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Sato N, Endo M, Nishi H, Fujiwara S, Tsuzuki M. Polyphosphate-kinase-1 dependent polyphosphate hyperaccumulation for acclimation to nutrient loss in the cyanobacterium, Synechocystis sp. PCC 6803. FRONTIERS IN PLANT SCIENCE 2024; 15:1441626. [PMID: 39145186 PMCID: PMC11322815 DOI: 10.3389/fpls.2024.1441626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 07/15/2024] [Indexed: 08/16/2024]
Abstract
Polyphosphate is prevalent in living organisms. To obtain insights into polyphosphate synthesis and its physiological significance in cyanobacteria, we characterize sll0290, a homolog of the polyphosphate-kinase-1 gene, in the freshwater cyanobacterium Synechocystis sp. PCC 6803. The Sll0290 protein structure reveals characteristics of Ppk1. A Synechocystis sll0290 disruptant and sll0290-overexpressing Escherichia coli transformant demonstrated loss and gain of polyphosphate synthesis ability, respectively. Accordingly, sll0290 is identified as ppk1. The disruptant (Δppk1) grows normally with aeration of ordinary air (0.04% CO2), consistent with its photosynthesis comparable to the wild type level, which contrasts with a previously reported high-CO2 (5%) requirement for Δppk1 in an alkaline hot spring cyanobacterium, Synechococcus OS-B'. Synechocystis Δppk1 is defective in polyphosphate hyperaccumulation and survival competence at the stationary phase, and also under sulfur-starvation conditions, implying that sulfur limitation is one of the triggers to induce polyphosphate hyperaccumulation in stationary cells. Furthermore, Δppk1 is defective in the enhancement of total phosphorus contents under sulfur-starvation conditions, a phenomenon that is only partially explained by polyphosphate hyperaccumulation. This study therefore demonstrates that in Synechocystis, ppk1 is not essential for low-CO2 acclimation but plays a crucial role in dynamic P-metabolic regulation, including polyP hyperaccumulation, to maintain physiological fitness under sulfur-starvation conditions.
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Affiliation(s)
- Norihiro Sato
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
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Barske T, Spät P, Schubert H, Walke P, Maček B, Hagemann M. The Role of Serine/Threonine-Specific Protein Kinases in Cyanobacteria - SpkB Is Involved in Acclimation to Fluctuating Conditions in Synechocystis sp. PCC 6803. Mol Cell Proteomics 2023; 22:100656. [PMID: 37797745 PMCID: PMC10651672 DOI: 10.1016/j.mcpro.2023.100656] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 08/31/2023] [Accepted: 10/01/2023] [Indexed: 10/07/2023] Open
Abstract
Protein phosphorylation via serine/threonine protein kinases (Spk) is a widespread mechanism to adjust cellular processes toward changing environmental conditions. To study their role(s) in cyanobacteria, we investigated a collection of 11 completely segregated spk mutants among the 12 annotated Spks in the model cyanobacterium Synechocystis sp. PCC 6803. Screening of the mutant collection revealed that especially the mutant defective in SpkB encoded by slr1697 showed clear deviations regarding carbon metabolism, that is, reduced growth rates at low CO2 or in the presence of glucose, and different glycogen accumulation patterns compared to WT. Alterations in the proteome of ΔspkB indicated changes of the cell surface but also metabolic functions. A phospho-proteome analysis revealed the absence of any phosphorylation in two proteins, while decreased phosphorylation of the carboxysome-associated protein CcmM and increased phosphorylation of the allophycocyanin alpha subunit ApcA was detected in ΔspkB. Furthermore, the regulatory PII protein appeared less phosphorylated in the mutant compared to WT, which was verified in Western blot experiments, indicating a clearly delayed PII phosphorylation in cells shifted from nitrate-containing to nitrate-free medium. Our results indicate that SpkB is an important regulator in Synechocystis that is involved in phosphorylation of the PII protein and additional proteins.
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Affiliation(s)
- Thomas Barske
- Department of Plant Physiology, Institute of Biosciences, University of Rostock, Rostock, Germany
| | - Philipp Spät
- Department of Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany; Department of Quantitative Proteomics, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Hendrik Schubert
- Department of Aquatic Ecology, Institute of Biosciences, University of Rostock, Rostock, Germany
| | - Peter Walke
- Department of Plant Physiology, Institute of Biosciences, University of Rostock, Rostock, Germany
| | - Boris Maček
- Department of Quantitative Proteomics, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Martin Hagemann
- Department of Plant Physiology, Institute of Biosciences, University of Rostock, Rostock, Germany; Interdisciplinary Faculty, Department Life, Light and Matter, University of Rostock, Rostock, Germany.
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Lucius S, Theune M, Arrivault S, Hildebrandt S, Mullineaux CW, Gutekunst K, Hagemann M. CP12 fine-tunes the Calvin-Benson cycle and carbohydrate metabolism in cyanobacteria. FRONTIERS IN PLANT SCIENCE 2022; 13:1028794. [PMID: 36330266 PMCID: PMC9623430 DOI: 10.3389/fpls.2022.1028794] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 09/26/2022] [Indexed: 06/12/2023]
Abstract
The regulatory protein CP12 can bind glyceraldehyde 3-phosphate dehydrogenase (GapDH) and phosphoribulokinase (PRK) in oxygenic phototrophs, thereby switching on and off the flux through the Calvin-Benson cycle (CBC) under light and dark conditions, respectively. However, it can be assumed that CP12 is also regulating CBC flux under further conditions associated with redox changes. To prove this hypothesis, the mutant Δcp12 of the model cyanobacterium Synechocystis sp. PCC 6803 was compared to wild type and different complementation strains. Fluorescence microscopy showed for the first time the in vivo kinetics of assembly and disassembly of the CP12-GapDH-PRK complex, which was absent in the mutant Δcp12. Metabolome analysis revealed differences in the contents of ribulose 1,5-bisphosphate and dihydroxyacetone phosphate, the products of the CP12-regulated enzymes GapDH and PRK, between wild type and mutant Δcp12 under changing CO2 conditions. Growth of Δcp12 was not affected at constant light under different inorganic carbon conditions, however, the addition of glucose inhibited growth in darkness as well as under diurnal conditions. The growth defect in the presence of glucose is associated with the inability of Δcp12 to utilize external glucose. These phenotypes could be complemented by ectopic expression of the native CP12 protein, however, expression of CP12 variants with missing redox-sensitive cysteine pairs only partly restored the growth with glucose. These experiments indicated that the loss of GapDH-inhibition via CP12 is more critical than PRK association. Measurements of the NAD(P)H oxidation revealed an impairment of light intensity-dependent redox state regulation in Δcp12. Collectively, our results indicate that CP12-dependent regulation of the CBC is crucial for metabolic adjustment under conditions leading to redox changes such as diurnal conditions, glucose addition, and different CO2 conditions in cyanobacteria.
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Affiliation(s)
- Stefan Lucius
- Department Plant Physiology, University Rostock, Rostock, Germany
| | - Marius Theune
- Molecular Plant Physiology, Bioenergetics in Photoautotrophs, University Kassel, Kassel, Germany
- Botanical Institute, University Kiel, Kiel, Germany
| | - Stéphanie Arrivault
- Max Planck Institute of Molecular Plant Physiology, Emeritus Group System Regulation, Potsdam, Germany
| | | | - Conrad W. Mullineaux
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Kirstin Gutekunst
- Molecular Plant Physiology, Bioenergetics in Photoautotrophs, University Kassel, Kassel, Germany
- Botanical Institute, University Kiel, Kiel, Germany
| | - Martin Hagemann
- Department Plant Physiology, University Rostock, Rostock, Germany
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Bantu L, Chauhan S, Srikumar A, Hirakawa Y, Suzuki I, Hagemann M, Prakash JSS. A membrane-bound cAMP receptor protein, SyCRP1 mediates inorganic carbon response in Synechocystis sp. PCC 6803. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194803. [PMID: 35272049 DOI: 10.1016/j.bbagrm.2022.194803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/24/2022] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
The availability of inorganic carbon (Ci) as the source for photosynthesis is fluctuating in aquatic environments. Despite the involvement of transcriptional regulators CmpR and NdhR in regulating genes encoding Ci transporters at limiting CO2, the Ci-sensing mechanism is largely unknown among cyanobacteria. Here we report that a cAMP-dependent transcription factor SyCRP1 mediates Ci response in Synechocystis. The mutant ∆sycrp1 exhibited a slow-growth phenotype and reduced maximum rate of bicarbonate-dependent photosynthetic electron transport (Vmax) compared to wild-type at the scarcity of CO2. The number of carboxysomes was decreased significantly in the ∆sycrp1 at low CO2 consistent with its reduced Vmax. The DNA microarray analysis revealed the upregulation of genes encoding Ci transporters in ∆sycrp1. The membrane-localized SyCRP1 was released into the cytosol in wild-type cells shifted from low to high CO2 or upon cAMP treatment. Soluble His-tagged SyCRP1 was shown to target DNA-binding sites upstream of the Ci-regulated genes sbtA and ccmK3. In addition, cAMP enhanced the binding of SyCRP1 to its target sites. Our data collectively suggest that the Ci is sensed through the second messenger cAMP releasing membrane-bound SyCRP1 into cytoplasm under sufficient CO2 conditions. Hence, SyCRP1 is a possible regulator of carbon concentrating mechanism, and such a regulation might be mediated via sensing Ci levels through cAMP in Synechocystis.
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Affiliation(s)
- Lingaswamy Bantu
- From the Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Suraj Chauhan
- From the Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Afshan Srikumar
- From the Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Yoshihisa Hirakawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennoudai 1-1-1, Tsukuba 305-8572, Japan
| | - Iwane Suzuki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennoudai 1-1-1, Tsukuba 305-8572, Japan
| | - Martin Hagemann
- Plant Physiology Department, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany
| | - Jogadhenu S S Prakash
- From the Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
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Artier J, Walker RM, Miller NT, Zhang M, Price GD, Burnap RL. Modeling and mutagenesis of amino acid residues critical for CO 2 hydration by specialized NDH-1 complexes in cyanobacteria. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148503. [PMID: 34610280 DOI: 10.1016/j.bbabio.2021.148503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/24/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
The uptake of inorganic carbon in cyanobacteria is facilitated by an energetically intensive CO2-concentrating mechanism (CCM). This includes specialized Type-1 NDH complexes that function to couple photosynthetic redox energy to CO2 hydration forming the bicarbonate that accumulates to high cytoplasmic concentrations during the operation of the CCM, required for effective carbon fixation. Here we used a Synechococcus PCC7942 expression system to investigate the role of conserved histidine and cysteine residues in the CupB (also designated, ChpX) protein, which has been hypothesized to participate in a vectoral CO2 hydration reaction near the interface between CupB protein and the proton-pumping subunits of the NDH-1 complex. A homology model has been constructed and most of the targeted conserved residues are in the vicinity of a Zn ion modeled to form the catalytic site of deprotonation and CO2 hydration. Growth and CO2 uptake assays show that the most severe defects in activity among the targeted residues are due to a substitution of the predicted Zn ligand, CupB-His86. Mutations at other sites produced intermediate effects. Proteomic analysis revealed that some amino acid substitution mutations of CupB caused the induction of bicarbonate uptake proteins to a greater extent than complete deletion of CupB, despite growth under CO2-enriched conditions. The results are discussed in terms of hypotheses on the catalytic function of this unusual enzyme.
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Affiliation(s)
- Juliana Artier
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Ross M Walker
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Neil T Miller
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Minquan Zhang
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - G Dean Price
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Robert L Burnap
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA.
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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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A new insight into role of phosphoketolase pathway in Synechocystis sp. PCC 6803. Sci Rep 2020; 10:22018. [PMID: 33328526 PMCID: PMC7744508 DOI: 10.1038/s41598-020-78475-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/25/2020] [Indexed: 11/29/2022] Open
Abstract
Phosphoketolase (PKET) pathway is predominant in cyanobacteria (around 98%) but current opinion is that it is virtually inactive under autotrophic ambient CO2 condition (AC-auto). This creates an evolutionary paradox due to the existence of PKET pathway in obligatory photoautotrophs. We aim to answer the paradox with the aid of bioinformatic analysis along with metabolic, transcriptomic, fluxomic and mutant data integrated into a multi-level kinetic model. We discussed the problems linked to neglected isozyme, pket2 (sll0529) and inconsistencies towards the explanation of residual flux via PKET pathway in the case of silenced pket1 (slr0453) in Synechocystis sp. PCC 6803. Our in silico analysis showed: (1) 17% flux reduction via RuBisCO for Δpket1 under AC-auto, (2) 11.2–14.3% growth decrease for Δpket2 in turbulent AC-auto, and (3) flux via PKET pathway reaching up to 252% of the flux via phosphoglycerate mutase under AC-auto. All results imply that PKET pathway plays a crucial role under AC-auto by mitigating the decarboxylation occurring in OPP pathway and conversion of pyruvate to acetyl CoA linked to EMP glycolysis under the carbon scarce environment. Finally, our model predicted that PKETs have low affinity to S7P as a substrate.
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Barchewitz T, Guljamow A, Meissner S, Timm S, Henneberg M, Baumann O, Hagemann M, Dittmann E. Non-canonical localization of RubisCO under high-light conditions in the toxic cyanobacterium Microcystis aeruginosa PCC7806. Environ Microbiol 2019; 21:4836-4851. [PMID: 31637830 DOI: 10.1111/1462-2920.14837] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/11/2019] [Accepted: 10/18/2019] [Indexed: 01/25/2023]
Abstract
The frequent production of the hepatotoxin microcystin (MC) and its impact on the lifestyle of bloom-forming cyanobacteria are poorly understood. Here, we report that MC interferes with the assembly and the subcellular localization of RubisCO, in Microcystis aeruginosa PCC7806. Immunofluorescence, electron microscopic and cellular fractionation studies revealed a pronounced heterogeneity in the subcellular localization of RubisCO. At high cell density, RubisCO particles are largely separate from carboxysomes in M. aeruginosa and relocate to the cytoplasmic membrane under high-light conditions. We hypothesize that the binding of MC to RubisCO promotes its membrane association and enables an extreme versatility of the enzyme. Steady-state levels of the RubisCO CO2 fixation product 3-phosphoglycerate are significantly higher in the MC-producing wild type. We also detected noticeable amounts of the RubisCO oxygenase reaction product secreted into the medium that may support the mutual interaction of M. aeruginosa with its heterotrophic microbial community.
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Affiliation(s)
- Tino Barchewitz
- Department of Microbiology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476 Potsdam-Golm, Germany
| | - Arthur Guljamow
- Department of Microbiology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476 Potsdam-Golm, Germany
| | - Sven Meissner
- Department of Microbiology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476 Potsdam-Golm, Germany
| | - Stefan Timm
- Department of Plant Physiology, Institute Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany
| | - Manja Henneberg
- Department of Plant Physiology, Institute Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany
| | - Otto Baumann
- Department of Zoophysiology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476 Potsdam-Golm, Germany
| | - Martin Hagemann
- Department of Plant Physiology, Institute Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany
| | - Elke Dittmann
- Department of Microbiology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476 Potsdam-Golm, Germany
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Abernathy MH, Czajka JJ, Allen DK, Hill NC, Cameron JC, Tang YJ. Cyanobacterial carboxysome mutant analysis reveals the influence of enzyme compartmentalization on cellular metabolism and metabolic network rigidity. Metab Eng 2019; 54:222-231. [PMID: 31029860 DOI: 10.1016/j.ymben.2019.04.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 04/13/2019] [Accepted: 04/22/2019] [Indexed: 12/18/2022]
Abstract
Cyanobacterial carboxysomes encapsulate carbonic anhydrase and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Genetic deletion of the major structural proteins encoded within the ccm operon in Synechococcus sp. PCC 7002 (ΔccmKLMN) disrupts carboxysome formation and significantly affects cellular physiology. Here we employed both metabolite pool size analysis and isotopically nonstationary metabolic flux analysis (INST-MFA) to examine metabolic regulation in cells lacking carboxysomes. Under high CO2 environments (1%), the ΔccmKLMN mutant could recover growth and had a similar central flux distribution as the control strain, with the exceptions of moderately decreased photosynthesis and elevated biomass protein content and photorespiration activity. Metabolite analyses indicated that the ΔccmKLMN strain had significantly larger pool sizes of pyruvate (>18 folds), UDPG (uridine diphosphate glucose), and aspartate as well as higher levels of secreted organic acids (e.g., malate and succinate). These results suggest that the ΔccmKLMN mutant is able to largely maintain a fluxome similar to the control strain by changing in intracellular metabolite concentrations and metabolite overflows under optimal growth conditions. When CO2 was insufficient (0.2%), provision of acetate moderately promoted mutant growth. Interestingly, the removal of microcompartments may loosen the flux network and promote RuBisCO side-reactions, facilitating redirection of central metabolites to competing pathways (i.e., pyruvate to heterologous lactate production). This study provides important insights into metabolic regulation via enzyme compartmentation and cyanobacterial compensatory responses.
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Affiliation(s)
- Mary H Abernathy
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, MO 63130, USA
| | - Jeffrey J Czajka
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, MO 63130, USA
| | - Douglas K Allen
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; United States Department of Agriculture, Agricultural Research Service, St. Louis, MO 63132, USA
| | - Nicholas C Hill
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Jeffrey C Cameron
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA; Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO 80309, USA; National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA.
| | - Yinjie J Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, MO 63130, USA.
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Zhang CC, Zhou CZ, Burnap RL, Peng L. Carbon/Nitrogen Metabolic Balance: Lessons from Cyanobacteria. TRENDS IN PLANT SCIENCE 2018; 23:1116-1130. [PMID: 30292707 DOI: 10.1016/j.tplants.2018.09.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 09/07/2018] [Accepted: 09/11/2018] [Indexed: 05/20/2023]
Abstract
Carbon and nitrogen are the two most abundant nutrient elements for all living organisms, and their metabolism is tightly coupled. What are the signaling mechanisms that cells use to sense and control the carbon/nitrogen (C/N) metabolic balance following environmental changes? Based on studies in cyanobacteria, it was found that 2-phosphoglycolate derived from the oxygenase activity of Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) and 2-oxoglutarate from the Krebs cycle act as the carbon- and nitrogen-starvation signals, respectively, and their concentration ratio likely reflects the status of the C/N metabolic balance. We will present and discuss the regulatory principles underlying the signaling mechanisms, which are likely to be conserved in other photosynthetic organisms. These concepts may also contribute to developments in the field of biofuel engineering or improvements in crop productivity.
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Affiliation(s)
- Cheng-Cai Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan, Hubei 430072, People's Republic of China; Aix-Marseille Université, CNRS, LCB, France.
| | - Cong-Zhao Zhou
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230027, People's Republic of China
| | - Robert L Burnap
- Department of Microbiology and Molecular Genetics, Henry Bellmon Research Center, Oklahoma State University, Stillwater, OK 74078, USA
| | - Ling Peng
- Aix-Marseille Université, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, Equipe Labellisée Ligue Contre le Cancer, CINaM UMR 7325, 13288 Marseille, France
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11
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Dai W, Chen M, Myers C, Ludtke SJ, Pettitt BM, King JA, Schmid MF, Chiu W. Visualizing Individual RuBisCO and Its Assembly into Carboxysomes in Marine Cyanobacteria by Cryo-Electron Tomography. J Mol Biol 2018; 430:4156-4167. [PMID: 30138616 DOI: 10.1016/j.jmb.2018.08.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 07/29/2018] [Accepted: 08/13/2018] [Indexed: 12/31/2022]
Abstract
Cyanobacteria are photosynthetic organisms responsible for ~25% of the organic carbon fixation on earth. A key step in carbon fixation is catalyzed by ribulose bisphosphate carboxylase/oxygenase (RuBisCO), the most abundant enzyme in the biosphere. Applying Zernike phase-contrast electron cryo-tomography and automated annotation, we identified individual RuBisCO molecules and their assembly intermediates leading to the formation of carboxysomes inside Syn5 cyanophage infected cyanobacteria Synechococcus sp. WH8109 cells. Surprisingly, more RuBisCO molecules were found to be present as cytosolic free-standing complexes or clusters than as packaged assemblies inside carboxysomes. Cytosolic RuBisCO clusters and partially assembled carboxysomes identified in the cell tomograms support a concurrent assembly model involving both the protein shell and the enclosed RuBisCO. In mature carboxysomes, RuBisCO is neither randomly nor strictly icosahedrally packed within protein shells of variable sizes. A time-averaged molecular dynamics simulation showed a semi-liquid probability distribution of the RuBisCO in carboxysomes and correlated well with carboxysome subtomogram averages. Our structural observations reveal the various stages of RuBisCO assemblies, which could be important for understanding cellular function.
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Affiliation(s)
- Wei Dai
- Department of Cell Biology and Neuroscience & Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ 08854, USA.
| | - Muyuan Chen
- Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher Myers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Steven J Ludtke
- Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - B Montgomery Pettitt
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jonathan A King
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael F Schmid
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Wah Chiu
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA; Departments of Bioengineering and of Microbiology and Immunoplogy, James H. Clark Center, Stanford University, Stanford, CA 94305, USA.
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12
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Kopka J, Schmidt S, Dethloff F, Pade N, Berendt S, Schottkowski M, Martin N, Dühring U, Kuchmina E, Enke H, Kramer D, Wilde A, Hagemann M, Friedrich A. Systems analysis of ethanol production in the genetically engineered cyanobacterium Synechococcus sp. PCC 7002. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:56. [PMID: 28286551 PMCID: PMC5340023 DOI: 10.1186/s13068-017-0741-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/23/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND Future sustainable energy production can be achieved using mass cultures of photoautotrophic microorganisms, which are engineered to synthesize valuable products directly from CO2 and sunlight. As cyanobacteria can be cultivated in large scale on non-arable land, these phototrophic bacteria have become attractive organisms for production of biofuels. Synechococcus sp. PCC 7002, one of the cyanobacterial model organisms, provides many attractive properties for biofuel production such as tolerance of seawater and high light intensities. RESULTS Here, we performed a systems analysis of an engineered ethanol-producing strain of the cyanobacterium Synechococcus sp. PCC 7002, which was grown in artificial seawater medium over 30 days applying a 12:12 h day-night cycle. Biosynthesis of ethanol resulted in a final accumulation of 0.25% (v/v) ethanol, including ethanol lost due to evaporation. The cultivation experiment revealed three production phases. The highest production rate was observed in the initial phase when cells were actively growing. In phase II growth of the producer strain stopped, but ethanol production rate was still high. Phase III was characterized by a decrease of both ethanol production and optical density of the culture. Metabolomics revealed that the carbon drain due to ethanol diffusion from the cell resulted in the expected reduction of pyruvate-based intermediates. Carbon-saving strategies successfully compensated the decrease of central intermediates of carbon metabolism during the first phase of fermentation. However, during long-term ethanol production the producer strain showed clear indications of intracellular carbon limitation. Despite the decreased levels of glycolytic and tricarboxylic acid cycle intermediates, soluble sugars and even glycogen accumulated in the producer strain. The changes in carbon assimilation patterns are partly supported by proteome analysis, which detected decreased levels of many enzymes and also revealed the stress phenotype of ethanol-producing cells. Strategies towards improved ethanol production are discussed. CONCLUSIONS Systems analysis of ethanol production in Synechococcus sp. PCC 7002 revealed initial compensation followed by increasing metabolic limitation due to excessive carbon drain from primary metabolism.
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Affiliation(s)
- Joachim Kopka
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Stefanie Schmidt
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Frederik Dethloff
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Max-Planck-Institute of Psychiatry, Kraepelinstraße 2-10, 80804 Munich, Germany
| | - Nadin Pade
- Institute of Biological Sciences, Plant Physiology, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany
| | - Susanne Berendt
- Algenol Biofuels Germany GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | | | - Nico Martin
- Algenol Biofuels Germany GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Ulf Dühring
- Algenol Biofuels Germany GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Ekaterina Kuchmina
- Institute of Biology III, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Heike Enke
- Algenol Biofuels Germany GmbH, Magnusstraße 11, 12489 Berlin, Germany
- Cyano Biotech GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Dan Kramer
- Algenol Biofuels Germany GmbH, Magnusstraße 11, 12489 Berlin, Germany
- Cyano Biotech GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Annegret Wilde
- Institute of Biology III, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Martin Hagemann
- Institute of Biological Sciences, Plant Physiology, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany
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13
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Holland SC, Artier J, Miller NT, Cano M, Yu J, Ghirardi ML, Burnap RL. Impacts of genetically engineered alterations in carbon sink pathways on photosynthetic performance. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.09.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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14
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Jablonsky J, Papacek S, Hagemann M. Different strategies of metabolic regulation in cyanobacteria: from transcriptional to biochemical control. Sci Rep 2016; 6:33024. [PMID: 27611502 PMCID: PMC5017163 DOI: 10.1038/srep33024] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/17/2016] [Indexed: 12/23/2022] Open
Abstract
Cyanobacteria Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803 show similar changes in the metabolic response to changed CO2 conditions but exhibit significant differences at the transcriptomic level. This study employs a systems biology approach to investigate the difference in metabolic regulation of Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803. Presented multi-level kinetic model for Synechocystis sp. PCC 6803 is a new approach integrating and analysing metabolomic, transcriptomic and fluxomics data obtained under high and ambient CO2 levels. Modelling analysis revealed that higher number of different isozymes in Synechocystis 6803 improves homeostatic stability of several metabolites, especially 3PGA by 275%, against changes in gene expression, compared to Synechococcus sp. PCC 7942. Furthermore, both cyanobacteria have the same amount of phosphoglycerate mutases but Synechocystis 6803 exhibits only ~20% differences in their mRNA levels after shifts from high to ambient CO2 level, in comparison to ~500% differences in the case of Synechococcus sp. PCC 7942. These and other data imply that the biochemical control dominates over transcriptional regulation in Synechocystis 6803 to acclimate central carbon metabolism in the environment of variable inorganic carbon availability without extra cost carried by large changes in the proteome.
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Affiliation(s)
- Jiri Jablonsky
- Institute of Complex Systems, FFPW, University of South Bohemia, Cenakva, Czech Republic
| | - Stepan Papacek
- Institute of Complex Systems, FFPW, University of South Bohemia, Cenakva, Czech Republic
| | - Martin Hagemann
- Department of Plant Physiology, University of Rostock, Einsteinstr. 3, D-18059 Rostock, Germany
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15
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Orf I, Timm S, Bauwe H, Fernie AR, Hagemann M, Kopka J, Nikoloski Z. Can cyanobacteria serve as a model of plant photorespiration? - a comparative meta-analysis of metabolite profiles. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2941-2952. [PMID: 26969741 DOI: 10.1093/jxb/erw068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Photorespiration is a process that is crucial for the survival of oxygenic phototrophs in environments that favour the oxygenation reaction of Rubisco. While photorespiration is conserved among cyanobacteria, algae, and embryophytes, it evolved to different levels of complexity in these phyla. The highest complexity is found in embryophytes, where the pathway involves four cellular compartments and respective transport processes. The complexity of photorespiration in embryophytes raises the question whether a simpler system, such as cyanobacteria, may serve as a model to facilitate our understanding of the common key aspects of photorespiration. In this study, we conducted a meta-analysis of publicly available metabolite profiles from the embryophyte Arabidopsis thaliana and the cyanobacterium Synechocystis sp. PCC 6803 grown under conditions that either activate or suppress photorespiration. The comparative meta-analysis evaluated the similarity of metabolite profiles, the variability of metabolite pools, and the patterns of metabolite ratios. Our results show that the metabolic signature of photorespiration is in part conserved between the compared model organisms under conditions that favour the oxygenation reaction. Therefore, our findings support the claim that cyanobacteria can serve as prokaryotic models of photorespiration in embryophytes.
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Affiliation(s)
- Isabel Orf
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam OT Golm, Germany
| | - Stefan Timm
- Universität Rostock, Abteilung Pflanzenphysiologie, Albert-Einstein-Str. 3, 18059 Rostock, Germany
| | - Hermann Bauwe
- Universität Rostock, Abteilung Pflanzenphysiologie, Albert-Einstein-Str. 3, 18059 Rostock, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam OT Golm, Germany
| | - Martin Hagemann
- Universität Rostock, Abteilung Pflanzenphysiologie, Albert-Einstein-Str. 3, 18059 Rostock, Germany
| | - Joachim Kopka
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam OT Golm, Germany
| | - Zoran Nikoloski
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam OT Golm, Germany
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16
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Rademacher N, Kern R, Fujiwara T, Mettler-Altmann T, Miyagishima SY, Hagemann M, Eisenhut M, Weber APM. Photorespiratory glycolate oxidase is essential for the survival of the red alga Cyanidioschyzon merolae under ambient CO2 conditions. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3165-75. [PMID: 26994474 PMCID: PMC4867895 DOI: 10.1093/jxb/erw118] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Photorespiration is essential for all organisms performing oxygenic photosynthesis. The evolution of photorespiratory metabolism began among cyanobacteria and led to a highly compartmented pathway in plants. A molecular understanding of photorespiration in eukaryotic algae, such as glaucophytes, rhodophytes, and chlorophytes, is essential to unravel the evolution of this pathway. However, mechanistic detail of the photorespiratory pathway in red algae is scarce. The unicellular red alga Cyanidioschyzon merolae represents a model for the red lineage. Its genome is fully sequenced, and tools for targeted gene engineering are available. To study the function and importance of photorespiration in red algae, we chose glycolate oxidase (GOX) as the target. GOX catalyses the conversion of glycolate into glyoxylate, while hydrogen peroxide is generated as a side-product. The function of the candidate GOX from C. merolae was verified by the fact that recombinant GOX preferred glycolate over L-lactate as a substrate. Yellow fluorescent protein-GOX fusion proteins showed that GOX is targeted to peroxisomes in C. merolae The GOX knockout mutant lines showed a high-carbon-requiring phenotype with decreased growth and reduced photosynthetic activity compared to the wild type under ambient air conditions. Metabolite analyses revealed glycolate and glycine accumulation in the mutant cells after a shift from high CO2 conditions to ambient air. In summary, or results demonstrate that photorespiratory metabolism is essential for red algae. The use of a peroxisomal GOX points to a high photorespiratory flux as an ancestral feature of all photosynthetic eukaryotes.
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Affiliation(s)
- Nadine Rademacher
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Ramona Kern
- University Rostock, Department Plant Physiology, Albert-Einstein-Straße 3, 18059 Rostock, Germany
| | - Takayuki Fujiwara
- Division of Symbiosis and Cell Evolution, National Institute of Genetics, 1111 Yata, Mishima 411-8540, Shizuoka, Japan
| | - Tabea Mettler-Altmann
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Shin-Ya Miyagishima
- Division of Symbiosis and Cell Evolution, National Institute of Genetics, 1111 Yata, Mishima 411-8540, Shizuoka, Japan Japan Science and Technology Agency, CREST, 4-1-8 Honcho, Kawaguchi 332-0012, Saitama, Japan
| | - Martin Hagemann
- University Rostock, Department Plant Physiology, Albert-Einstein-Straße 3, 18059 Rostock, Germany
| | - Marion Eisenhut
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
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17
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Klähn S, Orf I, Schwarz D, Matthiessen JKF, Kopka J, Hess WR, Hagemann M. Integrated Transcriptomic and Metabolomic Characterization of the Low-Carbon Response Using an ndhR Mutant of Synechocystis sp. PCC 6803. PLANT PHYSIOLOGY 2015; 169:1540-56. [PMID: 25630438 PMCID: PMC4634042 DOI: 10.1104/pp.114.254045] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 01/27/2015] [Indexed: 05/17/2023]
Abstract
The acquisition and assimilation of inorganic carbon (Ci) represents the largest flux of inorganic matter in photosynthetic organisms; hence, this process is tightly regulated. We examined the Ci-dependent transcriptional and metabolic regulation in wild-type Synechocystis sp. PCC 6803 compared with a mutant defective in the main transcriptional repressor for Ci acquisition genes, the NAD(P)H dehydrogenase transcriptional regulator NdhR. The analysis revealed that many protein-coding transcripts that are normally repressed in the presence of high CO2 (HC) concentrations were strongly expressed in ∆ndhR, whereas other messenger RNAs were strongly down-regulated in mutant cells, suggesting a potential activating role for NdhR. A conserved NdhR-binding motif was identified in the promoters of derepressed genes. Interestingly, the expression of some NdhR-regulated genes remained further inducible under low-CO2 conditions, indicating the involvement of additional NdhR-independent Ci-regulatory mechanisms. Intriguingly, we also observed that the abundance of 52 antisense RNAs and 34 potential noncoding RNAs was affected by Ci supply, although most of these molecules were not regulated through NdhR. Thus, antisense and noncoding RNAs could contribute to NdhR-independent carbon regulation. In contrast to the transcriptome, the metabolome in ∆ndhR cells was similar to that of wild-type cells under HC conditions. This observation and the delayed metabolic responses to the low-CO2 shift in ∆ndhR, specifically the lack of transient increases in the photorespiratory pathway intermediates 2-phosphoglycolate, glycolate, and glycine, suggest that the deregulation of gene expression in the ΔndhR mutant successfully preacclimates cyanobacterial cells to lowered Ci supply under HC conditions.
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Affiliation(s)
- Stephan Klähn
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
| | - Isabel Orf
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
| | - Doreen Schwarz
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
| | - Jasper K F Matthiessen
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
| | - Joachim Kopka
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
| | - Martin Hagemann
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
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18
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Sandrini G, Cunsolo S, Schuurmans JM, Matthijs HCP, Huisman J. Changes in gene expression, cell physiology and toxicity of the harmful cyanobacterium Microcystis aeruginosa at elevated CO2. Front Microbiol 2015; 6:401. [PMID: 25999931 PMCID: PMC4419860 DOI: 10.3389/fmicb.2015.00401] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 04/17/2015] [Indexed: 12/31/2022] Open
Abstract
Rising CO2 concentrations may have large effects on aquatic microorganisms. In this study, we investigated how elevated pCO2 affects the harmful freshwater cyanobacterium Microcystis aeruginosa. This species is capable of producing dense blooms and hepatotoxins called microcystins. Strain PCC 7806 was cultured in chemostats that were shifted from low to high pCO2 conditions. This resulted in a transition from a C-limited to a light-limited steady state, with a ~2.7-fold increase of the cyanobacterial biomass and ~2.5-fold more microcystin per cell. Cells increased their chlorophyll a and phycocyanin content, and raised their PSI/PSII ratio at high pCO2. Surprisingly, cells had a lower dry weight and contained less carbohydrates, which might be an adaptation to improve the buoyancy of Microcystis when light becomes more limiting at high pCO2. Only 234 of the 4691 genes responded to elevated pCO2. For instance, expression of the carboxysome, RuBisCO, photosystem and C metabolism genes did not change significantly, and only a few N assimilation genes were expressed differently. The lack of large-scale changes in the transcriptome could suit a buoyant species that lives in eutrophic lakes with strong CO2 fluctuations very well. However, we found major responses in inorganic carbon uptake. At low pCO2, cells were mainly dependent on bicarbonate uptake, whereas at high pCO2 gene expression of the bicarbonate uptake systems was down-regulated and cells shifted to CO2 and low-affinity bicarbonate uptake. These results show that the need for high-affinity bicarbonate uptake systems ceases at elevated CO2. Moreover, the combination of an increased cyanobacterial abundance, improved buoyancy, and higher toxin content per cell indicates that rising atmospheric CO2 levels may increase the problems associated with the harmful cyanobacterium Microcystis in eutrophic lakes.
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Affiliation(s)
- Giovanni Sandrini
- Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of AmsterdamAmsterdam, Netherlands
| | - Serena Cunsolo
- Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of AmsterdamAmsterdam, Netherlands
| | - J. Merijn Schuurmans
- Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of AmsterdamAmsterdam, Netherlands
- Department of Aquatic Ecology, Netherlands Institute of EcologyWageningen, Netherlands
| | - Hans C. P. Matthijs
- Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of AmsterdamAmsterdam, Netherlands
| | - Jef Huisman
- Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of AmsterdamAmsterdam, Netherlands
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19
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Allahverdiyeva Y, Isojärvi J, Zhang P, Aro EM. Cyanobacterial Oxygenic Photosynthesis is Protected by Flavodiiron Proteins. Life (Basel) 2015; 5:716-43. [PMID: 25761262 PMCID: PMC4390876 DOI: 10.3390/life5010716] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/04/2015] [Accepted: 02/25/2015] [Indexed: 12/13/2022] Open
Abstract
Flavodiiron proteins (FDPs, also called flavoproteins, Flvs) are modular enzymes widely present in Bacteria and Archaea. The evolution of cyanobacteria and oxygenic photosynthesis occurred in concert with the modulation of typical bacterial FDPs. Present cyanobacterial FDPs are composed of three domains, the β-lactamase-like, flavodoxin-like and flavin-reductase like domains. Cyanobacterial FDPs function as hetero- and homodimers and are involved in the regulation of photosynthetic electron transport. Whilst Flv2 and Flv4 proteins are limited to specific cyanobacterial species (β-cyanobacteria) and function in photoprotection of Photosystem II, Flv1 and Flv3 proteins, functioning in the "Mehler-like" reaction and safeguarding Photosystem I under fluctuating light conditions, occur in nearly all cyanobacteria and additionally in green algae, mosses and lycophytes. Filamentous cyanobacteria have additional FDPs in heterocyst cells, ensuring a microaerobic environment for the function of the nitrogenase enzyme under the light. Here, the evolution, occurrence and functional mechanisms of various FDPs in oxygenic photosynthetic organisms are discussed.
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Affiliation(s)
- Yagut Allahverdiyeva
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland.
| | - Janne Isojärvi
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland.
| | - Pengpeng Zhang
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland.
| | - Eva-Mari Aro
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland.
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Burnap RL, Hagemann M, Kaplan A. Regulation of CO2 Concentrating Mechanism in Cyanobacteria. Life (Basel) 2015; 5:348-71. [PMID: 25636131 PMCID: PMC4390856 DOI: 10.3390/life5010348] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 01/15/2015] [Accepted: 01/21/2015] [Indexed: 12/31/2022] Open
Abstract
In this chapter, we mainly focus on the acclimation of cyanobacteria to the changing ambient CO2 and discuss mechanisms of inorganic carbon (Ci) uptake, photorespiration, and the regulation among the metabolic fluxes involved in photoautotrophic, photomixotrophic and heterotrophic growth. The structural components for several of the transport and uptake mechanisms are described and the progress towards elucidating their regulation is discussed in the context of studies, which have documented metabolomic changes in response to changes in Ci availability. Genes for several of the transport and uptake mechanisms are regulated by transcriptional regulators that are in the LysR-transcriptional regulator family and are known to act in concert with small molecule effectors, which appear to be well-known metabolites. Signals that trigger changes in gene expression and enzyme activity correspond to specific "regulatory metabolites" whose concentrations depend on the ambient Ci availability. Finally, emerging evidence for an additional layer of regulatory complexity involving small non-coding RNAs is discussed.
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Affiliation(s)
- Robert L Burnap
- Department of Microbiology and Molecular Genetics, Henry Bellmon Research Center, Oklahoma State University, Stillwater, OK 74078, USA.
| | - Martin Hagemann
- Institute Biosciences, Department Plant Physiology, University of Rostock, Albert-Einstein-Straße 3, Rostock D-18059, Germany.
| | - Aaron Kaplan
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, Givat Ram, Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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21
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Haimovich-Dayan M, Lieman-Hurwitz J, Orf I, Hagemann M, Kaplan A. Does 2-phosphoglycolate serve as an internal signal molecule of inorganic carbon deprivation in the cyanobacterium Synechocystis sp. PCC 6803? Environ Microbiol 2015; 17:1794-804. [PMID: 25297829 DOI: 10.1111/1462-2920.12638] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 09/19/2014] [Accepted: 09/22/2014] [Indexed: 11/30/2022]
Abstract
Cyanobacteria possess CO2 -concentrating mechanisms (CCM) that functionally compensate for the poor affinity of their ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) to CO2 . It was proposed that 2-phosphoglycolate (2PG), produced by the oxygenase activity of Rubisco and metabolized via photorespiratory routes, serves as a signal molecule for the induction of CCM-related genes under limiting CO2 level (LC) conditions. However, in vivo evidence is still missing. Since 2PG does not permeate the cells, we manipulated its internal concentration. Four putative phosphoglycolate phosphatases (PGPases) encoding genes (slr0458, sll1349, slr0586 and slr1762) were identified in the cyanobacterium Synechocystis PCC 6803. Expression of slr0458 in Escherichia coli led to a significant rise in PGPase activity. A Synechocystis mutant overexpressing (OE) slr0458 was constructed. Compared with the wild type (WT), the mutant grew slower under limiting CO2 concentration and the intracellular 2PG level was considerably smaller than in the wild type, the transcript abundance of LC-induced genes including cmpA, sbtA and ndhF3 was reduced, and the OE cells acclimated slower to LC - indicated by the delayed rise in the apparent photosynthetic affinity to inorganic carbon. Data obtained here implicated 2PG in the acclimation of this cyanobacterium to LC but also indicated that other, yet to be identified components, are involved.
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Affiliation(s)
- Maya Haimovich-Dayan
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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de Araujo C, Arefeen D, Tadesse Y, Long BM, Price GD, Rowlett RS, Kimber MS, Espie GS. Identification and characterization of a carboxysomal γ-carbonic anhydrase from the cyanobacterium Nostoc sp. PCC 7120. PHOTOSYNTHESIS RESEARCH 2014; 121:135-50. [PMID: 24907906 DOI: 10.1007/s11120-014-0018-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 05/19/2014] [Indexed: 05/26/2023]
Abstract
Carboxysomes are proteinaceous microcompartments that encapsulate carbonic anhydrase (CA) and ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco); carboxysomes, therefore, catalyze reversible HCO3 (-) dehydration and the subsequent fixation of CO2. The N- and C-terminal domains of the β-carboxysome scaffold protein CcmM participate in a network of protein-protein interactions that are essential for carboxysome biogenesis, organization, and function. The N-terminal domain of CcmM in the thermophile Thermosynechococcus elongatus BP-1 is also a catalytically active, redox regulated γ-CA. To experimentally determine if CcmM from a mesophilic cyanobacterium is active, we cloned, expressed and purified recombinant, full-length CcmM from Nostoc sp. PCC 7120 as well as the N-terminal 209 amino acid γ-CA-like domain. Both recombinant proteins displayed ethoxyzolamide-sensitive CA activity in mass spectrometric assays, as did the carboxysome-enriched TP fraction. NstCcmM209 was characterized as a moderately active and efficient γ-CA with a k cat of 2.0 × 10(4) s(-1) and k cat/K m of 4.1 × 10(6) M(-1) s(-1) at 25 °C and pH 8, a pH optimum between 8 and 9.5 and a temperature optimum spanning 25-35 °C. NstCcmM209 also catalyzed the hydrolysis of the CO2 analog carbonyl sulfide. Circular dichroism and intrinsic tryptophan fluorescence analysis demonstrated that NstCcmM209 was progressively and irreversibly denatured above 50 °C. NstCcmM209 activity was inhibited by the reducing agent tris(hydroxymethyl)phosphine, an effect that was fully reversed by a molar excess of diamide, a thiol oxidizing agent, consistent with oxidative activation being a universal regulatory mechanism of CcmM orthologs. Immunogold electron microscopy and Western blot analysis of TP pellets indicated that Rubisco and CcmM co-localize and are concentrated in Nostoc sp. PCC 7120 carboxysomes.
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Affiliation(s)
- Charlotte de Araujo
- Department of Cell & Systems Biology, University of Toronto, Mississauga, ON, Canada
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23
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Liang B, Wu TD, Sun HJ, Vali H, Guerquin-Kern JL, Wang CH, Bosak T. Cyanophycin mediates the accumulation and storage of fixed carbon in non-heterocystous filamentous cyanobacteria from coniform mats. PLoS One 2014; 9:e88142. [PMID: 24516596 PMCID: PMC3917874 DOI: 10.1371/journal.pone.0088142] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 01/06/2014] [Indexed: 11/19/2022] Open
Abstract
Thin, filamentous, non-heterocystous, benthic cyanobacteria (Subsection III) from some marine, lacustrine and thermal environments aggregate into macroscopic cones and conical stromatolites. We investigate the uptake and storage of inorganic carbon by cone-forming cyanobacteria from Yellowstone National Park using high-resolution stable isotope mapping of labeled carbon (H(13)CO3 (-)) and immunoassays. Observations and incubation experiments in actively photosynthesizing enrichment cultures and field samples reveal the presence of abundant cyanophycin granules in the active growth layer of cones. These ultrastructurally heterogeneous granules rapidly accumulate newly fixed carbon and store 18% of the total particulate labeled carbon after 120 mins of incubation. The intracellular distribution of labeled carbon during the incubation experiment demonstrates an unexpectedly large contribution of PEP carboxylase to carbon fixation, and a large flow of carbon and nitrogen toward cyanophycin in thin filamentous, non-heterocystous cyanobacteria. This pattern does not occur in obvious response to a changing N or C status. Instead, it may suggest an unusual interplay between the regulation of carbon concentration mechanisms and accumulation of photorespiratory products that facilitates uptake of inorganic C and reduces photorespiration in the dense, surface-attached communities of cyanobacteria from Subsection III.
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Affiliation(s)
- Biqing Liang
- Institute of Earth Sciences, Academia Sinica, Nangang, Taipei, Taiwan, ROC
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Earth Sciences, National Cheng Kung University, Tainan 701, Taiwan, ROC
| | - Ting-Di Wu
- INSERM, U759, Orsay, France
- Institut Curie, Laboratoire de Microscopie Ionique, Orsay, France
| | - Hao-Jhe Sun
- Department of Life Sciences, National Central University, Jhongli City, Taiwan, ROC
| | - Hojatollah Vali
- Facility for Electron Microscopy Research, McGill University, Montreal, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, Canada
| | - Jean-Luc Guerquin-Kern
- INSERM, U759, Orsay, France
- Institut Curie, Laboratoire de Microscopie Ionique, Orsay, France
| | - Chung-Ho Wang
- Institute of Earth Sciences, Academia Sinica, Nangang, Taipei, Taiwan, ROC
| | - Tanja Bosak
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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24
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Nagarajan S, Srivastava S, Sherman LA. Essential role of the plasmid hik31 operon in regulating central metabolism in the dark in Synechocystis sp. PCC 6803. Mol Microbiol 2013; 91:79-97. [PMID: 24237382 DOI: 10.1111/mmi.12442] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2013] [Indexed: 12/13/2022]
Abstract
The plasmid hik31 operon (P3, slr6039-slr6041) is located on the pSYSX plasmid in Synechocystis sp. PCC 6803. A P3 mutant (ΔP3) had a growth defect in the dark and a pigment defect that was worsened by the addition of glucose. The glucose defect was from incomplete metabolism of the substrate, was pH dependent, and completely overcome by the addition of bicarbonate. Addition of organic carbon and nitrogen sources partly alleviated the defects of the mutant in the dark. Electron micrographs of the mutant revealed larger cells with division defects, glycogen limitation, lack of carboxysomes, deteriorated thylakoids and accumulation of polyhydroxybutyrate and cyanophycin. A microarray experiment over two days of growth in light-dark plus glucose revealed downregulation of several photosynthesis, amino acid biosynthesis, energy metabolism genes; and an upregulation of cell envelope and transport and binding genes in the mutant. ΔP3 had an imbalance in carbon and nitrogen levels and many sugar catabolic and cell division genes were negatively affected after the first dark period. The mutant suffered from oxidative and osmotic stress, macronutrient limitation, and an energy deficit. Therefore, the P3 operon is an important regulator of central metabolism and cell division in the dark.
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Affiliation(s)
- Sowmya Nagarajan
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
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25
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Savakis PE, Angermayr SA, Hellingwerf KJ. Synthesis of 2,3-butanediol by Synechocystis sp. PCC6803 via heterologous expression of a catabolic pathway from lactic acid- and enterobacteria. Metab Eng 2013; 20:121-30. [DOI: 10.1016/j.ymben.2013.09.008] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 09/25/2013] [Accepted: 09/26/2013] [Indexed: 02/08/2023]
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26
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Rae BD, Long BM, Badger MR, Price GD. Functions, compositions, and evolution of the two types of carboxysomes: polyhedral microcompartments that facilitate CO2 fixation in cyanobacteria and some proteobacteria. Microbiol Mol Biol Rev 2013; 77:357-79. [PMID: 24006469 PMCID: PMC3811607 DOI: 10.1128/mmbr.00061-12] [Citation(s) in RCA: 242] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cyanobacteria are the globally dominant photoautotrophic lineage. Their success is dependent on a set of adaptations collectively termed the CO2-concentrating mechanism (CCM). The purpose of the CCM is to support effective CO2 fixation by enhancing the chemical conditions in the vicinity of the primary CO2-fixing enzyme, D-ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), to promote the carboxylase reaction and suppress the oxygenase reaction. In cyanobacteria and some proteobacteria, this is achieved by encapsulation of RubisCO within carboxysomes, which are examples of a group of proteinaceous bodies called bacterial microcompartments. Carboxysomes encapsulate the CO2-fixing enzyme within the selectively permeable protein shell and simultaneously encapsulate a carbonic anhydrase enzyme for CO2 supply from a cytoplasmic bicarbonate pool. These bodies appear to have arisen twice and undergone a process of convergent evolution. While the gross structures of all known carboxysomes are ostensibly very similar, with shared gross features such as a selectively permeable shell layer, each type of carboxysome encapsulates a phyletically distinct form of RubisCO enzyme. Furthermore, the specific proteins forming structures such as the protein shell or the inner RubisCO matrix are not identical between carboxysome types. Each type has evolutionarily distinct forms of the same proteins, as well as proteins that are entirely unrelated to one another. In light of recent developments in the study of carboxysome structure and function, we present this review to summarize the knowledge of the structure and function of both types of carboxysome. We also endeavor to cast light on differing evolutionary trajectories which may have led to the differences observed in extant carboxysomes.
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Affiliation(s)
- Benjamin D Rae
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, ACT, Australia
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27
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Hagemann M, Fernie AR, Espie GS, Kern R, Eisenhut M, Reumann S, Bauwe H, Weber APM. Evolution of the biochemistry of the photorespiratory C2 cycle. PLANT BIOLOGY (STUTTGART, GERMANY) 2013; 15:639-647. [PMID: 23198988 DOI: 10.1111/j.1438-8677.2012.00677.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 08/23/2012] [Indexed: 05/23/2023]
Abstract
Oxygenic photosynthesis would not be possible without photorespiration in the present day O2 -rich atmosphere. It is now generally accepted that cyanobacteria-like prokaryotes first evolved oxygenic photosynthesis, which was later conveyed via endosymbiosis into a eukaryotic host, which then gave rise to the different groups of algae and streptophytes. For photosynthetic CO2 fixation, all these organisms use RubisCO, which catalyses both the carboxylation and the oxygenation of ribulose 1,5-bisphosphate. One of the reaction products of the oxygenase reaction, 2-phosphoglycolate (2PG), represents the starting point of the photorespiratory C2 cycle, which is considered largely responsible for recapturing organic carbon via conversion to the Calvin-Benson cycle (CBC) intermediate 3-phosphoglycerate, thereby detoxifying critical intermediates. Here we discuss possible scenarios for the evolution of this process toward the well-defined 2PG metabolism in extant plants. While the origin of the C2 cycle core enzymes can be clearly dated back towards the different endosymbiotic events, the evolutionary scenario that allowed the compartmentalised high flux photorespiratory cycle is uncertain, but probably occurred early during the algal radiation. The change in atmospheric CO2 /O2 ratios promoting the acquisition of different modes for inorganic carbon concentration mechanisms, as well as the evolutionary specialisation of peroxisomes, clearly had a dramatic impact on further aspects of land plant photorespiration.
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Affiliation(s)
- M Hagemann
- Institute of Biosciences, Plant Physiology, University of Rostock, Rostock, Germany.
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28
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Fernie AR, Bauwe H, Eisenhut M, Florian A, Hanson DT, Hagemann M, Keech O, Mielewczik M, Nikoloski Z, Peterhänsel C, Roje S, Sage R, Timm S, von Cammerer S, Weber APM, Westhoff P. Perspectives on plant photorespiratory metabolism. PLANT BIOLOGY (STUTTGART, GERMANY) 2013; 15:748-753. [PMID: 23231538 DOI: 10.1111/j.1438-8677.2012.00693.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 09/21/2012] [Indexed: 06/01/2023]
Abstract
Being intimately intertwined with (C3) photosynthesis, photorespiration is an incredibly high flux-bearing pathway. Traditionally, the photorespiratory cycle was viewed as closed pathway to refill the Calvin-Benson cycle with organic carbon. However, given the network nature of metabolism, it hence follows that photorespiration will interact with many other pathways. In this article, we review current understanding of these interactions and attempt to define key priorities for future research, which will allow us greater fundamental comprehension of general metabolic and developmental consequences of perturbation of this crucial metabolic process.
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Affiliation(s)
- A R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
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29
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Phosphoglycerate mutases function as reverse regulated isoenzymes in Synechococcus elongatus PCC 7942. PLoS One 2013; 8:e58281. [PMID: 23484009 PMCID: PMC3590821 DOI: 10.1371/journal.pone.0058281] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 02/01/2013] [Indexed: 11/19/2022] Open
Abstract
Phosphoglycerate-mutase (PGM) is an ubiquitous glycolytic enzyme, which in eukaryotic cells can be found in different compartments. In prokaryotic cells, several PGMs are annotated/localized in one compartment. The identification and functional characterization of PGMs in prokaryotes is therefore important for better understanding of metabolic regulation. Here we introduce a method, based on a multi-level kinetic model of the primary carbon metabolism in cyanobacterium Synechococcus elongatus PCC 7942, that allows the identification of a specific function for a particular PGM. The strategy employs multiple parameter estimation runs in high CO2, combined with simulations testing a broad range of kinetic parameters against the changes in transcript levels of annotated PGMs. Simulations are evaluated for a match in metabolic level in low CO2, to reveal trends that can be linked to the function of a particular PGM. A one-isoenzyme scenario shows that PGM2 is a major regulator of glycolysis, while PGM1 and PGM4 make the system robust against environmental changes. Strikingly, combining two PGMs with reverse transcriptional regulation allows both features. A conclusion arising from our analysis is that a two-enzyme PGM system is required to regulate the flux between glycolysis and the Calvin-Benson cycle, while an additional PGM increases the robustness of the system.
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30
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Schwarz D, Orf I, Kopka J, Hagemann M. Recent applications of metabolomics toward cyanobacteria. Metabolites 2013; 3:72-100. [PMID: 24957891 PMCID: PMC3901253 DOI: 10.3390/metabo3010072] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 01/23/2013] [Accepted: 01/23/2013] [Indexed: 11/16/2022] Open
Abstract
Our knowledge on cyanobacterial molecular biology increased tremendously by the application of the "omics" techniques. Only recently, metabolomics was applied systematically to model cyanobacteria. Metabolomics, the quantitative estimation of ideally the complete set of cellular metabolites, is particularly well suited to mirror cellular metabolism and its flexibility under diverse conditions. Traditionally, small sets of metabolites are quantified in targeted metabolome approaches. The development of separation technologies coupled to mass-spectroscopy- or nuclear-magnetic-resonance-based identification of low molecular mass molecules presently allows the profiling of hundreds of metabolites of diverse chemical nature. Metabolome analysis was applied to characterize changes in the cyanobacterial primary metabolism under diverse environmental conditions or in defined mutants. The resulting lists of metabolites and their steady state concentrations in combination with transcriptomics can be used in system biology approaches. The application of stable isotopes in fluxomics, i.e. the quantitative estimation of carbon and nitrogen fluxes through the biochemical network, has only rarely been applied to cyanobacteria, but particularly this technique will allow the making of kinetic models of cyanobacterial systems. The further application of metabolomics in the concert of other "omics" technologies will not only broaden our knowledge, but will also certainly strengthen the base for the biotechnological application of cyanobacteria.
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Affiliation(s)
- Doreen Schwarz
- Institut Biowissenschaften, Pflanzenphysiologie, Universität Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany.
| | - Isabel Orf
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Golm, Germany.
| | - Joachim Kopka
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Golm, Germany.
| | - Martin Hagemann
- Institut Biowissenschaften, Pflanzenphysiologie, Universität Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany.
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