It provides important information for the engineering of fully functional carboxysomes and CO2-fixing modules in higher plants. The study strengthens our synthetic biology toolbox for generating BMC-based organelles with tunable activities and new scaffolding biomaterials for metabolic improvement and molecule delivery.
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Zhou J, Meng H, Zhang W, Li Y. Production of Industrial Chemicals from CO 2 by Engineering Cyanobacteria. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1080:97-116. [PMID: 30091093 DOI: 10.1007/978-981-13-0854-3_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
As photosynthetic prokaryotes, cyanobacteria can directly convert CO2 to organic compounds and grow rapidly using sunlight as the sole source of energy. The direct biosynthesis of chemicals from CO2 and sunlight in cyanobacteria is therefore theoretically more attractive than using glucose as carbon source in heterotrophic bacteria. To date, more than 20 different target chemicals have been synthesized from CO2 in cyanobacteria. However, the yield and productivity of the constructed strains is about 100-fold lower than what can be obtained using heterotrophic bacteria, and only a few products reached the gram level. The main bottleneck in optimizing cyanobacterial cell factories is the relative complexity of the metabolism of photoautotrophic bacteria. In heterotrophic bacteria, energy metabolism is integrated with the carbon metabolism, so that glucose can provide both energy and carbon for the synthesis of target chemicals. By contrast, the energy and carbon metabolism of cyanobacteria are separated. First, solar energy is converted into chemical energy and reducing power via the light reactions of photosynthesis. Subsequently, CO2 is reduced to organic compounds using this chemical energy and reducing power. Finally, the reduced CO2 provides the carbon source and chemical energy for the synthesis of target chemicals and cell growth. Consequently, the unique nature of the cyanobacterial energy and carbon metabolism determines the specific metabolic engineering strategies required for these organisms. In this chapter, we will describe the specific characteristics of cyanobacteria regarding their metabolism of carbon and energy, summarize and analyze the specific strategies for the production of chemicals in cyanobacteria, and propose metabolic engineering strategies which may be most suitable for cyanobacteria.
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Affiliation(s)
- Jie Zhou
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hengkai Meng
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Wei Zhang
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yin Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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21
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Rohnke BA, Singh SP, Pattanaik B, Montgomery BL. RcaE-Dependent Regulation of Carboxysome Structural Proteins Has a Central Role in Environmental Determination of Carboxysome Morphology and Abundance in Fremyella diplosiphon. mSphere 2018; 3:e00617-17. [PMID: 29404416 PMCID: PMC5784247 DOI: 10.1128/msphere.00617-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 01/08/2018] [Indexed: 11/20/2022] Open
Abstract
Carboxysomes are central to the carbon dioxide-concentrating mechanism (CCM) and carbon fixation in cyanobacteria. Although the structure is well understood, roles of environmental cues in the synthesis, positioning, and functional tuning of carboxysomes have not been systematically studied. Fremyella diplosiphon is a model cyanobacterium for assessing impacts of environmental light cues on photosynthetic pigmentation and tuning of photosynthetic efficiency during complementary chromatic acclimation (CCA), which is controlled by the photoreceptor RcaE. Given the central role of carboxysomes in photosynthesis, we investigated roles of light-dependent RcaE signaling in carboxysome structure and function. A ΔrcaE mutant exhibits altered carboxysome size and number, ccm gene expression, and carboxysome protein accumulation relative to the wild-type (WT) strain. Several Ccm proteins, including carboxysome shell proteins and core-nucleating factors, overaccumulate in ΔrcaE cells relative to WT cells. Additionally, levels of carboxysome cargo RuBisCO in the ΔrcaE mutant are lower than or unchanged from those in the WT strain. This shift in the ratios of carboxysome shell and nucleating components to the carboxysome cargo appears to drive carboxysome morphology and abundance dynamics. Carboxysomes are also occasionally mislocalized spatially to the periphery of spherical mutants within thylakoid membranes, suggesting that carboxysome positioning is impacted by cell shape. The RcaE photoreceptor links perception of external light cues to regulating carboxysome structure and function and, thus, to the cellular capacity for carbon fixation. IMPORTANCE Carboxysomes are proteinaceous subcellular compartments, or bacterial organelles, found in cyanobacteria that consist of a protein shell surrounding a core primarily composed of the enzyme ribulose-1,5-biphosphate carboxylase/oxygenase (RuBisCO) that is central to the carbon dioxide-concentrating mechanism (CCM) and carbon fixation. Whereas significant insights have been gained regarding the structure and synthesis of carboxysomes, limited attention has been given to how their size, abundance, and protein composition are regulated to ensure optimal carbon fixation in dynamic environments. Given the centrality of carboxysomes in photosynthesis, we provide an analysis of the role of a photoreceptor, RcaE, which functions in matching photosynthetic pigmentation to the external environment during complementary chromatic acclimation and thereby optimizing photosynthetic efficiency, in regulating carboxysome dynamics. Our data highlight a role for RcaE in perceiving external light cues and regulating carboxysome structure and function and, thus, in the cellular capacity for carbon fixation and organismal fitness.
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Affiliation(s)
- Brandon A. Rohnke
- Department of Energy—Plant Research Laboratory, Michigan State University, Plant Biology Laboratories, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Shailendra P. Singh
- Department of Energy—Plant Research Laboratory, Michigan State University, Plant Biology Laboratories, East Lansing, Michigan, USA
| | - Bagmi Pattanaik
- Department of Energy—Plant Research Laboratory, Michigan State University, Plant Biology Laboratories, East Lansing, Michigan, USA
| | - Beronda L. Montgomery
- Department of Energy—Plant Research Laboratory, Michigan State University, Plant Biology Laboratories, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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22
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Mackinder LCM. The Chlamydomonas CO 2 -concentrating mechanism and its potential for engineering photosynthesis in plants. THE NEW PHYTOLOGIST 2018; 217:54-61. [PMID: 28833179 DOI: 10.1111/nph.14749] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/04/2017] [Indexed: 05/19/2023]
Abstract
Contents Summary I. Introduction 54 II. Recent advances in our understanding of the Chlamydomonas CCM 55 III. Current gaps in our understanding of the Chlamydomonas CCM 58 IV. Approaches to rapidly advance our understanding of the Chlamydomonas CCM 58 V. Engineering a CCM into higher plants 58 VI. Conclusion and outlook 59 Acknowledgements 60 References 60 SUMMARY: To meet the food demands of a rising global population, innovative strategies are required to increase crop yields. Improvements in plant photosynthesis by genetic engineering show considerable potential towards this goal. One prospective approach is to introduce a CO2 -concentrating mechanism into crop plants to increase carbon fixation by supplying the central carbon-fixing enzyme, Rubisco, with a higher concentration of its substrate, CO2 . A promising donor organism for the molecular machinery of this mechanism is the eukaryotic alga Chlamydomonas reinhardtii. This review summarizes the recent advances in our understanding of carbon concentration in Chlamydomonas, outlines the most pressing gaps in our knowledge and discusses strategies to transfer a CO2 -concentrating mechanism into higher plants to increase photosynthetic performance.
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23
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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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24
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Faulkner M, Rodriguez-Ramos J, Dykes GF, Owen SV, Casella S, Simpson DM, Beynon RJ, Liu LN. Direct characterization of the native structure and mechanics of cyanobacterial carboxysomes. NANOSCALE 2017; 9:10662-10673. [PMID: 28616951 PMCID: PMC5708340 DOI: 10.1039/c7nr02524f] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Carboxysomes are proteinaceous organelles that play essential roles in enhancing carbon fixation in cyanobacteria and some proteobacteria. These self-assembling organelles encapsulate Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) and carbonic anhydrase using a protein shell structurally resembling an icosahedral viral capsid. The protein shell serves as a physical barrier to protect enzymes from the cytosol and a selectively permeable membrane to mediate transport of enzyme substrates and products. The structural and mechanical nature of native carboxysomes remain unclear. Here, we isolate functional β-carboxysomes from the cyanobacterium Synechococcus elongatus PCC7942 and perform the first characterization of the macromolecular architecture and inherent physical mechanics of single β-carboxysomes using electron microscopy, atomic force microscopy (AFM) and proteomics. Our results illustrate that the intact β-carboxysome comprises three structural domains, a single-layered icosahedral shell, an inner layer and paracrystalline arrays of interior Rubisco. We also observe the protein organization of the shell and partial β-carboxysomes that likely serve as the β-carboxysome assembly intermediates. Furthermore, the topography and intrinsic mechanics of functional β-carboxysomes are determined in native conditions using AFM and AFM-based nanoindentation, revealing the flexible organization and soft mechanical properties of β-carboxysomes compared to rigid viruses. Our study provides new insights into the natural characteristics of β-carboxysome organization and nanomechanics, which can be extended to diverse bacterial microcompartments and are important considerations for the design and engineering of functional carboxysomes in other organisms to supercharge photosynthesis. It offers an approach for inspecting the structural and mechanical features of synthetic metabolic organelles and protein scaffolds in bioengineering.
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Affiliation(s)
- Matthew Faulkner
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | | | - Gregory F Dykes
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Siân V Owen
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Selene Casella
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Deborah M Simpson
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Robert J Beynon
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Lu-Ning Liu
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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25
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Giessen TW, Silver PA. Engineering carbon fixation with artificial protein organelles. Curr Opin Biotechnol 2017; 46:42-50. [DOI: 10.1016/j.copbio.2017.01.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/05/2017] [Indexed: 10/20/2022]
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26
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Young EJ, Burton R, Mahalik JP, Sumpter BG, Fuentes-Cabrera M, Kerfeld CA, Ducat DC. Engineering the Bacterial Microcompartment Domain for Molecular Scaffolding Applications. Front Microbiol 2017; 8:1441. [PMID: 28824573 PMCID: PMC5534457 DOI: 10.3389/fmicb.2017.01441] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 07/17/2017] [Indexed: 01/03/2023] Open
Abstract
As synthetic biology advances the intricacy of engineered biological systems, the importance of spatial organization within the cellular environment must not be marginalized. Increasingly, biological engineers are investigating means to control spatial organization within the cell, mimicking strategies used by natural pathways to increase flux and reduce cross-talk. A modular platform for constructing a diverse set of defined, programmable architectures would greatly assist in improving yields from introduced metabolic pathways and increasing insulation of other heterologous systems. Here, we review recent research on the shell proteins of bacterial microcompartments and discuss their potential application as "building blocks" for a range of customized intracellular scaffolds. We summarize the state of knowledge on the self-assembly of BMC shell proteins and discuss future avenues of research that will be important to realize the potential of BMC shell proteins as predictively assembling and programmable biological materials for bioengineering.
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Affiliation(s)
- Eric J. Young
- Biochemistry and Molecular Biology, Michigan State University, East LansingMI, United States
- MSU-DOE Plant Research Laboratory, East LansingMI, United States
| | - Rodney Burton
- MSU-DOE Plant Research Laboratory, East LansingMI, United States
| | - Jyoti P. Mahalik
- Computational Sciences and Engineering, Oak Ridge National Laboratory, Oak RidgeTN, United States
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak RidgeTN, United States
| | - Bobby G. Sumpter
- Computational Sciences and Engineering, Oak Ridge National Laboratory, Oak RidgeTN, United States
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak RidgeTN, United States
| | - Miguel Fuentes-Cabrera
- Computational Sciences and Engineering, Oak Ridge National Laboratory, Oak RidgeTN, United States
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak RidgeTN, United States
| | - Cheryl A. Kerfeld
- Biochemistry and Molecular Biology, Michigan State University, East LansingMI, United States
- MSU-DOE Plant Research Laboratory, East LansingMI, United States
- Molecular Biophysics and Integrated Bioimaging Division, Berkeley National Laboratory, BerkeleyCA, United States
| | - Daniel C. Ducat
- Biochemistry and Molecular Biology, Michigan State University, East LansingMI, United States
- MSU-DOE Plant Research Laboratory, East LansingMI, United States
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27
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Rae BD, Long BM, Förster B, Nguyen ND, Velanis CN, Atkinson N, Hee WY, Mukherjee B, Price GD, McCormick AJ. Progress and challenges of engineering a biophysical CO2-concentrating mechanism into higher plants. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3717-3737. [PMID: 28444330 DOI: 10.1093/jxb/erx133] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Growth and productivity in important crop plants is limited by the inefficiencies of the C3 photosynthetic pathway. Introducing CO2-concentrating mechanisms (CCMs) into C3 plants could overcome these limitations and lead to increased yields. Many unicellular microautotrophs, such as cyanobacteria and green algae, possess highly efficient biophysical CCMs that increase CO2 concentrations around the primary carboxylase enzyme, Rubisco, to enhance CO2 assimilation rates. Algal and cyanobacterial CCMs utilize distinct molecular components, but share several functional commonalities. Here we outline the recent progress and current challenges of engineering biophysical CCMs into C3 plants. We review the predicted requirements for a functional biophysical CCM based on current knowledge of cyanobacterial and algal CCMs, the molecular engineering tools and research pipelines required to translate our theoretical knowledge into practice, and the current challenges to achieving these goals.
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Affiliation(s)
- Benjamin D Rae
- Australian Research Council Centre of Excellence for Translational Photosynthesis
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton ACT 2601, Australia
| | - Benedict M Long
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton ACT 2601, Australia
| | - Britta Förster
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton ACT 2601, Australia
| | - Nghiem D Nguyen
- Australian Research Council Centre of Excellence for Translational Photosynthesis
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton ACT 2601, Australia
| | - Christos N Velanis
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Nicky Atkinson
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Wei Yih Hee
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton ACT 2601, Australia
| | - Bratati Mukherjee
- Australian Research Council Centre of Excellence for Translational Photosynthesis
- Research School of Biology, The Australian National University, 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, 134 Linnaeus Way, Acton ACT 2601, Australia
| | - Alistair J McCormick
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
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28
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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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Introducing extra NADPH consumption ability significantly increases the photosynthetic efficiency and biomass production of cyanobacteria. Metab Eng 2016; 38:217-227. [PMID: 27497972 DOI: 10.1016/j.ymben.2016.08.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/28/2016] [Accepted: 08/04/2016] [Indexed: 11/20/2022]
Abstract
Increasing photosynthetic efficiency is crucial to increasing biomass production to meet the growing demands for food and energy. Previous theoretical arithmetic analysis suggests that the light reactions and dark reactions are imperfectly coupled due to shortage of ATP supply, or accumulation of NADPH. Here we hypothesized that solely increasing NADPH consumption might improve the coupling of light reactions and dark reactions, thereby increasing the photosynthetic efficiency and biomass production. To test this hypothesis, an NADPH consumption pathway was constructed in cyanobacterium Synechocystis sp. PCC 6803. The resulting extra NADPH-consuming mutant grew much faster and achieved a higher biomass concentration. Analyses of photosynthesis characteristics showed the activities of photosystem II and photosystem I and the light saturation point of the NADPH-consuming mutant all significantly increased. Thus, we demonstrated that introducing extra NADPH consumption ability is a promising strategy to increase photosynthetic efficiency and to enable utilization of high-intensity lights.
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Encapsulation of multiple cargo proteins within recombinant Eut nanocompartments. Appl Microbiol Biotechnol 2016; 100:9187-9200. [PMID: 27450681 DOI: 10.1007/s00253-016-7737-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 07/07/2016] [Accepted: 07/10/2016] [Indexed: 01/08/2023]
Abstract
Spatial organization via encapsulation of enzymes within recombinant nanocompartments may increase efficiency in multienzyme cascades. Previously, we reported the encapsulation of single cargo proteins within nanocompartments in the heterologous host Escherichia coli. This was achieved by coexpression of the Salmonella enterica LT2 ethanolamine utilization bacterial microcompartment shell proteins EutS or EutSMNLK, with a signal sequence EutC1-19 cargo protein fusion. Optimization of this system, leading to the targeting of more than one cargo protein, requires an understanding of the encapsulation mechanism. In this work, we report that the signal sequence EutC1-19 targets cargo to the interior of nanocompartments via a hydrophobic interaction with a helix on shell protein EutS. We confirm that EutC1-19 does not interact with other Eut BMC shell proteins, EutMNLK. Furthermore, we show that a second signal sequence EutE1-21 interacts specifically with the same helix on EutS. Both signal sequences appear to compete for the same EutS helix to simultaneously colocalize two cargo proteins to the interior of recombinant nanocompartments. This work offers the first insights into signal sequence-shell protein interactions required for cargo sequestration within Eut BMCs. It also provides a basis for the future engineering of Eut nanocompartments as a platform for the potential colocalization of multienzyme cascades for synthetic biology applications.
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Erb TJ, Zarzycki J. Biochemical and synthetic biology approaches to improve photosynthetic CO 2-fixation. Curr Opin Chem Biol 2016; 34:72-79. [PMID: 27400232 DOI: 10.1016/j.cbpa.2016.06.026] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 01/08/2023]
Abstract
There is an urgent need to improve agricultural productivity to secure future food and biofuel supply. Here, we summarize current approaches that aim at improving photosynthetic CO2-fixation. We critically review, compare and comment on the four major lines of research towards this aim, which focus on (i) improving RubisCO, the CO2-fixing enzyme in photosynthesis, (ii) implementing CO2-concentrating mechanisms, (iii) establishing synthetic photorespiration bypasses, and (iv) engineering synthetic CO2-fixation pathways.
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Affiliation(s)
- Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Biochemistry & Synthetic Biology of Microbial Metabolism Group, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany; LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, 35043 Marburg, Germany.
| | - Jan Zarzycki
- Max Planck Institute for Terrestrial Microbiology, Biochemistry & Synthetic Biology of Microbial Metabolism Group, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
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Hanson MR, Lin MT, Carmo-Silva AE, Parry MA. Towards engineering carboxysomes into C3 plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:38-50. [PMID: 26867858 PMCID: PMC4970904 DOI: 10.1111/tpj.13139] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 01/29/2016] [Accepted: 02/02/2016] [Indexed: 05/18/2023]
Abstract
Photosynthesis in C3 plants is limited by features of the carbon-fixing enzyme Rubisco, which exhibits a low turnover rate and can react with O2 instead of CO2 , leading to photorespiration. In cyanobacteria, bacterial microcompartments, known as carboxysomes, improve the efficiency of photosynthesis by concentrating CO2 near the enzyme Rubisco. Cyanobacterial Rubisco enzymes are faster than those of C3 plants, though they have lower specificity toward CO2 than the land plant enzyme. Replacement of land plant Rubisco by faster bacterial variants with lower CO2 specificity will improve photosynthesis only if a microcompartment capable of concentrating CO2 can also be installed into the chloroplast. We review current information about cyanobacterial microcompartments and carbon-concentrating mechanisms, plant transformation strategies, replacement of Rubisco in a model C3 plant with cyanobacterial Rubisco and progress toward synthesizing a carboxysome in chloroplasts.
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Affiliation(s)
- Maureen R. Hanson
- Department of Molecular Biology and Genetics, Cornell University, Biotechnology Building, Ithaca, NY 14853 USA
| | - Myat T. Lin
- Department of Molecular Biology and Genetics, Cornell University, Biotechnology Building, Ithaca, NY 14853 USA
| | | | - Martin A.J. Parry
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, United Kingdom
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Gonzalez-Esquer CR, Newnham SE, Kerfeld CA. Bacterial microcompartments as metabolic modules for plant synthetic biology. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:66-75. [PMID: 26991644 DOI: 10.1111/tpj.13166] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 03/04/2016] [Accepted: 03/08/2016] [Indexed: 05/28/2023]
Abstract
Bacterial microcompartments (BMCs) are megadalton-sized protein assemblies that enclose segments of metabolic pathways within cells. They increase the catalytic efficiency of the encapsulated enzymes while sequestering volatile or toxic intermediates from the bulk cytosol. The first BMCs discovered were the carboxysomes of cyanobacteria. Carboxysomes compartmentalize the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) with carbonic anhydrase. They enhance the carboxylase activity of RuBisCO by increasing the local concentration of CO2 in the vicinity of the enzyme's active site. As a metabolic module for carbon fixation, carboxysomes could be transferred to eukaryotic organisms (e.g. plants) to increase photosynthetic efficiency. Within the scope of synthetic biology, carboxysomes and other BMCs hold even greater potential when considered a source of building blocks for the development of nanoreactors or three-dimensional scaffolds to increase the efficiency of either native or heterologously expressed enzymes. The carboxysome serves as an ideal model system for testing approaches to engineering BMCs because their expression in cyanobacteria provides a sensitive screen for form (appearance of polyhedral bodies) and function (ability to grow on air). We recount recent progress in the re-engineering of the carboxysome shell and core to offer a conceptual framework for the development of BMC-based architectures for applications in plant synthetic biology.
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Affiliation(s)
| | - Sarah E Newnham
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Berkeley Synthetic Biology Institute, UC Berkeley, Berkeley, CA, USA
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, USA
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Kerfeld CA, Melnicki MR. Assembly, function and evolution of cyanobacterial carboxysomes. CURRENT OPINION IN PLANT BIOLOGY 2016; 31:66-75. [PMID: 27060669 DOI: 10.1016/j.pbi.2016.03.009] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 05/19/2023]
Abstract
All cyanobacteria contain carboxysomes, RuBisCO-encapsulating bacterial microcompartments that function as prokaryotic organelles. The two carboxysome types, alpha and beta, differ fundamentally in components, assembly, and species distribution. Alpha carboxysomes share a highly-conserved gene organization, with evidence of horizontal gene transfer from chemoautotrophic proteobacteria to the picocyanobacteria, and seem to co-assemble shells concomitantly with aggregation of cargo enzymes. In contrast, beta carboxysomes assemble an enzymatic core first, with an encapsulation peptide playing a critical role in formation of the surrounding shell. Based on similarities in assembly, and phylogenetic analysis of the pentameric shell protein conserved across all bacterial microcompartments, beta carboxysomes appear to be more closely related to the microcompartments of heterotrophic bacteria (metabolosomes) than to alpha carboxysomes, which appear deeply divergent. Beta carboxysomes can be found in the basal cyanobacterial clades that diverged before the ancestor of the chloroplast and have recently been shown to be able to encapsulate functional RuBisCO enzymes resurrected from ancestrally-reconstructed sequences, consistent with an ancient origin. Alpha and beta carboxysomes are not only distinct units of evolution, but are now emerging as genetic/metabolic modules for synthetic biology; heterologous expression and redesign of both the shell and the enzymatic core have recently been achieved.
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Affiliation(s)
- Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Matthew R Melnicki
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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Long BM, Rae BD, Rolland V, Förster B, Price GD. Cyanobacterial CO2-concentrating mechanism components: function and prospects for plant metabolic engineering. CURRENT OPINION IN PLANT BIOLOGY 2016; 31:1-8. [PMID: 26999306 DOI: 10.1016/j.pbi.2016.03.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/25/2016] [Accepted: 03/02/2016] [Indexed: 05/21/2023]
Abstract
Global population growth is projected to outpace plant-breeding improvements in major crop yields within decades. To ensure future food security, multiple creative efforts seek to overcome limitations to crop yield. Perhaps the greatest limitation to increased crop yield is photosynthetic inefficiency, particularly in C3 crop plants. Recently, great strides have been made toward crop improvement by researchers seeking to introduce the cyanobacterial CO2-concentrating mechanism (CCM) into plant chloroplasts. This strategy recognises the C3 chloroplast as lacking a CCM, and being a primordial cyanobacterium at its essence. Hence the collection of solute transporters, enzymes, and physical structures that make cyanobacterial CO2-fixation so efficient are viewed as a natural source of genetic material for C3 chloroplast improvement. Also we highlight recent outstanding research aimed toward the goal of introducing a cyanobacterial CCM into C3 chloroplasts and consider future research directions.
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Affiliation(s)
- Benedict M Long
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia.
| | - Benjamin D Rae
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Vivien Rolland
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Britta Förster
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - G Dean Price
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
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Sun Y, Casella S, Fang Y, Huang F, Faulkner M, Barrett S, Liu LN. Light Modulates the Biosynthesis and Organization of Cyanobacterial Carbon Fixation Machinery through Photosynthetic Electron Flow. PLANT PHYSIOLOGY 2016; 171:530-41. [PMID: 26956667 PMCID: PMC4854705 DOI: 10.1104/pp.16.00107] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 03/06/2016] [Indexed: 05/08/2023]
Abstract
Cyanobacteria have evolved effective adaptive mechanisms to improve photosynthesis and CO2 fixation. The central CO2-fixing machinery is the carboxysome, which is composed of an icosahedral proteinaceous shell encapsulating the key carbon fixation enzyme, Rubisco, in the interior. Controlled biosynthesis and ordered organization of carboxysomes are vital to the CO2-fixing activity of cyanobacterial cells. However, little is known about how carboxysome biosynthesis and spatial positioning are physiologically regulated to adjust to dynamic changes in the environment. Here, we used fluorescence tagging and live-cell confocal fluorescence imaging to explore the biosynthesis and subcellular localization of β-carboxysomes within a model cyanobacterium, Synechococcus elongatus PCC7942, in response to light variation. We demonstrated that β-carboxysome biosynthesis is accelerated in response to increasing light intensity, thereby enhancing the carbon fixation activity of the cell. Inhibition of photosynthetic electron flow impairs the accumulation of carboxysomes, indicating a close coordination between β-carboxysome biogenesis and photosynthetic electron transport. Likewise, the spatial organization of carboxysomes in the cell correlates with the redox state of photosynthetic electron transport chain. This study provides essential knowledge for us to modulate the β-carboxysome biosynthesis and function in cyanobacteria. In translational terms, the knowledge is instrumental for design and synthetic engineering of functional carboxysomes into higher plants to improve photosynthesis performance and CO2 fixation.
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Affiliation(s)
- Yaqi Sun
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom (Y.S., S.C., Y.F., F.H., M.F., L.-N.L.); and Department of Physics, University of Liverpool, Liverpool L69 7ZE, United Kingdom (S.B.)
| | - Selene Casella
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom (Y.S., S.C., Y.F., F.H., M.F., L.-N.L.); and Department of Physics, University of Liverpool, Liverpool L69 7ZE, United Kingdom (S.B.)
| | - Yi Fang
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom (Y.S., S.C., Y.F., F.H., M.F., L.-N.L.); and Department of Physics, University of Liverpool, Liverpool L69 7ZE, United Kingdom (S.B.)
| | - Fang Huang
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom (Y.S., S.C., Y.F., F.H., M.F., L.-N.L.); and Department of Physics, University of Liverpool, Liverpool L69 7ZE, United Kingdom (S.B.)
| | - Matthew Faulkner
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom (Y.S., S.C., Y.F., F.H., M.F., L.-N.L.); and Department of Physics, University of Liverpool, Liverpool L69 7ZE, United Kingdom (S.B.)
| | - Steve Barrett
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom (Y.S., S.C., Y.F., F.H., M.F., L.-N.L.); and Department of Physics, University of Liverpool, Liverpool L69 7ZE, United Kingdom (S.B.)
| | - Lu-Ning Liu
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom (Y.S., S.C., Y.F., F.H., M.F., L.-N.L.); and Department of Physics, University of Liverpool, Liverpool L69 7ZE, United Kingdom (S.B.)
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37
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The Structural Basis of Coenzyme A Recycling in a Bacterial Organelle. PLoS Biol 2016; 14:e1002399. [PMID: 26959993 PMCID: PMC4784909 DOI: 10.1371/journal.pbio.1002399] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 02/03/2016] [Indexed: 12/29/2022] Open
Abstract
Bacterial Microcompartments (BMCs) are proteinaceous organelles that encapsulate critical segments of autotrophic and heterotrophic metabolic pathways; they are functionally diverse and are found across 23 different phyla. The majority of catabolic BMCs (metabolosomes) compartmentalize a common core of enzymes to metabolize compounds via a toxic and/or volatile aldehyde intermediate. The core enzyme phosphotransacylase (PTAC) recycles Coenzyme A and generates an acyl phosphate that can serve as an energy source. The PTAC predominantly associated with metabolosomes (PduL) has no sequence homology to the PTAC ubiquitous among fermentative bacteria (Pta). Here, we report two high-resolution PduL crystal structures with bound substrates. The PduL fold is unrelated to that of Pta; it contains a dimetal active site involved in a catalytic mechanism distinct from that of the housekeeping PTAC. Accordingly, PduL and Pta exemplify functional, but not structural, convergent evolution. The PduL structure, in the context of the catalytic core, completes our understanding of the structural basis of cofactor recycling in the metabolosome lumen. This study describes the structure of a novel phosphotransacylase enzyme that facilitates the recycling of the essential cofactor acetyl-CoA within a bacterial organelle and discusses the properties of the enzyme's active site and how it is packaged into the organelle. In metabolism, molecules with “high-energy” bonds (e.g., ATP and Acetyl~CoA) are critical for both catabolic and anabolic processes. Accordingly, the retention of these bonds during biochemical transformations is incredibly important. The phosphotransacylase (Pta) enzyme catalyzes the conversion between acyl-CoA and acyl-phosphate. This reaction directly links an acyl-CoA with ATP generation via substrate-level phosphorylation, producing short-chain fatty acids (e.g., acetate), and also provides a path for short-chain fatty acids to enter central metabolism. Due to this key function, Pta is conserved across the bacterial kingdom. Recently, a new type of phosphotransacylase was described that shares no evolutionary relation to Pta. This enzyme, PduL, is exclusively associated with organelles called bacterial microcompartments, which are used to catabolize various compounds. Not only does PduL facilitate substrate level phosphorylation, but it also is critical for cofactor recycling within, and product efflux from, the organelle. We solved the structure of this convergent phosphotransacylase and show that it is completely structurally different from Pta, including its active site architecture. We also discuss features of the protein important to its packaging in the organelle.
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Cai F, Bernstein SL, Wilson SC, Kerfeld CA. Production and Characterization of Synthetic Carboxysome Shells with Incorporated Luminal Proteins. PLANT PHYSIOLOGY 2016; 170:1868-77. [PMID: 26792123 PMCID: PMC4775138 DOI: 10.1104/pp.15.01822] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 01/16/2016] [Indexed: 05/19/2023]
Abstract
Spatial segregation of metabolism, such as cellular-localized CO2 fixation in C4 plants or in the cyanobacterial carboxysome, enhances the activity of inefficient enzymes by selectively concentrating them with their substrates. The carboxysome and other bacterial microcompartments (BMCs) have drawn particular attention for bioengineering of nanoreactors because they are self-assembling proteinaceous organelles. All BMCs share an architecturally similar, selectively permeable shell that encapsulates enzymes. Fundamental to engineering carboxysomes and other BMCs for applications in plant synthetic biology and metabolic engineering is understanding the structural determinants of cargo packaging and shell permeability. Here we describe the expression of a synthetic operon in Escherichia coli that produces carboxysome shells. Protein domains native to the carboxysome core were used to encapsulate foreign cargo into the synthetic shells. These synthetic shells can be purified to homogeneity with or without luminal proteins. Our results not only further the understanding of protein-protein interactions governing carboxysome assembly, but also establish a platform to study shell permeability and the structural basis of the function of intact BMC shells both in vivo and in vitro. This system will be especially useful for developing synthetic carboxysomes for plant engineering.
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Affiliation(s)
- Fei Cai
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 (F.C., S.L.B., S.C.W., C.A.K.); Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (F.C., S.L.B., S.C.W., C.A.K.); and MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (C.A.K.)
| | - Susan L Bernstein
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 (F.C., S.L.B., S.C.W., C.A.K.); Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (F.C., S.L.B., S.C.W., C.A.K.); and MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (C.A.K.)
| | - Steven C Wilson
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 (F.C., S.L.B., S.C.W., C.A.K.); Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (F.C., S.L.B., S.C.W., C.A.K.); and MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (C.A.K.)
| | - Cheryl A Kerfeld
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 (F.C., S.L.B., S.C.W., C.A.K.); Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (F.C., S.L.B., S.C.W., C.A.K.); and MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (C.A.K.)
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Cyanobacterial chassis engineering for enhancing production of biofuels and chemicals. Appl Microbiol Biotechnol 2016; 100:3401-13. [DOI: 10.1007/s00253-016-7374-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 01/29/2016] [Accepted: 02/01/2016] [Indexed: 10/22/2022]
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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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41
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Kerfeld CA. Plug-and-play for improving primary productivity. AMERICAN JOURNAL OF BOTANY 2015; 102:1949-1950. [PMID: 26656128 DOI: 10.3732/ajb.1500409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 09/15/2015] [Indexed: 06/05/2023]
Affiliation(s)
- Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720 USA; Department of Plant and Microbial Biology, UC Berkeley, Berkeley, California 94720 USA; and Berkeley Synthetic Biology Institute, Berkeley, California 94720 USA
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42
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Aussignargues C, Paasch BC, Gonzalez-Esquer R, Erbilgin O, Kerfeld CA. Bacterial microcompartment assembly: The key role of encapsulation peptides. Commun Integr Biol 2015; 8:e1039755. [PMID: 26478774 PMCID: PMC4594438 DOI: 10.1080/19420889.2015.1039755] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/03/2015] [Accepted: 04/06/2015] [Indexed: 12/14/2022] Open
Abstract
Bacterial microcompartments (BMCs) are proteinaceous organelles used by a broad range of bacteria to segregate and optimize metabolic reactions. Their functions are diverse, and can be divided into anabolic (carboxysome) and catabolic (metabolosomes) processes, depending on their cargo enzymes. The assembly pathway for the β-carboxysome has been characterized, revealing that biogenesis proceeds from the inside out. The enzymes coalesce into a procarboxysome, followed by encapsulation in a protein shell that is recruited to the procarboxysome by a short (∼17 amino acids) extension on the C-terminus of one of the encapsulated proteins. A similar extension is also found on the N- or C-termini of a subset of metabolosome core enzymes. These encapsulation peptides (EPs) are characterized by a primary structure predicted to form an amphipathic α-helix that interacts with shell proteins. Here, we review the features, function and widespread occurrence of EPs among metabolosomes, and propose an expanded role for EPs in the assembly of diverse BMCs.
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Affiliation(s)
| | - Bradley C Paasch
- DOE Plant Research Laboratory; Michigan State University ; East Lansing, MI USA
| | | | - Onur Erbilgin
- Department of Plant and Microbial Biology; University of California, Berkeley ; Berkeley, CA USA
| | - Cheryl A Kerfeld
- DOE Plant Research Laboratory; Michigan State University ; East Lansing, MI USA ; Department of Plant and Microbial Biology; University of California, Berkeley ; Berkeley, CA USA ; Physical Biosciences Division; Lawrence Berkeley National Laboratory ; Berkeley, CA USA ; Berkeley Synthetic Biology Institute ; Berkeley, CA USA
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