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Muth-Pawlak D, Kakko L, Kallio P, Aro EM. Interplay between photosynthetic electron flux and organic carbon sinks in sucrose-excreting Synechocystis sp. PCC 6803 revealed by omics approaches. Microb Cell Fact 2024; 23:188. [PMID: 38951789 PMCID: PMC11218172 DOI: 10.1186/s12934-024-02462-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/17/2024] [Indexed: 07/03/2024] Open
Abstract
BACKGROUND Advancing the engineering of photosynthesis-based prokaryotic cell factories is important for sustainable chemical production and requires a deep understanding of the interplay between bioenergetic and metabolic pathways. Rearrangements in photosynthetic electron flow to increase the efficient use of the light energy for carbon fixation must be balanced with a strong carbon sink to avoid photoinhibition. In the cyanobacterium Synechocystis sp. PCC 6803, the flavodiiron protein Flv3 functions as an alternative electron acceptor of photosystem I and represents an interesting engineering target for reorganizing electron flow in attempts to enhance photosynthetic CO2 fixation and increase production yield. RESULTS We have shown that inactivation of Flv3 in engineered sucrose-excreting Synechocystis (S02:Δflv3) induces a transition from photoautotrophic sucrose production to mixotrophic growth sustained by sucrose re-uptake and the formation of intracellular carbon sinks such as glycogen and polyhydroxybutyrate. The growth of S02:Δflv3 exceeds that of the sucrose-producing strain (S02) and demonstrates unforeseen proteomic and metabolomic changes over the course of the nine-day cultivation. In the absence of Flv3, a down-regulation of proteins related to photosynthetic light reactions and CO2 assimilation occurred concomitantly with up-regulation of those related to glycolytic pathways, before any differences in sucrose production between S02 and S02:Δflv3 strains were observed. Over time, increased sucrose degradation in S02:Δflv3 led to the upregulation of respiratory pathway components, such as the plastoquinone reductase complexes NDH-11 and NDH-2 and the terminal respiratory oxidases Cyd and Cox, which transfer electrons to O2. While glycolytic metabolism is significantly up-regulated in S02:Δflv3 to provide energy for the cell, the accumulation of intracellular storage compounds and the increase in respiration serve as indirect sinks for photosynthetic electrons. CONCLUSIONS Our results show that the presence of strong carbon sink in the engineered sucrose-producing Synechocystis S02 strain, operating under high light, high CO2 and salt stress, cannot compensate for the lack of Flv3 by directly balancing the light transducing source and carbon fixing sink reactions. Instead, the cells immediately sense the imbalance, leading to extensive reprogramming of cellular bioenergetic, metabolic and ion transport pathways that favor mixotrophic growth rather than enhancing photoautotrophic sucrose production.
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Affiliation(s)
- Dorota Muth-Pawlak
- Department of Life Technologies, Molecular Plant Biology, University of Turku, Turku, FIN-20014, Finland.
| | - Lauri Kakko
- Department of Life Technologies, Molecular Plant Biology, University of Turku, Turku, FIN-20014, Finland
| | - Pauli Kallio
- Department of Life Technologies, Molecular Plant Biology, University of Turku, Turku, FIN-20014, Finland
| | - Eva-Mari Aro
- Department of Life Technologies, Molecular Plant Biology, University of Turku, Turku, FIN-20014, Finland
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2
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Zhai Y, Tong S, Chen L, Zhang Y, Amin FR, Khalid H, Liu F, Duan Y, Chen W, Chen G, Li D. The enhancement of energy supply in syngas-fermenting microorganisms. ENVIRONMENTAL RESEARCH 2024; 252:118813. [PMID: 38574985 DOI: 10.1016/j.envres.2024.118813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024]
Abstract
After the second industrial revolution, social productivity developed rapidly, and the use of fossil fuels such as coal, oil, and natural gas increased greatly in industrial production. The burning of these fossil fuels releases large amounts of greenhouse gases such as CO2, which has caused greenhouse effects and global warming. This has endangered the planet's ecological balance and brought many species, including animals and plants, to the brink of extinction. Thus, it is crucial to address this problem urgently. One potential solution is the use of syngas fermentation with microbial cell factories. This process can produce chemicals beneficial to humans, such as ethanol as a fuel while consuming large quantities of harmful gases, CO and CO2. However, syngas-fermenting microorganisms often face a metabolic energy deficit, resulting in slow cell growth, metabolic disorders, and low product yields. This problem limits the large-scale industrial application of engineered microorganisms. Therefore, it is imperative to address the energy barriers of these microorganisms. This paper provides an overview of the current research progress in addressing energy barriers in bacteria, including the efficient capture of external energy and the regulation of internal energy metabolic flow. Capturing external energy involves summarizing studies on overexpressing natural photosystems and constructing semiartificial photosynthesis systems using photocatalysts. The regulation of internal energy metabolic flows involves two parts: regulating enzymes and metabolic pathways. Finally, the article discusses current challenges and future perspectives, with a focus on achieving both sustainability and profitability in an economical and energy-efficient manner. These advancements can provide a necessary force for the large-scale industrial application of syngas fermentation microbial cell factories.
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Affiliation(s)
- Yida Zhai
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China; Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Sheng Tong
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Limei Chen
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Yuan Zhang
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Farrukh Raza Amin
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Habiba Khalid
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Fuguo Liu
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Yu Duan
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China; Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Wuxi Chen
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China.
| | - Demao Li
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China.
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3
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Artins A, Martins MCM, Meyer C, Fernie AR, Caldana C. Sensing and regulation of C and N metabolism - novel features and mechanisms of the TOR and SnRK1 signaling pathways. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1268-1280. [PMID: 38349940 DOI: 10.1111/tpj.16684] [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: 12/16/2022] [Revised: 01/25/2024] [Accepted: 02/02/2024] [Indexed: 02/15/2024]
Abstract
Carbon (C) and nitrogen (N) metabolisms are tightly integrated to allow proper plant growth and development. Photosynthesis is dependent on N invested in chlorophylls, enzymes, and structural components of the photosynthetic machinery, while N uptake and assimilation rely on ATP, reducing equivalents, and C-skeletons provided by photosynthesis. The direct connection between N availability and photosynthetic efficiency allows the synthesis of precursors for all metabolites and building blocks in plants. Thus, the capacity to sense and respond to sudden changes in C and N availability is crucial for plant survival and is mediated by complex yet efficient signaling pathways such as TARGET OF RAPAMYCIN (TOR) and SUCROSE-NON-FERMENTING-1-RELATED PROTEIN KINASE 1 (SnRK1). In this review, we present recent advances in mechanisms involved in sensing C and N status as well as identifying current gaps in our understanding. We finally attempt to provide new perspectives and hypotheses on the interconnection of diverse signaling pathways that will allow us to understand the integration and orchestration of the major players governing the regulation of the CN balance.
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Affiliation(s)
- Anthony Artins
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Golm, Germany
| | - Marina C M Martins
- in Press - Scientific Consulting and Communication Services, 05089-030, São Paulo, São Paulo, Brazil
| | - Christian Meyer
- Institut Jean-Pierre Bourgin (IJPB), INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Golm, Germany
| | - Camila Caldana
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Golm, Germany
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4
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Karikomi M, Katayama N, Osanai T. Pyruvate kinase 2 from Synechocystis sp. PCC 6803 increased substrate affinity via glucose-6-phosphate and ribose-5-phosphate for phosphoenolpyruvate consumption. PLANT MOLECULAR BIOLOGY 2024; 114:60. [PMID: 38758412 PMCID: PMC11101554 DOI: 10.1007/s11103-023-01401-0] [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: 06/08/2023] [Accepted: 11/30/2023] [Indexed: 05/18/2024]
Abstract
Pyruvate kinase (Pyk, EC 2.7.1.40) is a glycolytic enzyme that generates pyruvate and adenosine triphosphate (ATP) from phosphoenolpyruvate (PEP) and adenosine diphosphate (ADP), respectively. Pyk couples pyruvate and tricarboxylic acid metabolisms. Synechocystis sp. PCC 6803 possesses two pyk genes (encoded pyk1, sll0587 and pyk2, sll1275). A previous study suggested that pyk2 and not pyk1 is essential for cell viability; however, its biochemical analysis is yet to be performed. Herein, we biochemically analyzed Synechocystis Pyk2 (hereafter, SyPyk2). The optimum pH and temperature of SyPyk2 were 7.0 and 55 °C, respectively, and the Km values for PEP and ADP under optimal conditions were 1.5 and 0.053 mM, respectively. SyPyk2 is activated in the presence of glucose-6-phosphate (G6P) and ribose-5-phosphate (R5P); however, it remains unaltered in the presence of adenosine monophosphate (AMP) or fructose-1,6-bisphosphate. These results indicate that SyPyk2 is classified as PykA type rather than PykF, stimulated by sugar monophosphates, such as G6P and R5P, but not by AMP. SyPyk2, considering substrate affinity and effectors, can play pivotal roles in sugar catabolism under nonphotosynthetic conditions.
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Affiliation(s)
- Masahiro Karikomi
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-Ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Noriaki Katayama
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-Ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Takashi Osanai
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-Ku, Kawasaki, Kanagawa, 214-8571, Japan.
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5
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Sendker FL, Lo YK, Heimerl T, Bohn S, Persson LJ, Mais CN, Sadowska W, Paczia N, Nußbaum E, Del Carmen Sánchez Olmos M, Forchhammer K, Schindler D, Erb TJ, Benesch JLP, Marklund EG, Bange G, Schuller JM, Hochberg GKA. Emergence of fractal geometries in the evolution of a metabolic enzyme. Nature 2024; 628:894-900. [PMID: 38600380 PMCID: PMC11041685 DOI: 10.1038/s41586-024-07287-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 03/08/2024] [Indexed: 04/12/2024]
Abstract
Fractals are patterns that are self-similar across multiple length-scales1. Macroscopic fractals are common in nature2-4; however, so far, molecular assembly into fractals is restricted to synthetic systems5-12. Here we report the discovery of a natural protein, citrate synthase from the cyanobacterium Synechococcus elongatus, which self-assembles into Sierpiński triangles. Using cryo-electron microscopy, we reveal how the fractal assembles from a hexameric building block. Although different stimuli modulate the formation of fractal complexes and these complexes can regulate the enzymatic activity of citrate synthase in vitro, the fractal may not serve a physiological function in vivo. We use ancestral sequence reconstruction to retrace how the citrate synthase fractal evolved from non-fractal precursors, and the results suggest it may have emerged as a harmless evolutionary accident. Our findings expand the space of possible protein complexes and demonstrate that intricate and regulatable assemblies can evolve in a single substitution.
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Affiliation(s)
- Franziska L Sendker
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Yat Kei Lo
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Thomas Heimerl
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Stefan Bohn
- Cryo-EM Platform and Institute of Structural Biology, Helmholtz Munich, Neuherberg, Germany
| | - Louise J Persson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | - Wiktoria Sadowska
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Nicole Paczia
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Eva Nußbaum
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, Tübingen, Germany
| | | | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, Tübingen, Germany
| | - Daniel Schindler
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
- MaxGENESYS Biofoundry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Tobias J Erb
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Justin L P Benesch
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Max Planck Fellow Group Molecular Physiology of Microbes, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jan M Schuller
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany.
| | - Georg K A Hochberg
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany.
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6
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Hudson EP. The Calvin Benson cycle in bacteria: New insights from systems biology. Semin Cell Dev Biol 2024; 155:71-83. [PMID: 37002131 DOI: 10.1016/j.semcdb.2023.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/21/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023]
Abstract
The Calvin Benson cycle in phototrophic and chemolithoautotrophic bacteria has ecological and biotechnological importance, which has motivated study of its regulation. I review recent advances in our understanding of how the Calvin Benson cycle is regulated in bacteria and the technologies used to elucidate regulation and modify it, and highlight differences between and photoautotrophic and chemolithoautotrophic models. Systems biology studies have shown that in oxygenic phototrophic bacteria, Calvin Benson cycle enzymes are extensively regulated at post-transcriptional and post-translational levels, with multiple enzyme activities connected to cellular redox status through thioredoxin. In chemolithoautotrophic bacteria, regulation is primarily at the transcriptional level, with effector metabolites transducing cell status, though new methods should now allow facile, proteome-wide exploration of biochemical regulation in these models. A biotechnological objective is to enhance CO2 fixation in the cycle and partition that carbon to a product of interest. Flux control of CO2 fixation is distributed over multiple enzymes, and attempts to modulate gene Calvin cycle gene expression show a robust homeostatic regulation of growth rate, though the synthesis rates of products can be significantly increased. Therefore, de-regulation of cycle enzymes through protein engineering may be necessary to increase fluxes. Non-canonical Calvin Benson cycles, if implemented with synthetic biology, could have reduced energy demand and enzyme loading, thus increasing the attractiveness of these bacteria for industrial applications.
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Affiliation(s)
- Elton P Hudson
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.
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7
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Santos-Merino M, Sakkos JK, Singh AK, Ducat DC. Coordination of carbon partitioning and photosynthesis by a two-component signaling network in Synechococcus elongatus PCC 7942. Metab Eng 2024; 81:38-52. [PMID: 37925065 DOI: 10.1016/j.ymben.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/26/2023] [Accepted: 11/02/2023] [Indexed: 11/06/2023]
Abstract
Photosynthetic organisms need to balance the rate of photosynthesis with the utilization of photosynthetic products by downstream reactions. While such "source/sink" pathways are well-interrogated in plants, analogous regulatory systems are unknown or poorly studied in single-celled algal and cyanobacterial species. Towards the identification of energy/sugar sensors in cyanobacteria, we utilized an engineered strain of Synechococcus elongatus PCC 7942 that allows experimental manipulation of carbon status. We conducted a screening of all two-component systems (TCS) and serine/threonine kinases (STKs) encoded in S. elongatus PCC 7942 by analyzing phenotypes consistent with sucrose-induced relaxation of sink inhibition. We narrowed the candidate sensor proteins by analyzing changes observed after sucrose feeding. We show that a clustered TCS network containing RpaA, CikB, ManS and NblS are involved in the regulation of genes related to photosynthesis, pigment synthesis, and Rubisco concentration in response to sucrose. Altogether, these results highlight a regulatory TCS group that may play under-appreciated functions in carbon partitioning and energy balancing in cyanobacteria.
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Affiliation(s)
- María Santos-Merino
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, United States
| | - Jonathan K Sakkos
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, United States
| | - Amit K Singh
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, United States
| | - Daniel C Ducat
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, United States; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, United States.
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8
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Lu KJ, Chang CW, Wang CH, Chen FYH, Huang IY, Huang PH, Yang CH, Wu HY, Wu WJ, Hsu KC, Ho MC, Tsai MD, Liao JC. An ATP-sensitive phosphoketolase regulates carbon fixation in cyanobacteria. Nat Metab 2023; 5:1111-1126. [PMID: 37349485 PMCID: PMC10365998 DOI: 10.1038/s42255-023-00831-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/25/2023] [Indexed: 06/24/2023]
Abstract
Regulation of CO2 fixation in cyanobacteria is important both for the organism and global carbon balance. Here we show that phosphoketolase in Synechococcus elongatus PCC7942 (SeXPK) possesses a distinct ATP-sensing mechanism, where a drop in ATP level allows SeXPK to divert precursors of the RuBisCO substrate away from the Calvin-Benson-Bassham cycle. Deleting the SeXPK gene increased CO2 fixation particularly during light-dark transitions. In high-density cultures, the Δxpk strain showed a 60% increase in carbon fixation and unexpectedly resulted in sucrose secretion without any pathway engineering. Using cryo-EM analysis, we discovered that these functions were enabled by a unique allosteric regulatory site involving two subunits jointly binding two ATP, which constantly suppresses the activity of SeXPK until the ATP level drops. This magnesium-independent ATP allosteric site is present in many species across all three domains of life, where it may also play important regulatory functions.
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Affiliation(s)
- Kuan-Jen Lu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chiung-Wen Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chun-Hsiung Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | | | - Irene Y Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Pin-Hsuan Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Cheng-Han Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Hsiang-Yi Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Wen-Jin Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Kai-Cheng Hsu
- Graduate Institute of Cancer Biology and Drug Discovery, Taipei Medical University, Taipei, Taiwan
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.
| | - James C Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
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9
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Cipriano R, Martins JPR, Conde LT, da Silva MM, Silva DM, Gontijo ABPL, Falqueto AR. Anatomical and physiological responses of Aechmea blanchetiana (Bromeliaceae) induced by silicon and sodium chloride stress during in vitro culture. PeerJ 2023; 11:e14624. [PMID: 36647445 PMCID: PMC9840392 DOI: 10.7717/peerj.14624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 12/02/2022] [Indexed: 01/12/2023] Open
Abstract
Salt stress is one of the most severe abiotic stresses affecting plant growth and development. The application of silicon (Si) is an alternative that can increase the tolerance of plants to various types of biotic and abiotic stresses. The objective was to evaluate salt stress's effect in vitro and Si's mitigation potential on Aechmea blanchetiana plants. For this purpose, plants already established in vitro were transferred to a culture medium with 0 or 14 µM of Si (CaSiO3). After growth for 30 days, a stationary liquid medium containing different concentrations of NaCl (0, 100, 200, or 300 µM) was added to the flasks. Anatomical and physiological analyses were performed after growth for 45 days. The plants cultivated with excess NaCl presented reduced root diameter and effective photochemical quantum yield of photosystem II (PSII) (ΦPSII) and increased non-photochemical dissipation of fluorescence (qN). Plants that grew with the presence of Si also had greater content of photosynthetic pigments and activity of the enzymes of the antioxidant system, as well as higher values of maximum quantum yield of PSII (FV/FM), photochemical dissipation coefficient of fluorescence (qP) and fresh weight bioaccumulation of roots and shoots. The anatomical, physiological and biochemical responses, and growth induced by Si mitigated the effect of salt stress on the A. blanchetiana plants cultivated in vitro, which can be partly explained by the tolerance of this species to grow in sandbank (Restinga) areas.
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Affiliation(s)
- Rosiane Cipriano
- Plant Ecophysiology Laboratory, Federal University of Espírito Santo, São Mateus, Espírito Santo, Brazil,Plant Tissue Culture Laboratory, Federal University of Espírito Santo, São Mateus, Espírito Santo, Brazil
| | | | - Lorenzo Toscano Conde
- Plant Tissue Culture Laboratory, Federal University of Espírito Santo, São Mateus, Espírito Santo, Brazil
| | - Mariela Mattos da Silva
- Center for the Study of Photosynthesis, Federal University of Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Diolina Moura Silva
- Center for the Study of Photosynthesis, Federal University of Espírito Santo, Vitória, Espírito Santo, Brazil
| | | | - Antelmo Ralph Falqueto
- Plant Ecophysiology Laboratory, Federal University of Espírito Santo, São Mateus, Espírito Santo, Brazil
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10
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Babele PK, Srivastava A, Selim KA, Kumar A. Millet-inspired systems metabolic engineering of NUE in crops. Trends Biotechnol 2022; 41:701-713. [PMID: 36566140 DOI: 10.1016/j.tibtech.2022.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/20/2022] [Accepted: 10/27/2022] [Indexed: 12/24/2022]
Abstract
The use of nitrogen (N) fertilizers in agriculture has a great ability to increase crop productivity. However, their excessive use has detrimental effects on the environment. Therefore, it is necessary to develop crop varieties with improved nitrogen use efficiency (NUE) that require less N but have substantial yields. Orphan crops such as millets are cultivated in limited regions and are well adapted to lower input conditions. Therefore, they serve as a rich source of beneficial traits that can be transferred into major crops to improve their NUE. This review highlights the tremendous potential of systems biology to unravel the enzymes and pathways involved in the N metabolism of millets, which can open new possibilities to generate transgenic crops with improved NUE.
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Affiliation(s)
- Piyoosh K Babele
- Rani Lakshmi Bai Central Agricultural University, Jhansi 284003, Uttar Pradesh, India.
| | - Amit Srivastava
- University of Jyväskylä, Nanoscience Centre, Department of Biological and Environmental Science, 40014 Jyväskylä, Finland
| | - Khaled A Selim
- Organismic Interactions Department, Interfaculty Institute for Microbiology and Infection Medicine, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Anil Kumar
- Rani Lakshmi Bai Central Agricultural University, Jhansi 284003, Uttar Pradesh, India
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11
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Pichaiyotinkul P, Ruankaew N, Incharoensakdi A, Monshupanee T. Enhanced polyglucan contents in divergent cyanobacteria under nutrient-deprived photoautotrophy: transcriptional and metabolic changes in response to increased glycogen accumulation in nitrogen-deprived Synechocystis sp. PCC 6803. World J Microbiol Biotechnol 2022; 39:27. [PMID: 36437374 DOI: 10.1007/s11274-022-03476-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 11/17/2022] [Indexed: 11/29/2022]
Abstract
Cyanobacteria accumulate polyglucan as main carbohydrate storage. Here, the cellular polyglucan content was determined in 27 cyanobacterial strains from 25 genera. The polyglucan contents were significantly enhanced in 20 and 23 strains under nitrogen (-N) and phosphate (-P) deprivation, respectively. High polyglucan accumulation was not associated with particular evolutionary groups but was strain specific. The highest polyglucan accumulations of 46.2% and 52.5% (w/w dry weight; DW) were obtained under -N in Synechocystis sp. PCC 6803 (hereafter Synechocystis) and Chroococcus limneticus, respectively. In Synechocystis, 80-97% (w/w) of the polyglucan was glycogen. Transcriptome and metabolome analyses during glycogen accumulation under -N were determined in Synechocystis. The genes responsible for the supply of the substrates for glycogen synthesis: glycerate-1,3-phosphate and fructose-1,6-phosphate, were significantly up-regulated. The genes encoding the enzymes converting succinate to malate in TCA cycle, were significantly down-regulated. The genes encoding the regulator proteins which inhibits metabolism at lower part of glycolysis pathway, were also significantly up-regulated. The transcript levels of PII protein and the level of 2-oxoglutarate, which form a complex that inhibits lower part of glycolysis pathway, were significantly increased. Thus, the increased Synechocystis glycogen accumulation under -N was likely to be mediated by the increased supply of glycogen synthesis substrates and metabolic inhibitions at lower part of glycolysis pathway and TCA cycle.
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Affiliation(s)
| | - Nathanich Ruankaew
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, 10330, Bangkok, Thailand
| | - Aran Incharoensakdi
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, 10330, Bangkok, Thailand.,Academy of Science, Royal Society of Thailand, 10300, Bangkok, Thailand
| | - Tanakarn Monshupanee
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, 10330, Bangkok, Thailand.
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12
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Iskhakova ZI, Zhuravleva DE, Heim C, Hartmann MD, Laykov AV, Forchhammer K, Kayumov AR. PotN represents a novel energy‐state sensing PII subfamily, occurring in firmicutes. FEBS J 2022; 289:5305-5321. [DOI: 10.1111/febs.16431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 02/19/2022] [Accepted: 03/10/2022] [Indexed: 01/19/2023]
Affiliation(s)
| | | | - Christopher Heim
- Department of Protein Evolution Max Planck Institute for Developmental Biology Tübingen Germany
| | - Marcus D. Hartmann
- Department of Protein Evolution Max Planck Institute for Developmental Biology Tübingen Germany
| | | | - Karl Forchhammer
- Institut für Mikrobiologie Eberhard‐Karls‐Universität Tübingen Germany
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13
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New views on PII signaling: from nitrogen sensing to global metabolic control. Trends Microbiol 2022; 30:722-735. [DOI: 10.1016/j.tim.2021.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 11/20/2022]
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14
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Andrews F, Faulkner M, Toogood HS, Scrutton NS. Combinatorial use of environmental stresses and genetic engineering to increase ethanol titres in cyanobacteria. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:240. [PMID: 34920731 PMCID: PMC8684110 DOI: 10.1186/s13068-021-02091-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/05/2021] [Indexed: 06/07/2023]
Abstract
Current industrial bioethanol production by yeast through fermentation generates carbon dioxide. Carbon neutral bioethanol production by cyanobacteria uses biological fixation (photosynthesis) of carbon dioxide or other waste inorganic carbon sources, whilst being sustainable and renewable. The first ethanologenic cyanobacterial process was developed over two decades ago using Synechococcus elongatus PCC 7942, by incorporating the recombinant pdc and adh genes from Zymomonas mobilis. Further engineering has increased bioethanol titres 24-fold, yet current levels are far below what is required for industrial application. At the heart of the problem is that the rate of carbon fixation cannot be drastically accelerated and carbon partitioning towards bioethanol production impacts on cell fitness. Key progress has been achieved by increasing the precursor pyruvate levels intracellularly, upregulating synthetic genes and knocking out pathways competing for pyruvate. Studies have shown that cyanobacteria accumulate high proportions of carbon reserves that are mobilised under specific environmental stresses or through pathway engineering to increase ethanol production. When used in conjunction with specific genetic knockouts, they supply significantly more carbon for ethanol production. This review will discuss the progress in generating ethanologenic cyanobacteria through chassis engineering, and exploring the impact of environmental stresses on increasing carbon flux towards ethanol production.
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Affiliation(s)
- Fraser Andrews
- EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN, UK
| | - Matthew Faulkner
- EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN, UK
| | - Helen S Toogood
- EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN, UK
| | - Nigel S Scrutton
- EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN, UK.
- C3 Biotechnologies Ltd, 20 Mannin Way, Lancaster Business Park, Caton Road, Lancaster, LA1 3SW, Lancashire, UK.
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15
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Prediction of Genes That Function in Methanogenesis and CO 2 Pathways in Extremophiles. Microorganisms 2021; 9:microorganisms9112211. [PMID: 34835337 PMCID: PMC8621995 DOI: 10.3390/microorganisms9112211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 12/04/2022] Open
Abstract
Gaet’ale (GAL) and Mud’ara (MUP) are two hypersaline ponds located in the Danakil Depression recharged by underground water from the surrounding highlands. These two ponds have different pH, salinity, and show variation in the concentration of many ionic components. Metagenomic analysis concludes that GAL is dominated by bacteria as in the case of the other hypersaline and acidic ponds in the Danakil Depression. However, Archaea dominated the ponds of MUP. In the current study, the application of SEED and KEGG helped to map the ordered steps of specific enzyme catalyzed reaction in converting CO2 into cell products. We predict that highly efficient and light-independent carbon fixation involving phosphoenolpyruvate carboxylase takes place in MUP. On the contrary, genes encoding enzymes involved in hydrogenotrophic and acetoclastic methanogenesis appeared solely in ponds of GAL, implying the biological source of the hazardous methane gas in that environment. Based on the investigation of the sources of the genes of interest, it is clear that cooperative interactions between members of the two communities and syntrophic metabolism is the main strategy adapted to utilize inorganic carbon as a carbon source in both MUP and GAL. This insight can be used to design biotechnological applications of microbial communities in production of methane biogas or to minimize CO2 emissions.
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16
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Kallio P, Kugler A, Pyytövaara S, Stensjö K, Allahverdiyeva Y, Gao X, Lindblad P, Lindberg P. Photoautotrophic production of renewable ethylene by engineered cyanobacteria: Steering the cell metabolism towards biotechnological use. PHYSIOLOGIA PLANTARUM 2021; 173:579-590. [PMID: 33864400 DOI: 10.1111/ppl.13430] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/05/2021] [Accepted: 04/13/2021] [Indexed: 06/12/2023]
Abstract
Ethylene is a volatile hydrocarbon with a massive global market in the plastic industry. The ethylene now used for commercial applications is produced exclusively from nonrenewable petroleum sources, while competitive biotechnological production systems do not yet exist. This review focuses on the currently developed photoautotrophic bioproduction strategies that enable direct solar-driven conversion of CO2 into ethylene, based on the use of genetically engineered photosynthetic cyanobacteria expressing heterologous ethylene forming enzyme (EFE) from Pseudomonas syringae. The emphasis is on the different engineering strategies to express EFE and to direct the cellular carbon flux towards the primary metabolite 2-oxoglutarate, highlighting associated metabolic constraints, and technical considerations on cultivation strategies and conditional parameters. While the research field has progressed towards more robust strains with better production profiles, and deeper understanding of the associated metabolic limitations, it is clear that there is room for significant improvement to reach industrial relevance. At the same time, existing information and the development of synthetic biology tools for engineering cyanobacteria open new possibilities for improving the prospects for the sustainable production of renewable ethylene.
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Affiliation(s)
- Pauli Kallio
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, Finland
| | - Amit Kugler
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Uppsala, Sweden
| | - Samuli Pyytövaara
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, Finland
| | - Karin Stensjö
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Uppsala, Sweden
| | - Yagut Allahverdiyeva
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, Finland
| | - Xiang Gao
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Uppsala, Sweden
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Uppsala, Sweden
| | - Pia Lindberg
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Uppsala, Sweden
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17
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Orthwein T, Huergo LF, Forchhammer K, Selim KA. Kinetic Analysis of a Protein-protein Complex to Determine its Dissociation Constant (K D) and the Effective Concentration (EC 50) of an Interplaying Effector Molecule Using Bio-layer Interferometry. Bio Protoc 2021; 11:e4152. [PMID: 34604457 DOI: 10.21769/bioprotoc.4152] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/07/2021] [Accepted: 06/21/2021] [Indexed: 11/02/2022] Open
Abstract
Biolayer interferometry (BLI) is an emerging analytical tool that allows the study of protein complexes in real time to determine protein complex kinetic parameters. This article describes a protocol to determine the KD of a protein complex using a 6×His tagged fusion protein as bait immobilized on the NTA sensor chip of the FortéBio® Octet K2 System (Sartorius). We also describe how to determine the half maximal effective concentration (EC50, also known as IC50 for inhibiting effectors) of a metabolite. The complete protocol allows the determination of protein complex KD and small molecular effector EC50 within 8 h, measured in triplicates. Graphic abstract: Principle of the Biolayer interferometry measurement. (Middle, top) Exemplary result of the BLI measurement using Octet® (Raw Data). Wavelength shift (Δλ) against time. (A) Baseline 1. Baseline measurement. When the sensor is equilibrated in the kinetics buffer. The light is reflected with no difference. (B) Load. The his-tagged proteins (ligand) are loaded onto the sensor surface. The light is reflected with a shift of the wavelength. (C) Baseline 2. The loaded sensor is equilibrated in the kinetics buffer. No further wavelength shift appears. (D) Association. The loaded sensor is dipped into the analyte solution. The analyte binds to the immobilized ligand along with an increased wavelength shift. (E) Dissociation. Afterward, the sensor is dipped again into the kinetics buffer without the analyte. Some analyte molecules dissociate. The wavelength shift decreases. (Subfigures A-E) The left side shows the position of the sensor during the measurement seen in the representative BLI measurement, marked with the figure label. The right side shows the light path in the sensor. Black waves represent the light emitted to the sensor surface. The red waves show the light reflected from the sensor surface back to the detector.
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Affiliation(s)
- Tim Orthwein
- Organismic Interactions Department, Interfaculty Institute for Microbiology and Infection Medicine, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Luciano F Huergo
- Setor Litoral, Federal University of Paraná (UFPR), Matinhos, Brazil
| | - Karl Forchhammer
- Organismic Interactions Department, Interfaculty Institute for Microbiology and Infection Medicine, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Khaled A Selim
- Organismic Interactions Department, Interfaculty Institute for Microbiology and Infection Medicine, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Pharmaceutical and Drug Industries Research Division, National Research Center, Giza, Egypt
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18
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The Oxoglutarate Binding Site and Regulatory Mechanism Are Conserved in Ammonium Transporter Inhibitors GlnKs from Methanococcales. Int J Mol Sci 2021; 22:ijms22168631. [PMID: 34445335 PMCID: PMC8395244 DOI: 10.3390/ijms22168631] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022] Open
Abstract
Protein inhibition is a natural regulatory process to control cellular metabolic fluxes. PII-family signal-transducing effectors are in this matter key regulators of the nitrogen metabolism. Their interaction with their various targets is governed by the cellular nitrogen level and the energy charge. Structural studies on GlnK, a PII-family inhibitor of the ammonium transporters (Amt), showed that the T-loops responsible for channel obstruction are displaced upon the binding of 2-oxoglutarate, magnesium and ATP in a conserved cleft. However, GlnK from Methanocaldococcus jannaschii was shown to bind 2-oxoglutarate on the tip of its T-loop, causing a moderate disruption to GlnK-Amt interaction, raising the question if methanogenic archaea use a singular adaptive strategy. Here we show that membrane fractions of Methanothermococcus thermolithotrophicus released GlnKs only in the presence of Mg-ATP and 2-oxoglutarate. This observation led us to structurally characterize the two GlnK isoforms apo or in complex with ligands. Together, our results show that the 2-oxoglutarate binding interface is conserved in GlnKs from Methanococcales, including Methanocaldococcus jannaschii, emphasizing the importance of a free carboxy-terminal group to facilitate ligand binding and to provoke the shift of the T-loop positions.
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19
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Spät P, Barske T, Maček B, Hagemann M. Alterations in the CO 2 availability induce alterations in the phosphoproteome of the cyanobacterium Synechocystis sp. PCC 6803. THE NEW PHYTOLOGIST 2021; 231:1123-1137. [PMID: 34058021 DOI: 10.1111/nph.17423] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 04/16/2021] [Indexed: 06/12/2023]
Abstract
Cyanobacteria are the only prokaryotes that perform plant-like oxygenic photosynthesis. They evolved an inorganic carbon-concentrating mechanism to adapt to low CO2 conditions. Quantitative phosphoproteomics was applied to analyze regulatory features during the acclimation to low CO2 conditions in the model cyanobacterium Synechocystis sp. PCC 6803. Overall, more than 2500 proteins were quantified, equivalent to c. 70% of the Synechocystis theoretical proteome. Proteins with changing abundances correlated largely with mRNA expression levels. Functional annotation of the noncorrelating proteins revealed an enrichment of key metabolic processes fundamental for maintaining cellular homeostasis. Furthermore, 105 phosphoproteins harboring over 200 site-specific phosphorylation events were identified. Subunits of the bicarbonate transporter BCT1 and the redox switch protein CP12 were among phosphoproteins with reduced phosphorylation levels at lower CO2 , whereas the serine/threonine protein kinase SpkC revealed increased phosphorylation levels. The corresponding ΔspkC mutant was characterized and showed decreased ability to acclimate to low CO2 conditions. Possible phosphorylation targets of SpkC including a BCT1 subunit were identified by phosphoproteomics. Collectively, our study highlights the importance of posttranscriptional regulation of protein abundances as well as posttranslational regulation by protein phosphorylation for the successful acclimation towards low CO2 conditions in Synechocystis and possibly among cyanobacteria.
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Affiliation(s)
- Philipp Spät
- Department of Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, D-72076, Germany
- Department of Quantitative Proteomics, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, D-72076, Germany
| | - Thomas Barske
- Department of Plant Physiology, Institute of Biosciences, University of Rostock, Rostock, D-18059, Germany
| | - Boris Maček
- Department of Quantitative Proteomics, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, D-72076, Germany
| | - Martin Hagemann
- Department of Plant Physiology, Institute of Biosciences, University of Rostock, Rostock, D-18059, Germany
- Department Life, Light and Matter, Interdisciplinary Faculty, University of Rostock, Rostock, D-18059, Germany
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20
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The novel P II-interactor PirC identifies phosphoglycerate mutase as key control point of carbon storage metabolism in cyanobacteria. Proc Natl Acad Sci U S A 2021; 118:2019988118. [PMID: 33526690 PMCID: PMC8018021 DOI: 10.1073/pnas.2019988118] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nitrogen limitation imposes a major transition in the lifestyle of nondiazotrophic cyanobacteria that is controlled by a complex interplay of regulatory factors involving the pervasive signal processor PII Immediately upon nitrogen limitation, newly fixed carbon is redirected toward glycogen synthesis. How the metabolic switch for diverting fixed carbon toward the synthesis of glycogen or of cellular building blocks is operated was so far poorly understood. Here, using the nondiazotrophic cyanobacterium Synechocystis sp. PCC 6803 as model system, we identified a novel PII interactor, the product of the sll0944 gene, which we named PirC. We show that PirC binds to and inhibits the activity of 2,3-phosphoglycerate-independent phosphoglycerate mutase (PGAM), the enzyme that deviates newly fixed CO2 toward lower glycolysis. The binding of PirC to either PII or PGAM is tuned by the metabolite 2-oxoglutarate (2-OG), which accumulates upon nitrogen starvation. In these conditions, the high levels of 2-OG dissociate the PirC-PII complex to promote PirC binding to and inhibition of PGAM. Accordingly, a PirC-deficient mutant showed strongly reduced glycogen levels upon nitrogen deprivation, whereas polyhydroxybutyrate granules were overaccumulated compared to wild-type. Metabolome analysis revealed an imbalance in 3-phosphoglycerate to pyruvate levels in the pirC mutant, confirming that PirC controls the carbon flux in cyanobacteria via mutually exclusive interaction with either PII or PGAM.
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21
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Split NanoLuc technology allows quantitation of interactions between PII protein and its receptors with unprecedented sensitivity and reveals transient interactions. Sci Rep 2021; 11:12535. [PMID: 34131190 PMCID: PMC8206089 DOI: 10.1038/s41598-021-91856-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/24/2021] [Indexed: 11/08/2022] Open
Abstract
PII proteins constitute a widespread signal transduction superfamily in the prokaryotic world. The canonical PII signal proteins sense metabolic state of the cells by binding the metabolite molecules ATP, ADP and 2-oxoglutarate. Depending on bound effector molecule, PII proteins interact with and modulate the activity of multiple target proteins. To investigate the complexity of interactions of PII with target proteins, analytical methods that do not disrupt the native cellular context are required. To this purpose, split luciferase proteins have been used to develop a novel complementation reporter called NanoLuc Binary Technology (NanoBiT). The luciferase NanoLuc is divided in two subunits: a 18 kDa polypeptide termed "Large BiT" and a 1.3 kDa peptide termed "Small BiT", which only weakly associate. When fused to proteins of interest, they reconstitute an active luciferase when the proteins of interest interact. Therefore, we set out to develop a new NanoBiT sensor based on the interaction of PII protein from Synechocystis sp. PCC6803 with PII-interacting protein X (PipX) and N-acetyl-L-glutamate kinase (NAGK). The novel NanoBiT sensor showed unprecedented sensitivity, which made it possible to detect even weak and transient interactions between PII variants and their interacting partners, thereby shedding new light in PII signalling processes.
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22
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Bolay P, Rozbeh R, Muro-Pastor MI, Timm S, Hagemann M, Florencio FJ, Forchhammer K, Klähn S. The Novel P II-Interacting Protein PirA Controls Flux into the Cyanobacterial Ornithine-Ammonia Cycle. mBio 2021; 12:e00229-21. [PMID: 33758091 PMCID: PMC8092223 DOI: 10.1128/mbio.00229-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 02/16/2021] [Indexed: 12/11/2022] Open
Abstract
Among prokaryotes, cyanobacteria have an exclusive position as they perform oxygenic photosynthesis. Cyanobacteria substantially differ from other bacteria in further aspects, e.g., they evolved a plethora of unique regulatory mechanisms to control primary metabolism. This is exemplified by the regulation of glutamine synthetase (GS) via small proteins termed inactivating factors (IFs). Here, we reveal another small protein, encoded by the ssr0692 gene in the model strain Synechocystis sp. PCC 6803, that regulates flux into the ornithine-ammonia cycle (OAC), the key hub of cyanobacterial nitrogen stockpiling and remobilization. This regulation is achieved by the interaction with the central carbon/nitrogen control protein PII, which commonly controls entry into the OAC by activating the key enzyme of arginine synthesis, N-acetyl-l-glutamate kinase (NAGK). In particular, the Ssr0692 protein competes with NAGK for PII binding and thereby prevents NAGK activation, which in turn lowers arginine synthesis. Accordingly, we termed it PII-interacting regulator of arginine synthesis (PirA). Similar to the GS IFs, PirA accumulates in response to ammonium upshift due to relief from repression by the global nitrogen control transcription factor NtcA. Consistent with this, the deletion of pirA affects the balance of metabolite pools of the OAC in response to ammonium shocks. Moreover, the PirA-PII interaction requires ADP and is prevented by PII mutations affecting the T-loop conformation, the major protein interaction surface of this signal processing protein. Thus, we propose that PirA is an integrator determining flux into N storage compounds not only depending on the N availability but also the energy state of the cell.IMPORTANCE Cyanobacteria contribute a significant portion to the annual oxygen yield and play important roles in biogeochemical cycles, e.g., as major primary producers. Due to their photosynthetic lifestyle, cyanobacteria also arouse interest as hosts for the sustainable production of fuel components and high-value chemicals. However, their broad application as microbial cell factories is hampered by limited knowledge about the regulation of metabolic fluxes in these organisms. Our research identified a novel regulatory protein that controls nitrogen flux, in particular arginine synthesis. Besides its role as a proteinogenic amino acid, arginine is a precursor for the cyanobacterial storage compound cyanophycin, which is of potential interest to biotechnology. Therefore, the obtained results will not only enhance our understanding of flux control in these organisms but also help to provide a scientific basis for targeted metabolic engineering and, hence, the design of photosynthesis-driven biotechnological applications.
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Affiliation(s)
- Paul Bolay
- Helmholtz Centre for Environmental Research, Department of Solar Materials, Leipzig, Germany
| | - Rokhsareh Rozbeh
- Interfaculty Institute for Microbiology and Infection Medicine, Organismic Interactions Department, Tübingen University, Tübingen, Germany
| | - M Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Sevilla, Spain
| | - Stefan Timm
- Department of Plant Physiology, University of Rostock, Rostock, Germany
| | - Martin Hagemann
- Department of Plant Physiology, University of Rostock, Rostock, Germany
| | - Francisco J Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Sevilla, Spain
| | - Karl Forchhammer
- Interfaculty Institute for Microbiology and Infection Medicine, Organismic Interactions Department, Tübingen University, Tübingen, Germany
| | - Stephan Klähn
- Helmholtz Centre for Environmental Research, Department of Solar Materials, Leipzig, Germany
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23
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Ito S, Hakamada T, Ogino T, Osanai T. Reconstitution of oxaloacetate metabolism in the tricarboxylic acid cycle in Synechocystis sp. PCC 6803: discovery of important factors that directly affect the conversion of oxaloacetate. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1449-1458. [PMID: 33280178 DOI: 10.1111/tpj.15120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
The tricarboxylic acid (TCA) cycle is one of the most important metabolic pathways in nature. Oxygenic photoautotrophic bacteria, cyanobacteria, have an unusual TCA cycle. The TCA cycle in cyanobacteria contains two unique enzymes that are not part of the TCA cycle in other organisms. In recent years, sustainable metabolite production from carbon dioxide using cyanobacteria has been looked at as a means to reduce the environmental burden of this gas. Among cyanobacteria, the unicellular cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis 6803) is an optimal host for sustainable metabolite production. Recently, metabolite production using the TCA cycle in Synechocystis 6803 has been carried out. Previous studies revealed that the branch point of the oxidative and reductive TCA cycles, oxaloacetate metabolism, plays a key role in metabolite production. However, the biochemical mechanisms regulating oxaloacetate metabolism in Synechocystis 6803 are poorly understood. Concentrations of oxaloacetate in Synechocystis 6803 are extremely low, such that in vivo analysis of oxaloacetate metabolism does not seem realistic. Therefore, using purified enzymes, we reconstituted oxaloacetate metabolism in Synechocystis 6803 in vitro to reveal the regulatory mechanisms involved. Reconstitution of oxaloacetate metabolism revealed that pH, Mg2+ and phosphoenolpyruvate are important factors affecting the conversion of oxaloacetate in the TCA cycle. Biochemical analyses of the enzymes involved in oxaloacetate metabolism in this and previous studies revealed the biochemical mechanisms underlying the effects of these factors on oxaloacetate conversion. In addition, we clarified the function of two l-malate dehydrogenase isozymes in oxaloacetate metabolism. These findings serve as a basis for various applications of the cyanobacterial TCA cycle.
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Affiliation(s)
- Shoki Ito
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Takumi Hakamada
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Tatsumi Ogino
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Takashi Osanai
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
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Gao X, Jing X, Liu X, Lindblad P. Biotechnological Production of the Sunscreen Pigment Scytonemin in Cyanobacteria: Progress and Strategy. Mar Drugs 2021; 19:129. [PMID: 33673485 PMCID: PMC7997468 DOI: 10.3390/md19030129] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 12/22/2022] Open
Abstract
Scytonemin is a promising UV-screen and antioxidant small molecule with commercial value in cosmetics and medicine. It is solely biosynthesized in some cyanobacteria. Recently, its biosynthesis mechanism has been elucidated in the model cyanobacterium Nostoc punctiforme PCC 73102. The direct precursors for scytonemin biosynthesis are tryptophan and p-hydroxyphenylpyruvate, which are generated through the shikimate and aromatic amino acid biosynthesis pathway. More upstream substrates are the central carbon metabolism intermediates phosphoenolpyruvate and erythrose-4-phosphate. Thus, it is a long route to synthesize scytonemin from the fixed atmospheric CO2 in cyanobacteria. Metabolic engineering has risen as an important biotechnological means for achieving sustainable high-efficiency and high-yield target metabolites. In this review, we summarized the biochemical properties of this molecule, its biosynthetic gene clusters and transcriptional regulations, the associated carbon flux-driving progresses, and the host selection and biosynthetic strategies, with the aim to expand our understanding on engineering suitable cyanobacteria for cost-effective production of scytonemin in future practices.
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Affiliation(s)
- Xiang Gao
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi’an 710021, China;
| | - Xin Jing
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi’an 710021, China;
| | - Xufeng Liu
- Microbial Chemistry, Department of Chemistry-Ångstrom, Uppsala University, Box 523, 751 20 Uppsala, Sweden;
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry-Ångstrom, Uppsala University, Box 523, 751 20 Uppsala, Sweden;
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Durall C, Kukil K, Hawkes JA, Albergati A, Lindblad P, Lindberg P. Production of succinate by engineered strains of Synechocystis PCC 6803 overexpressing phosphoenolpyruvate carboxylase and a glyoxylate shunt. Microb Cell Fact 2021; 20:39. [PMID: 33557832 PMCID: PMC7871529 DOI: 10.1186/s12934-021-01529-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/25/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Cyanobacteria are promising hosts for the production of various industrially important compounds such as succinate. This study focuses on introduction of the glyoxylate shunt, which is naturally present in only a few cyanobacteria, into Synechocystis PCC 6803. In order to test its impact on cell metabolism, engineered strains were evaluated for succinate accumulation under conditions of light, darkness and anoxic darkness. Each condition was complemented by treatments with 2-thenoyltrifluoroacetone, an inhibitor of succinate dehydrogenase enzyme, and acetate, both in nitrogen replete and deplete medium. RESULTS We were able to introduce genes encoding the glyoxylate shunt, aceA and aceB, encoding isocitrate lyase and malate synthase respectively, into a strain of Synechocystis PCC 6803 engineered to overexpress phosphoenolpyruvate carboxylase. Our results show that complete expression of the glyoxylate shunt results in higher extracellular succinate accumulation compared to the wild type control strain after incubation of cells in darkness and anoxic darkness in the presence of nitrate. Addition of the inhibitor 2-thenoyltrifluoroacetone increased succinate titers in all the conditions tested when nitrate was available. Addition of acetate in the presence of the inhibitor further increased the succinate accumulation, resulting in high levels when phosphoenolpyruvate carboxylase was overexpressed, compared to control strain. However, the highest succinate titer was obtained after dark incubation of an engineered strain with a partial glyoxylate shunt overexpressing isocitrate lyase in addition to phosphoenolpyruvate carboxylase, with only 2-thenoyltrifluoroacetone supplementation to the medium. CONCLUSIONS Heterologous expression of the glyoxylate shunt with its central link to the tricarboxylic acid cycle (TCA) for acetate assimilation provides insight on the coordination of the carbon metabolism in the cell. Phosphoenolpyruvate carboxylase plays an important role in directing carbon flux towards the TCA cycle.
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Affiliation(s)
- Claudia Durall
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, 751 20, Uppsala, Sweden
| | - Kateryna Kukil
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, 751 20, Uppsala, Sweden
| | - Jeffrey A Hawkes
- Analytical Chemistry, Department of Chemistry-BMC, Uppsala University, Box 599, 751 20, Uppsala, Sweden
| | - Alessia Albergati
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, 751 20, Uppsala, Sweden
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, 751 20, Uppsala, Sweden
| | - Pia Lindberg
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, 751 20, Uppsala, Sweden.
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The Protein-Protein Interaction Network Reveals a Novel Role of the Signal Transduction Protein PII in the Control of c-di-GMP Homeostasis in Azospirillum brasilense. mSystems 2020; 5:5/6/e00817-20. [PMID: 33144311 PMCID: PMC7646526 DOI: 10.1128/msystems.00817-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The PII proteins sense and integrate important metabolic signals which reflect the cellular nutrition and energy status. Such extraordinary ability was capitalized by nature in such a way that the various PII proteins regulate different facets of metabolism by controlling the activity of a range of target proteins by protein-protein interactions. Here, we determined the PII protein interaction network in the plant growth-promoting nitrogen-fixing bacterium Azospirillum brasilense. The interactome data along with metabolome analysis suggest that PII functions as a master metabolic regulator hub. We provide evidence that PII proteins act to regulate c-di-GMP levels in vivo and cell motility and adherence behaviors. The PII family comprises a group of widely distributed signal transduction proteins ubiquitous in prokaryotes and in the chloroplasts of plants. PII proteins sense the levels of key metabolites ATP, ADP, and 2-oxoglutarate, which affect the PII protein structure and thereby the ability of PII to interact with a range of target proteins. Here, we performed multiple ligand fishing assays with the PII protein orthologue GlnZ from the plant growth-promoting nitrogen-fixing bacterium Azospirillum brasilense to identify 37 proteins that are likely to be part of the PII protein-protein interaction network. Among the PII targets identified were enzymes related to nitrogen and fatty acid metabolism, signaling, coenzyme synthesis, RNA catabolism, and transcription. Direct binary PII-target complex was confirmed for 15 protein complexes using pulldown assays with recombinant proteins. Untargeted metabolome analysis showed that PII is required for proper homeostasis of important metabolites. Two enzymes involved in c-di-GMP metabolism were among the identified PII targets. A PII-deficient strain showed reduced c-di-GMP levels and altered aerotaxis and flocculation behavior. These data support that PII acts as a major metabolic hub controlling important enzymes and the homeostasis of key metabolites such as c-di-GMP in response to the prevailing nutritional status. IMPORTANCE The PII proteins sense and integrate important metabolic signals which reflect the cellular nutrition and energy status. Such extraordinary ability was capitalized by nature in such a way that the various PII proteins regulate different facets of metabolism by controlling the activity of a range of target proteins by protein-protein interactions. Here, we determined the PII protein interaction network in the plant growth-promoting nitrogen-fixing bacterium Azospirillum brasilense. The interactome data along with metabolome analysis suggest that PII functions as a master metabolic regulator hub. We provide evidence that PII proteins act to regulate c-di-GMP levels in vivo and cell motility and adherence behaviors.
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Veaudor T, Blanc-Garin V, Chenebault C, Diaz-Santos E, Sassi JF, Cassier-Chauvat C, Chauvat F. Recent Advances in the Photoautotrophic Metabolism of Cyanobacteria: Biotechnological Implications. Life (Basel) 2020; 10:life10050071. [PMID: 32438704 PMCID: PMC7281370 DOI: 10.3390/life10050071] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/16/2020] [Accepted: 05/18/2020] [Indexed: 12/13/2022] Open
Abstract
Cyanobacteria constitute the only phylum of oxygen-evolving photosynthetic prokaryotes that shaped the oxygenic atmosphere of our planet. Over time, cyanobacteria have evolved as a widely diverse group of organisms that have colonized most aquatic and soil ecosystems of our planet and constitute a large proportion of the biomass that sustains the biosphere. Cyanobacteria synthesize a vast array of biologically active metabolites that are of great interest for human health and industry, and several model cyanobacteria can be genetically manipulated. Hence, cyanobacteria are regarded as promising microbial factories for the production of chemicals from highly abundant natural resources, e.g., solar energy, CO2, minerals, and waters, eventually coupled to wastewater treatment to save costs. In this review, we summarize new important discoveries on the plasticity of the photoautotrophic metabolism of cyanobacteria, emphasizing the coordinated partitioning of carbon and nitrogen towards growth or compound storage, and the importance of these processes for biotechnological perspectives. We also emphasize the importance of redox regulation (including glutathionylation) on these processes, a subject which has often been overlooked.
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Affiliation(s)
- Théo Veaudor
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (T.V.); (V.B.-G.); (C.C.); (E.D.-S.); (C.C.-C.)
| | - Victoire Blanc-Garin
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (T.V.); (V.B.-G.); (C.C.); (E.D.-S.); (C.C.-C.)
| | - Célia Chenebault
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (T.V.); (V.B.-G.); (C.C.); (E.D.-S.); (C.C.-C.)
| | - Encarnación Diaz-Santos
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (T.V.); (V.B.-G.); (C.C.); (E.D.-S.); (C.C.-C.)
| | - Jean-François Sassi
- Commissariat à l’énergie atomique et aux énergies alternatives (CEA), Centre de Cadarache St Paul Lez, 13108 Durance, France;
| | - Corinne Cassier-Chauvat
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (T.V.); (V.B.-G.); (C.C.); (E.D.-S.); (C.C.-C.)
| | - Franck Chauvat
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (T.V.); (V.B.-G.); (C.C.); (E.D.-S.); (C.C.-C.)
- Correspondence: ; Tel.: +33-1-69-08-78-11
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