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Bolay P, Dodge N, Janssen K, Jensen PE, Lindberg P. Tailoring regulatory components for metabolic engineering in cyanobacteria. PHYSIOLOGIA PLANTARUM 2024; 176:e14316. [PMID: 38686633 DOI: 10.1111/ppl.14316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/26/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024]
Abstract
The looming climate crisis has prompted an ever-growing interest in cyanobacteria due to their potential as sustainable production platforms for the synthesis of energy carriers and value-added chemicals from CO2 and sunlight. Nonetheless, cyanobacteria are yet to compete with heterotrophic systems in terms of space-time yields and consequently production costs. One major drawback leading to the low production performance observed in cyanobacteria is the limited ability to utilize the full capacity of the photosynthetic apparatus and its associated systems, i.e. CO2 fixation and the directly connected metabolism. In this review, novel insights into various levels of metabolic regulation of cyanobacteria are discussed, including the potential of targeting these regulatory mechanisms to create a chassis with a phenotype favorable for photoautotrophic production. Compared to conventional metabolic engineering approaches, minor perturbations of regulatory mechanisms can have wide-ranging effects.
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Affiliation(s)
- Paul Bolay
- Microbial Chemistry, Department of Chemistry - Ångström, Uppsala University, Uppsala, SE, Sweden
| | - Nadia Dodge
- Plant Based Foods and Biochemistry, Food Analytics and Biotechnology, Department of Food Science, University of Copenhagen, Denmark
| | - Kim Janssen
- Microbial Chemistry, Department of Chemistry - Ångström, Uppsala University, Uppsala, SE, Sweden
| | - Poul Erik Jensen
- Plant Based Foods and Biochemistry, Food Analytics and Biotechnology, Department of Food Science, University of Copenhagen, Denmark
| | - Pia Lindberg
- Microbial Chemistry, Department of Chemistry - Ångström, Uppsala University, Uppsala, SE, Sweden
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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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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: 0] [Impact Index Per Article: 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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Miao R, Jahn M, Shabestary K, Peltier G, Hudson EP. CRISPR interference screens reveal growth-robustness tradeoffs in Synechocystis sp. PCC 6803 across growth conditions. THE PLANT CELL 2023; 35:3937-3956. [PMID: 37494719 PMCID: PMC10615215 DOI: 10.1093/plcell/koad208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/01/2023] [Accepted: 07/20/2023] [Indexed: 07/28/2023]
Abstract
Barcoded mutant libraries are a powerful tool for elucidating gene function in microbes, particularly when screened in multiple growth conditions. Here, we screened a pooled CRISPR interference library of the model cyanobacterium Synechocystis sp. PCC 6803 in 11 bioreactor-controlled conditions, spanning multiple light regimes and carbon sources. This gene repression library contained 21,705 individual mutants with high redundancy over all open reading frames and noncoding RNAs. Comparison of the derived gene fitness scores revealed multiple instances of gene repression being beneficial in 1 condition while generally detrimental in others, particularly for genes within light harvesting and conversion, such as antennae components at high light and PSII subunits during photoheterotrophy. Suboptimal regulation of such genes likely represents a tradeoff of reduced growth speed for enhanced robustness to perturbation. The extensive data set assigns condition-specific importance to many previously unannotated genes and suggests additional functions for central metabolic enzymes. Phosphoribulokinase, glyceraldehyde-3-phosphate dehydrogenase, and the small protein CP12 were critical for mixotrophy and photoheterotrophy, which implicates the ternary complex as important for redirecting metabolic flux in these conditions in addition to inactivation of the Calvin cycle in the dark. To predict the potency of sgRNA sequences, we applied machine learning on sgRNA sequences and gene repression data, which showed the importance of C enrichment and T depletion proximal to the PAM site. Fitness data for all genes in all conditions are compiled in an interactive web application.
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Affiliation(s)
- Rui Miao
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH—Royal Institute of Technology, Stockholm, SE-17165,Sweden
| | - Michael Jahn
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH—Royal Institute of Technology, Stockholm, SE-17165,Sweden
- Max Planck Unit for the Science of Pathogens, 10117 Berlin,Germany
| | - Kiyan Shabestary
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH—Royal Institute of Technology, Stockholm, SE-17165,Sweden
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ,UK
| | - Gilles Peltier
- Aix Marseille Univ, CEA, CNRS, Institut de Biosciences et Biotechnologies Aix-Marseille, CEA Cadarache, 13108 Saint Paul-Lez-Durance,France
| | - Elton P Hudson
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH—Royal Institute of Technology, Stockholm, SE-17165,Sweden
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Del Giudice A, Gurrieri L, Galantini L, Fanti S, Trost P, Sparla F, Fermani S. Conformational Disorder Analysis of the Conditionally Disordered Protein CP12 from Arabidopsis thaliana in Its Different Redox States. Int J Mol Sci 2023; 24:ijms24119308. [PMID: 37298260 DOI: 10.3390/ijms24119308] [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: 04/10/2023] [Revised: 05/18/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
CP12 is a redox-dependent conditionally disordered protein universally distributed in oxygenic photosynthetic organisms. It is primarily known as a light-dependent redox switch regulating the reductive step of the metabolic phase of photosynthesis. In the present study, a small angle X-ray scattering (SAXS) analysis of recombinant Arabidopsis CP12 (AtCP12) in a reduced and oxidized form confirmed the highly disordered nature of this regulatory protein. However, it clearly pointed out a decrease in the average size and a lower level of conformational disorder upon oxidation. We compared the experimental data with the theoretical profiles of pools of conformers generated with different assumptions and show that the reduced form is fully disordered, whereas the oxidized form is better described by conformers comprising both the circular motif around the C-terminal disulfide bond detected in previous structural analysis and the N-terminal disulfide bond. Despite the fact that disulfide bridges are usually thought to confer rigidity to protein structures, in the oxidized AtCP12, their presence coexists with a disordered nature. Our results rule out the existence of significant amounts of structured and compact conformations of free AtCP12 in a solution, even in its oxidized form, thereby highlighting the importance of recruiting partner proteins to complete its structured final folding.
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Affiliation(s)
| | - Libero Gurrieri
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Luciano Galantini
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy
| | - Silvia Fanti
- Department of Chemistry "G. Ciamician", University of Bologna, 40126 Bologna, Italy
| | - Paolo Trost
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Francesca Sparla
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Simona Fermani
- Department of Chemistry "G. Ciamician", University of Bologna, 40126 Bologna, Italy
- Interdepartmental Centre for Industrial Research Health Sciences & Technologies, University of Bologna, 40064 Bologna, Italy
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Toepel J, Karande R, Klähn S, Bühler B. Cyanobacteria as whole-cell factories: current status and future prospectives. Curr Opin Biotechnol 2023; 80:102892. [PMID: 36669448 DOI: 10.1016/j.copbio.2023.102892] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/08/2022] [Accepted: 12/20/2022] [Indexed: 01/20/2023]
Abstract
Cyanobacteria as phototrophic microorganisms bear great potential to produce chemicals from sustainable resources such as light and CO2. Most studies focus on either strain engineering or tackling metabolic constraints. Recently gained knowledge on internal electron and carbon fluxes and their regulation provides new opportunities to efficiently channel cellular resources toward product formation. Concomitantly, novel photobioreactor concepts are developed to ensure sufficient light supply. This review summarizes the newest developments in the field of cyanobacterial engineering to finally establish photosynthesis-based production processes. A holistic approach tackling genetic, metabolic, and biochemical engineering in parallel is considered essential to turn their application into an ecoefficient and economically feasible option for a future green bioeconomy.
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Affiliation(s)
- Jörg Toepel
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Rohan Karande
- Research and Transfer Center for bioactive Matter b-ACTmatter, University of Leipzig, Germany
| | - Stephan Klähn
- Department of Solar Materials, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Bruno Bühler
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.
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Selim KA, Haffner M, Mantovani O, Albrecht R, Zhu H, Hagemann M, Forchhammer K, Hartmann MD. Carbon signaling protein SbtB possesses atypical redox-regulated apyrase activity to facilitate regulation of bicarbonate transporter SbtA. Proc Natl Acad Sci U S A 2023; 120:e2205882120. [PMID: 36800386 PMCID: PMC9974498 DOI: 10.1073/pnas.2205882120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 12/15/2022] [Indexed: 02/18/2023] Open
Abstract
The PII superfamily consists of widespread signal transduction proteins found in all domains of life. In addition to canonical PII proteins involved in C/N sensing, structurally similar PII-like proteins evolved to fulfill diverse, yet poorly understood cellular functions. In cyanobacteria, the bicarbonate transporter SbtA is co-transcribed with the conserved PII-like protein, SbtB, to augment intracellular inorganic carbon levels for efficient CO2 fixation. We identified SbtB as a sensor of various adenine nucleotides including the second messenger nucleotides cyclic AMP (cAMP) and c-di-AMP. Moreover, many SbtB proteins possess a C-terminal extension with a disulfide bridge of potential redox-regulatory function, which we call R-loop. Here, we reveal an unusual ATP/ADP apyrase (diphosphohydrolase) activity of SbtB that is controlled by the R-loop. We followed the sequence of hydrolysis reactions from ATP over ADP to AMP in crystallographic snapshots and unravel the structural mechanism by which changes of the R-loop redox state modulate apyrase activity. We further gathered evidence that this redox state is controlled by thioredoxin, suggesting that it is generally linked to cellular metabolism, which is supported by physiological alterations in site-specific mutants of the SbtB protein. Finally, we present a refined model of how SbtB regulates SbtA activity, in which both the apyrase activity and its redox regulation play a central role. This highlights SbtB as a central switch point in cyanobacterial cell physiology, integrating not only signals from the energy state (adenyl-nucleotide binding) and the carbon supply via cAMP binding but also from the day/night status reported by the C-terminal redox switch.
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Affiliation(s)
- Khaled A. Selim
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, 72076Tübingen, Germany
- Department of Protein Evolution, Max Planck Institute for Biology, 72076Tübingen, Germany
| | - Michael Haffner
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, 72076Tübingen, Germany
| | - Oliver Mantovani
- Plant Physiology Department, Institute of Biological Sciences, Rostock University, 18059Rostock, Germany
| | - Reinhard Albrecht
- Department of Protein Evolution, Max Planck Institute for Biology, 72076Tübingen, Germany
| | - Hongbo Zhu
- Department of Protein Evolution, Max Planck Institute for Biology, 72076Tübingen, Germany
| | - Martin Hagemann
- Plant Physiology Department, Institute of Biological Sciences, Rostock University, 18059Rostock, Germany
| | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, 72076Tübingen, Germany
| | - Marcus D. Hartmann
- Department of Protein Evolution, Max Planck Institute for Biology, 72076Tübingen, Germany
- Interfaculty Institute of Biochemistry, Tübingen University, 72076Tübingen, Germany
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