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Ugya AY, Hasan DB, Ari HA, Sheng Y, Chen H, Wang Q. Antibiotic synergistic effect surge bioenergy potential and pathogen resistance of Chlorella variabilis biofilm. ENVIRONMENTAL RESEARCH 2024; 259:119521. [PMID: 38960350 DOI: 10.1016/j.envres.2024.119521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 06/21/2024] [Accepted: 06/29/2024] [Indexed: 07/05/2024]
Abstract
Tetracycline (TC) and ciprofloxacin (CF) induce a synergistic effect that alters the biochemical composition, leading to a decrease in the growth and photosynthetic efficiency of microalgae. But the current study provides a novel insight into stress-inducing techniques that trigger a change in macromolecules, leading to an increase in the bioenergy potential and pathogen resistance of Chlorella variabilis biofilm. The study revealed that in a closed system, a light intensity of 167 μmol/m2/s causes 93.5% degradation of TC and 16% degradation of CF after 7 days of exposure, hence availing the products for utilization by C. variabilis biofilm. The resistance to pathogens invasion was linked to 85% and 40% increase in the expression level of photosystem II oxygen-evolving enhancer protein 3 (PsbQ), and mitogen activated kinase (MAK) respectively. The results also indicate that a surge in light intensity triggers 49% increase in the expression level of lysophosphatidylcholine (LPC) (18:2), which is an important lipidomics that can easily undergo transesterification into bioenergy. The thermogravimetric result indicates that the biomass sample of C. variabilis biofilm cultivated under light intensity of 167 μmol/m2/s produces a higher residual mass of 45.5% and 57.5 under air and inert conditions, respectively. The Fourier transform infrared (FTIR) indicates a slight shift in the major functional groups, while the energy-dispersive X-ray spectroscopy (SEM-EDS) and X-ray fluorescence (XRF) indicate clear differences in the morphology and elemental composition of the biofilm biomass in support of the increase bioenergy potential of C. variabilis biofilm. The current study provides a vital understanding of a innovative method of cultivation of C. variabilis biofilm, which is resistant to pathogens and controls the balance between fatty acid and TAG synthesis leading to surge in bioenergy potential and environmental sustainability.
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Affiliation(s)
- Adamu Yunusa Ugya
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China; Henan Key Laboratory of Synthetic Biology and Biomanufacturing, Henan University, Kaifeng, China; Department of Environmental Management, Kaduna State University, Kaduna State, Nigeria
| | - Diya'uddeen Basheer Hasan
- Centre for Energy Research and Training (CERT), Ahmadu Bello University, Zaria, Kaduna State, Nigeria
| | | | - Yangyang Sheng
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Hui Chen
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China; Henan Key Laboratory of Synthetic Biology and Biomanufacturing, Henan University, Kaifeng, China
| | - Qiang Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China; Henan Key Laboratory of Synthetic Biology and Biomanufacturing, Henan University, Kaifeng, China.
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2
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Steichen S, Deshpande A, Mosey M, Loob J, Douchi D, Knoshaug EP, Brown S, Nielsen R, Weissman J, Carrillo LR, Laurens LML. Central transcriptional regulator controls photosynthetic growth and carbon storage in response to high light. Nat Commun 2024; 15:4842. [PMID: 38844786 PMCID: PMC11156908 DOI: 10.1038/s41467-024-49090-7] [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: 12/08/2023] [Accepted: 05/14/2024] [Indexed: 06/09/2024] Open
Abstract
Carbon capture and biochemical storage are some of the primary drivers of photosynthetic yield and productivity. To elucidate the mechanisms governing carbon allocation, we designed a photosynthetic light response test system for genetic and metabolic carbon assimilation tracking, using microalgae as simplified plant models. The systems biology mapping of high light-responsive photophysiology and carbon utilization dynamics between two variants of the same Picochlorum celeri species, TG1 and TG2 elucidated metabolic bottlenecks and transport rates of intermediates using instationary 13C-fluxomics. Simultaneous global gene expression dynamics showed 73% of the annotated genes responding within one hour, elucidating a singular, diel-responsive transcription factor, closely related to the CCA1/LHY clock genes in plants, with significantly altered expression in TG2. Transgenic P. celeri TG1 cells expressing the TG2 CCA1/LHY gene, showed 15% increase in growth rates and 25% increase in storage carbohydrate content, supporting a coordinating regulatory function for a single transcription factor.
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Affiliation(s)
- Seth Steichen
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Arnav Deshpande
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Megan Mosey
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Jessica Loob
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Damien Douchi
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Eric P Knoshaug
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Stuart Brown
- ExxonMobil Technology and Engineering Co. (EMTEC), CLD286 Annandale, 1545 Route 22 East, Annandale, NJ, 08801, USA
| | - Robert Nielsen
- ExxonMobil Technology and Engineering Co. (EMTEC), CLD286 Annandale, 1545 Route 22 East, Annandale, NJ, 08801, USA
| | - Joseph Weissman
- ExxonMobil Technology and Engineering Co. (EMTEC), CLD286 Annandale, 1545 Route 22 East, Annandale, NJ, 08801, USA
| | - L Ruby Carrillo
- ExxonMobil Technology and Engineering Co. (EMTEC), CLD286 Annandale, 1545 Route 22 East, Annandale, NJ, 08801, USA
| | - Lieve M L Laurens
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA.
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3
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Liu F, Gaul L, Giometto A, Wu M. A high throughput array microhabitat platform reveals how light and nitrogen colimit the growth of algal cells. Sci Rep 2024; 14:9860. [PMID: 38684720 PMCID: PMC11058252 DOI: 10.1038/s41598-024-59041-3] [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: 11/16/2023] [Accepted: 04/05/2024] [Indexed: 05/02/2024] Open
Abstract
A mechanistic understanding of algal growth is essential for maintaining a sustainable environment in an era of climate change and population expansion. It is known that algal growth is tightly controlled by complex interactive physical and chemical conditions. Many mathematical models have been proposed to describe the relation of algal growth and environmental parameters, but experimental verification has been difficult due to the lack of tools to measure cell growth under precise physical and chemical conditions. As such, current models depend on the specific testing systems, and the fitted growth kinetic constants vary widely for the same organisms in the existing literature. Here, we present a microfluidic platform where both light intensity and nutrient gradients can be well controlled for algal cell growth studies. In particular, light shading is avoided, a common problem in macroscale assays. Our results revealed that light and nitrogen colimit the growth of algal cells, with each contributing a Monod growth kinetic term in a multiplicative model. We argue that the microfluidic platform can lead towards a general culture system independent algal growth model with systematic screening of many environmental parameters. Our work advances technology for algal cell growth studies and provides essential information for future bioreactor designs and ecological predictions.
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Affiliation(s)
- Fangchen Liu
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - Larissa Gaul
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - Andrea Giometto
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, USA.
| | - Mingming Wu
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA.
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4
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Plouviez M, Dubreucq E. Key Proteomics Tools for Fundamental and Applied Microalgal Research. Proteomes 2024; 12:13. [PMID: 38651372 PMCID: PMC11036299 DOI: 10.3390/proteomes12020013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/28/2024] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
Microscopic, photosynthetic prokaryotes and eukaryotes, collectively referred to as microalgae, are widely studied to improve our understanding of key metabolic pathways (e.g., photosynthesis) and for the development of biotechnological applications. Omics technologies, which are now common tools in biological research, have been shown to be critical in microalgal research. In the past decade, significant technological advancements have allowed omics technologies to become more affordable and efficient, with huge datasets being generated. In particular, where studies focused on a single or few proteins decades ago, it is now possible to study the whole proteome of a microalgae. The development of mass spectrometry-based methods has provided this leap forward with the high-throughput identification and quantification of proteins. This review specifically provides an overview of the use of proteomics in fundamental (e.g., photosynthesis) and applied (e.g., lipid production for biofuel) microalgal research, and presents future research directions in this field.
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Affiliation(s)
- Maxence Plouviez
- School of Agriculture and Environment, Massey University, Palmerston North 4410, New Zealand
- The Cawthron Institute, Nelson 7010, New Zealand
| | - Eric Dubreucq
- Agropolymer Engineering and Emerging Technologies, L’Institut Agro Montpellier, 34060 Montpellier, France;
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Meloni M, Fanti S, Tedesco D, Gurrieri L, Trost P, Fermani S, Lemaire SD, Zaffagnini M, Henri J. Characterization of chloroplast ribulose-5-phosphate-3-epimerase from the microalga Chlamydomonas reinhardtii. PLANT PHYSIOLOGY 2024; 194:2263-2277. [PMID: 38134324 DOI: 10.1093/plphys/kiad680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/09/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023]
Abstract
Carbon fixation relies on Rubisco and 10 additional enzymes in the Calvin-Benson-Bassham cycle. Epimerization of xylulose-5-phosphate (Xu5P) into ribulose-5-phosphate (Ru5P) contributes to the regeneration of ribulose-1,5-bisphosphate, the substrate of Rubisco. Ribulose-5-phosphate-3-epimerase (RPE, EC 5.1.3.1) catalyzes the formation of Ru5P, but it can also operate in the pentose-phosphate pathway by catalyzing the reverse reaction. Here, we describe the structural and biochemical properties of the recombinant RPE isoform 1 from Chlamydomonas (Chlamydomonas reinhardtii) (CrRPE1). The enzyme is a homo-hexamer that contains a zinc ion in the active site and exposes a catalytic pocket on the top of an α8β8 triose isomerase-type barrel as observed in structurally solved RPE isoforms from both plant and non-plant sources. By optimizing and developing enzyme assays to monitor the reversible epimerization of Ru5P to Xu5P and vice versa, we determined the catalytic parameters that differ from those of other plant paralogs. Despite being identified as a putative target of multiple thiol-based redox modifications, CrRPE1 activity is not affected by both reductive and oxidative treatments, indicating that enzyme catalysis is insensitive to possible redox alterations of cysteine residues. We mapped phosphorylation sites on the crystal structure, and the specific location at the entrance of the catalytic cleft supports a phosphorylation-based regulatory mechanism. This work provides an accurate description of the structural features of CrRPE1 and an in-depth examination of its catalytic and regulatory properties highlighting the physiological relevance of this enzyme in the context of photosynthetic carbon fixation.
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Affiliation(s)
- Maria Meloni
- Laboratory of Molecular Plant Physiology, Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
- Sorbonne Université, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, UMR 7238, 4 Place Jussieu, 75005, Paris, France
| | - Silvia Fanti
- Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Daniele Tedesco
- Institute for Organic Synthesis and Photoreactivity, National Research Council (ISOF-CNR), Via Gobetti 101, 40129, Bologna, Italy
| | - Libero Gurrieri
- Laboratory of Molecular Plant Physiology, Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Paolo Trost
- Laboratory of Molecular Plant Physiology, Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Simona Fermani
- Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Stéphane D Lemaire
- Sorbonne Université, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, UMR 7238, 4 Place Jussieu, 75005, Paris, France
| | - Mirko Zaffagnini
- Laboratory of Molecular Plant Physiology, Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Julien Henri
- Sorbonne Université, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, UMR 7238, 4 Place Jussieu, 75005, Paris, France
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6
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Westhoff P, Weber APM. The role of metabolomics in informing strategies for improving photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1696-1713. [PMID: 38158893 DOI: 10.1093/jxb/erad508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
Photosynthesis plays a vital role in acclimating to and mitigating climate change, providing food and energy security for a population that is constantly growing, and achieving an economy with zero carbon emissions. A thorough comprehension of the dynamics of photosynthesis, including its molecular regulatory network and limitations, is essential for utilizing it as a tool to boost plant growth, enhance crop yields, and support the production of plant biomass for carbon storage. Photorespiration constrains photosynthetic efficiency and contributes significantly to carbon loss. Therefore, modulating or circumventing photorespiration presents opportunities to enhance photosynthetic efficiency. Over the past eight decades, substantial progress has been made in elucidating the molecular basis of photosynthesis, photorespiration, and the key regulatory mechanisms involved, beginning with the discovery of the canonical Calvin-Benson-Bassham cycle. Advanced chromatographic and mass spectrometric technologies have allowed a comprehensive analysis of the metabolite patterns associated with photosynthesis, contributing to a deeper understanding of its regulation. In this review, we summarize the results of metabolomics studies that shed light on the molecular intricacies of photosynthetic metabolism. We also discuss the methodological requirements essential for effective analysis of photosynthetic metabolism, highlighting the value of this technology in supporting strategies aimed at enhancing photosynthesis.
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Affiliation(s)
- Philipp Westhoff
- CEPLAS Plant Metabolomics and Metabolism Laboratory, Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
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7
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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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8
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Gurrieri L, Sparla F, Zaffagnini M, Trost P. Dark complexes of the Calvin-Benson cycle in a physiological perspective. Semin Cell Dev Biol 2024; 155:48-58. [PMID: 36889996 DOI: 10.1016/j.semcdb.2023.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK) are two enzymes of the Calvin Benson cycle that stand out for some peculiar properties they have in common: (i) they both use the products of light reactions for catalysis (NADPH for GAPDH, ATP for PRK), (ii) they are both light-regulated through thioredoxins and (iii) they are both involved in the formation of regulatory supramolecular complexes in the dark or low photosynthetic conditions, with or without the regulatory protein CP12. In the complexes, enzymes are transiently inactivated but ready to recover full activity after complex dissociation. Fully active GAPDH and PRK are in large excess for the functioning of the Calvin-Benson cycle, but they can limit the cycle upon complex formation. Complex dissociation contributes to photosynthetic induction. CP12 also controls PRK concentration in model photosynthetic organisms like Arabidopsis thaliana and Chlamydomonas reinhardtii. The review combines in vivo and in vitro data into an integrated physiological view of the role of GAPDH and PRK dark complexes in the regulation of photosynthesis.
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Affiliation(s)
- Libero Gurrieri
- University of Bologna, Department of Pharmacy and Biotechnology, Via Irnerio 42, 40126 Bologna, Italy.
| | - Francesca Sparla
- University of Bologna, Department of Pharmacy and Biotechnology, Via Irnerio 42, 40126 Bologna, Italy.
| | - Mirko Zaffagnini
- University of Bologna, Department of Pharmacy and Biotechnology, Via Irnerio 42, 40126 Bologna, Italy.
| | - Paolo Trost
- University of Bologna, Department of Pharmacy and Biotechnology, Via Irnerio 42, 40126 Bologna, Italy.
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9
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Clapero V, Arrivault S, Stitt M. Natural variation in metabolism of the Calvin-Benson cycle. Semin Cell Dev Biol 2024; 155:23-36. [PMID: 36959059 DOI: 10.1016/j.semcdb.2023.02.015] [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: 08/24/2022] [Revised: 02/24/2023] [Accepted: 02/24/2023] [Indexed: 03/25/2023]
Abstract
The Calvin-Benson cycle (CBC) evolved over 2 billion years ago but has been subject to massive selection due to falling atmospheric carbon dioxide, rising atmospheric oxygen and changing nutrient and water availability. In addition, large groups of organisms have evolved carbon-concentrating mechanisms (CCMs) that operate upstream of the CBC. Most previous studies of CBC diversity focused on Rubisco kinetics and regulation. Quantitative metabolite profiling provides a top-down strategy to uncover inter-species diversity in CBC operation. CBC profiles were recently published for twenty species including terrestrial C3 species, terrestrial C4 species that operate a biochemical CCM, and cyanobacteria and green algae that operate different types of biophysical CCM. Distinctive profiles were found for species with different modes of photosynthesis, revealing that evolution of the various CCMs was accompanied by co-evolution of the CBC. Diversity was also found between species that share the same mode of photosynthesis, reflecting lineage-dependent diversity of the CBC. Connectivity analysis uncovers constraints due to pathway and thermodynamic topology, and reveals that cross-species diversity in the CBC is driven by changes in the balance between regulated enzymes and in the balance between the CBC and the light reactions or end-product synthesis.
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Affiliation(s)
- Vittoria Clapero
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Golm, D-14476 Potsdam, Germany
| | - Stéphanie Arrivault
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Golm, D-14476 Potsdam, Germany.
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Golm, D-14476 Potsdam, Germany
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Naseema Rasheed R, Pourbakhtiar A, Mehdizadeh Allaf M, Baharlooeian M, Rafiei N, Alishah Aratboni H, Morones-Ramirez JR, Winck FV. Microalgal co-cultivation -recent methods, trends in omic-studies, applications, and future challenges. Front Bioeng Biotechnol 2023; 11:1193424. [PMID: 37799812 PMCID: PMC10548143 DOI: 10.3389/fbioe.2023.1193424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/08/2023] [Indexed: 10/07/2023] Open
Abstract
The burgeoning human population has resulted in an augmented demand for raw materials and energy sources, which in turn has led to a deleterious environmental impact marked by elevated greenhouse gas (GHG) emissions, acidification of water bodies, and escalating global temperatures. Therefore, it is imperative that modern society develop sustainable technologies to avert future environmental degradation and generate alternative bioproduct-producing technologies. A promising approach to tackling this challenge involves utilizing natural microbial consortia or designing synthetic communities of microorganisms as a foundation to develop diverse and sustainable applications for bioproduct production, wastewater treatment, GHG emission reduction, energy crisis alleviation, and soil fertility enhancement. Microalgae, which are photosynthetic microorganisms that inhabit aquatic environments and exhibit a high capacity for CO2 fixation, are particularly appealing in this context. They can convert light energy and atmospheric CO2 or industrial flue gases into valuable biomass and organic chemicals, thereby contributing to GHG emission reduction. To date, most microalgae cultivation studies have focused on monoculture systems. However, maintaining a microalgae monoculture system can be challenging due to contamination by other microorganisms (e.g., yeasts, fungi, bacteria, and other microalgae species), which can lead to low productivity, culture collapse, and low-quality biomass. Co-culture systems, which produce robust microorganism consortia or communities, present a compelling strategy for addressing contamination problems. In recent years, research and development of innovative co-cultivation techniques have substantially increased. Nevertheless, many microalgae co-culturing technologies remain in the developmental phase and have yet to be scaled and commercialized. Accordingly, this review presents a thorough literature review of research conducted in the last few decades, exploring the advantages and disadvantages of microalgae co-cultivation systems that involve microalgae-bacteria, microalgae-fungi, and microalgae-microalgae/algae systems. The manuscript also addresses diverse uses of co-culture systems, and growing methods, and includes one of the most exciting research areas in co-culturing systems, which are omic studies that elucidate different interaction mechanisms among microbial communities. Finally, the manuscript discusses the economic viability, future challenges, and prospects of microalgal co-cultivation methods.
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Affiliation(s)
| | - Asma Pourbakhtiar
- School of Chemical Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | | | - Maedeh Baharlooeian
- Department of Marine Biology, Faculty of Marine Science and Oceanography, Khorramshahr University of Marine Science and Technology, Khorramshahr, Iran
| | - Nahid Rafiei
- Regulatory Systems Biology Lab, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, Nuevo León, Mexico
| | - Hossein Alishah Aratboni
- Regulatory Systems Biology Lab, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, Nuevo León, Mexico
| | - Jose Ruben Morones-Ramirez
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, Nuevo León, Mexico
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Universidad Autonoma de Nuevo Leon (UANL), Av Universidad s/n, CD. Universitaria, San Nicolás de los Garza, Nuevo León, Mexico
| | - Flavia Vischi Winck
- Regulatory Systems Biology Lab, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
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Sporre E, Karlsen J, Schriever K, Asplund-Samuelsson J, Janasch M, Strandberg L, Karlsson A, Kotol D, Zeckey L, Piazza I, Syrén PO, Edfors F, Hudson EP. Metabolite interactions in the bacterial Calvin cycle and implications for flux regulation. Commun Biol 2023; 6:947. [PMID: 37723200 PMCID: PMC10507043 DOI: 10.1038/s42003-023-05318-8] [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: 01/27/2023] [Accepted: 09/01/2023] [Indexed: 09/20/2023] Open
Abstract
Metabolite-level regulation of enzyme activity is important for microbes to cope with environmental shifts. Knowledge of such regulations can also guide strain engineering for biotechnology. Here we apply limited proteolysis-small molecule mapping (LiP-SMap) to identify and compare metabolite-protein interactions in the proteomes of two cyanobacteria and two lithoautotrophic bacteria that fix CO2 using the Calvin cycle. Clustering analysis of the hundreds of detected interactions shows that some metabolites interact in a species-specific manner. We estimate that approximately 35% of interacting metabolites affect enzyme activity in vitro, and the effect is often minor. Using LiP-SMap data as a guide, we find that the Calvin cycle intermediate glyceraldehyde-3-phosphate enhances activity of fructose-1,6/sedoheptulose-1,7-bisphosphatase (F/SBPase) from Synechocystis sp. PCC 6803 and Cupriavidus necator in reducing conditions, suggesting a convergent feed-forward activation of the cycle. In oxidizing conditions, glyceraldehyde-3-phosphate inhibits Synechocystis F/SBPase by promoting enzyme aggregation. In contrast, the glycolytic intermediate glucose-6-phosphate activates F/SBPase from Cupriavidus necator but not F/SBPase from Synechocystis. Thus, metabolite-level regulation of the Calvin cycle is more prevalent than previously appreciated.
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Affiliation(s)
- Emil Sporre
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Jan Karlsen
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Karen Schriever
- Department of Fiber and Polymer Technology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Johannes Asplund-Samuelsson
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Markus Janasch
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
- Department of Biotechnology and Nanomedicine, SINTEF Industry, 7465, Trondheim, Norway
| | - Linnéa Strandberg
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Anna Karlsson
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - David Kotol
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Luise Zeckey
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Ilaria Piazza
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Per-Olof Syrén
- Department of Fiber and Polymer Technology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Edfors
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Elton P Hudson
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.
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12
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Geffen O, Achaintre D, Treves H. 13CO 2-labelling and Sampling in Algae for Flux Analysis of Photosynthetic and Central Carbon Metabolism. Bio Protoc 2023; 13:e4808. [PMID: 37719071 PMCID: PMC10501915 DOI: 10.21769/bioprotoc.4808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 09/19/2023] Open
Abstract
The flux in photosynthesis can be studied by performing 13CO2 pulse labelling and analysing the temporal labelling kinetics of metabolic intermediates using gas or liquid chromatography linked to mass spectrometry. Metabolic flux analysis (MFA) is the primary approach for analysing metabolic network function and quantifying intracellular metabolic fluxes. Different MFA approaches differ based on the metabolic state (steady vs. non-steady state) and the use of stable isotope tracers. The main methodology used to investigate metabolic systems is metabolite steady state associated with stable isotope labelling experiments. Specifically, in biological systems like photoautotrophic organisms, isotopic non-stationary 113C metabolic flux analysis at metabolic steady state with transient isotopic labelling (13C-INST-MFA) is required. The common requirement for metabolic steady state, alongside its very short half-timed reactions, complicates robust MFA of photosynthetic metabolism. While custom gas chambers design has addressed these challenges in various model plants, no similar tools were developed for liquid photosynthetic cultures (e.g., algae, cyanobacteria), where diffusion and equilibration of inorganic carbon species in the medium entails a new dimension of complexity. Recently, a novel tailor-made microfluidics labelling system has been introduced, supplying short 13CO2 pulses at steady state, and resolving fluxes across most photosynthetic metabolic pathways in algae. The system involves injecting algal cultures and medium containing pre-equilibrated inorganic 13C into a microfluidic mixer, followed by rapid metabolic quenching, enabling precise seconds-level label pulses. This was complemented by a 13CO2-bubbling-based open labelling system (photobioreactor), allowing long pulses (minutes-hours) required for investigating fluxes into central C metabolism and major products. This combined labelling procedure provides a comprehensive fluxome cover for most algal photosynthetic and central C metabolism pathways, thus allowing comparative flux analyses across algae and plants.
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Affiliation(s)
- Or Geffen
- School of Plant Sciences and Food Security, Faculty of Biology, Tel-Aviv University, Tel Aviv-Yafo, Israel
| | - David Achaintre
- School of Plant Sciences and Food Security, Faculty of Biology, Tel-Aviv University, Tel Aviv-Yafo, Israel
| | - Haim Treves
- School of Plant Sciences and Food Security, Faculty of Biology, Tel-Aviv University, Tel Aviv-Yafo, Israel
- Plant Metabolism Group, Faculty of Biology, Rhineland-Palatinate Technical University of Kaiserslautern-Landau, Kaiserslautern, Germany
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13
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Liu F, Gaul L, Giometto A, Wu M. Colimitation of light and nitrogen on algal growth revealed by an array microhabitat platform. ARXIV 2023:arXiv:2307.02646v1. [PMID: 37461420 PMCID: PMC10350088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Microalgae are key players in the global carbon cycle and emerging producers of biofuels. Algal growth is critically regulated by its complex microenvironment, including nitrogen and phosphorous levels, light intensity, and temperature. Mechanistic understanding of algal growth is important for maintaining a balanced ecosystem at a time of climate change and population expansion, as well as providing essential formulations for optimizing biofuel production. Current mathematical models for algal growth in complex environmental conditions are still in their infancy, due in part to the lack of experimental tools necessary to generate data amenable to theoretical modeling. Here, we present a high throughput microfluidic platform that allows for algal growth with precise control over light intensity and nutrient gradients, while also performing real-time microscopic imaging. We propose a general mathematical model that describes algal growth under multiple physical and chemical environments, which we have validated experimentally. We showed that light and nitrogen colimited the growth of the model alga Chlamydomonas reinhardtii following a multiplicative Monod kinetic model. The microfluidic platform presented here can be easily adapted to studies of other photosynthetic micro-organisms, and the algal growth model will be essential for future bioreactor designs and ecological predictions.
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Affiliation(s)
- Fangchen Liu
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - Larissa Gaul
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - Andrea Giometto
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - Mingming Wu
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
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14
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Transcriptome Analysis Reveals the Mechanisms of Tolerance to High Concentrations of Calcium Chloride Stress in Parachlorella kessleri. Int J Mol Sci 2022; 24:ijms24010651. [PMID: 36614098 PMCID: PMC9821113 DOI: 10.3390/ijms24010651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 01/03/2023] Open
Abstract
Salt stress is one of the abiotic stress factors that affect the normal growth and development of higher plants and algae. However, few research studies have focused on calcium stress, especially in algae. In this study, the mechanism of tolerance to high calcium stress of a Parachlorella kessleri strain was explored by the method of transcriptomics combined with physiological and morphological analysis. Concentrations of CaCl2 100 times (3.6 g/L) and 1000 times (36 g/L) greater than the standard culture were set up as stresses. The results revealed the algae could cope with high calcium stress mainly by strengthening photosynthesis, regulating osmotic pressure, and inducing antioxidant defense. Under the stress of 3.6 g/L CaCl2, the algae grew well with normal cell morphology. Although the chlorophyll content was significantly reduced, the photosynthetic efficiency was well maintained by up-regulating the expression of some photosynthesis-related genes. The cells reduced oxidative damage by inducing superoxide dismutase (SOD) activities and selenoprotein synthesis. A large number of free amino acids were produced to regulate the osmotic potential. When in higher CaCl2 stress of 36 g/L, the growth and chlorophyll content of algae were significantly inhibited. However, the algae still slowly grew and maintained the same photosynthetic efficiency, which resulted from significant up-regulation of massive photosynthesis genes. Antioxidant enzymes and glycerol were found to resist oxidative damage and osmotic stress, respectively. This study supplied algal research on CaCl2 stress and provided supporting data for further explaining the mechanism of plant salt tolerance.
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15
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Hui C, Schmollinger S, Strenkert D, Holbrook K, Montgomery HR, Chen S, Nelson HM, Weber PK, Merchant SS. Simple steps to enable reproducibility: culture conditions affecting Chlamydomonas growth and elemental composition. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:995-1014. [PMID: 35699388 DOI: 10.1111/tpj.15867] [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: 02/15/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 05/26/2023]
Abstract
Even subtle modifications in growth conditions elicit acclimation responses affecting the molecular and elemental makeup of organisms, both in the laboratory and in natural habitats. We systematically explored the effect of temperature, pH, nutrient availability, culture density, and access to CO2 and O2 in laboratory-grown algal cultures on growth rate, the ionome, and the ability to accumulate Fe. We found algal cells accumulate Fe in alkaline conditions, even more so when excess Fe is present, coinciding with a reduced growth rate. Using a combination of Fe-specific dyes, X-ray fluorescence microscopy, and NanoSIMS, we show that the alkaline-accumulated Fe was intracellularly sequestered into acidocalcisomes, which are localized towards the periphery of the cells. At high photon flux densities, Zn and Ca specifically over-accumulate, while Zn alone accumulates at low temperatures. The impact of aeration was probed by reducing shaking speeds and changing vessel fill levels; the former increased the Cu quota of cultures, the latter resulted in a reduction in P, Ca, and Mn at low fill levels. Trace element quotas were also affected in the stationary phase, where specifically Fe, Cu, and Zn accumulate. Cu accumulation here depends inversely on the Fe concentration of the medium. Individual laboratory strains accumulate Ca, P, and Cu to different levels. All together, we identified a set of specific changes to growth rate, elemental composition, and the capacity to store Fe in response to subtle differences in culturing conditions of Chlamydomonas, affecting experimental reproducibility. Accordingly, we recommend that these variables be recorded and reported as associated metadata.
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Affiliation(s)
- Colleen Hui
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
- Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
| | - Stefan Schmollinger
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
| | - Daniela Strenkert
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
| | - Kristen Holbrook
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Hayden R Montgomery
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Si Chen
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Hosea M Nelson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Peter K Weber
- Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, 94550, USA
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
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Chen YJ, Huang YL, Chen YH, Chang ST, Yeh TF. Biogenic Volatile Organic Compounds and Protein Expressions of Chamaecyparis formosensis and Chamaecyparis obtusa var. formosana Leaves under Different Light Intensities and Temperatures. PLANTS 2022; 11:plants11121535. [PMID: 35736687 PMCID: PMC9231097 DOI: 10.3390/plants11121535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 11/22/2022]
Abstract
Both Chamaecyparis formosensis and C. obtusa var. formosana are representative cypresses of high economic value in Taiwan, the southernmost subtropical region where cypresses are found. Both species show differences of their habitats. To find out the effects of environmental factors on the CO2 assimilation rate and the biogenic volatile organic compound (BVOC) emission of both species, saplings from both species were grown under different light intensity and temperature regimes. The results indicated that the net CO2 assimilation rates and total BVOC emission rates of both species increased with increasing light intensity. C. formosensis showed a higher magnitude of change, but C. obtusa var. formosana had considerably increased sesquiterpenoid and diterpenoid emission in BVOC under high light intensity. Both species grown under higher temperatures had significantly lower BVOC emission rates. Proteomic analyses revealed that compared to C. formosensis saplings, C. obtusa var. formosana saplings had less differentially expressed proteins in terms of protein species and fold changes in response to the growth conditions. These proteins participated mainly in photosynthesis, carbon metabolism, amino acid and protein processing, signal transduction, and stress mechanisms. These proteins might be the major regulatory factors affecting BVOC emission of these two species under different environments.
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Affiliation(s)
- Ying-Ju Chen
- School of Forestry and Resource Conservation, National Taiwan University, Taipei 10617, Taiwan; (Y.-J.C.); (Y.-L.H.); (Y.-H.C.)
- Division of Forest Chemistry, Taiwan Forestry Research Institute, Taipei 10070, Taiwan
| | - Ya-Lun Huang
- School of Forestry and Resource Conservation, National Taiwan University, Taipei 10617, Taiwan; (Y.-J.C.); (Y.-L.H.); (Y.-H.C.)
| | - Yu-Han Chen
- School of Forestry and Resource Conservation, National Taiwan University, Taipei 10617, Taiwan; (Y.-J.C.); (Y.-L.H.); (Y.-H.C.)
| | - Shang-Tzen Chang
- School of Forestry and Resource Conservation, National Taiwan University, Taipei 10617, Taiwan; (Y.-J.C.); (Y.-L.H.); (Y.-H.C.)
- Correspondence: (S.-T.C.); (T.-F.Y.)
| | - Ting-Feng Yeh
- School of Forestry and Resource Conservation, National Taiwan University, Taipei 10617, Taiwan; (Y.-J.C.); (Y.-L.H.); (Y.-H.C.)
- Correspondence: (S.-T.C.); (T.-F.Y.)
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17
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Le Moigne T, Sarti E, Nourisson A, Zaffagnini M, Carbone A, Lemaire SD, Henri J. Crystal structure of chloroplast fructose-1,6-bisphosphate aldolase from the green alga Chlamydomonas reinhardtii. J Struct Biol 2022; 214:107873. [DOI: 10.1016/j.jsb.2022.107873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 11/25/2022]
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18
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Saint-Sorny M, Brzezowski P, Arrivault S, Alric J, Johnson X. Interactions Between Carbon Metabolism and Photosynthetic Electron Transport in a Chlamydomonas reinhardtii Mutant Without CO 2 Fixation by RuBisCO. FRONTIERS IN PLANT SCIENCE 2022; 13:876439. [PMID: 35574084 PMCID: PMC9096841 DOI: 10.3389/fpls.2022.876439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/31/2022] [Indexed: 06/15/2023]
Abstract
A Chlamydomonas reinhardtii RuBisCO-less mutant, ΔrbcL, was used to study carbohydrate metabolism without fixation of atmospheric carbon. The regulatory mechanism(s) that control linear electron flow, known as "photosynthetic control," are amplified in ΔrbcL at the onset of illumination. With the aim to understand the metabolites that control this regulatory response, we have correlated the kinetics of primary carbon metabolites to chlorophyll fluorescence induction curves. We identify that ΔrbcL in the absence of acetate generates adenosine triphosphate (ATP) via photosynthetic electron transfer reactions. Also, metabolites of the Calvin Benson Bassham (CBB) cycle are responsive to the light. Indeed, ribulose 1,5-bisphosphate (RuBP), the last intermediate before carboxylation by Ribulose-1,5-bisphosphate carboxylase-oxygenase, accumulates significantly with time, and CBB cycle intermediates for RuBP regeneration, dihydroxyacetone phosphate (DHAP), pentose phosphates and ribose-5-phosphate (R5P) are rapidly accumulated in the first seconds of illumination, then consumed, showing that although the CBB is blocked, these enzymes are still transiently active. In opposition, in the presence of acetate, consumption of CBB cycle intermediates is strongly diminished, suggesting that the link between light and primary carbon metabolism is almost lost. Phosphorylated hexoses and starch accumulate significantly. We show that acetate uptake results in heterotrophic metabolism dominating phototrophic metabolism, with glyoxylate and tricarboxylic acid (TCA) cycle intermediates being the most highly represented metabolites, specifically succinate and malate. These findings allow us to hypothesize which metabolites and metabolic pathways are relevant to the upregulation of processes like cyclic electron flow that are implicated in photosynthetic control mechanisms.
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Affiliation(s)
- Maureen Saint-Sorny
- CEA, CNRS, UMR 7265, BIAM, CEA Cadarache, Aix-Marseille Université, Saint-Paul-lez-Durance, France
| | - Pawel Brzezowski
- CEA, CNRS, UMR 7265, BIAM, CEA Cadarache, Aix-Marseille Université, Saint-Paul-lez-Durance, France
| | | | - Jean Alric
- CEA, CNRS, UMR 7265, BIAM, CEA Cadarache, Aix-Marseille Université, Saint-Paul-lez-Durance, France
| | - Xenie Johnson
- CEA, CNRS, UMR 7265, BIAM, CEA Cadarache, Aix-Marseille Université, Saint-Paul-lez-Durance, France
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19
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Zhang N, Pazouki L, Nguyen H, Jacobshagen S, Bigge BM, Xia M, Mattoon EM, Klebanovych A, Sorkin M, Nusinow DA, Avasthi P, Czymmek KJ, Zhang R. Comparative Phenotyping of Two Commonly Used Chlamydomonas reinhardtii Background Strains: CC-1690 (21gr) and CC-5325 (The CLiP Mutant Library Background). PLANTS (BASEL, SWITZERLAND) 2022; 11:585. [PMID: 35270055 PMCID: PMC8912731 DOI: 10.3390/plants11050585] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/07/2022] [Accepted: 02/14/2022] [Indexed: 05/02/2023]
Abstract
The unicellular green alga Chlamydomonas reinhardtii is an excellent model organism to investigate many essential cellular processes in photosynthetic eukaryotes. Two commonly used background strains of Chlamydomonas are CC-1690 and CC-5325. CC-1690, also called 21gr, has been used for the Chlamydomonas genome project and several transcriptome analyses. CC-5325 is the background strain for the Chlamydomonas Library Project (CLiP). Photosynthetic performance in CC-5325 has not been evaluated in comparison with CC-1690. Additionally, CC-5325 is often considered to be cell-wall deficient, although detailed analysis is missing. The circadian rhythms in CC-5325 are also unclear. To fill these knowledge gaps and facilitate the use of the CLiP mutant library for various screens, we performed phenotypic comparisons between CC-1690 and CC-5325. Our results showed that CC-5325 grew faster heterotrophically in dark and equally well in mixotrophic liquid medium as compared to CC-1690. CC-5325 had lower photosynthetic efficiency and was more heat-sensitive than CC-1690. Furthermore, CC-5325 had an intact cell wall which had comparable integrity to that in CC-1690 but appeared to have reduced thickness. Additionally, CC-5325 could perform phototaxis, but could not maintain a sustained circadian rhythm of phototaxis as CC1690 did. Finally, in comparison to CC-1690, CC-5325 had longer cilia in the medium with acetate but slower swimming speed in the medium without nitrogen and acetate. Our results will be useful for researchers in the Chlamydomonas community to choose suitable background strains for mutant analysis and employ the CLiP mutant library for genome-wide mutant screens under appropriate conditions, especially in the areas of photosynthesis, thermotolerance, cell wall, and circadian rhythms.
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Affiliation(s)
- Ningning Zhang
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Leila Pazouki
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Huong Nguyen
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Sigrid Jacobshagen
- Department of Biology, Western Kentucky University, Bowling Green, KY 42101, USA;
| | - Brae M. Bigge
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA; (B.M.B.); (P.A.)
| | - Ming Xia
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Erin M. Mattoon
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
- Plant and Microbial Biosciences Program, Division of Biology and Biomedical Sciences, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Anastasiya Klebanovych
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Maria Sorkin
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
- Plant and Microbial Biosciences Program, Division of Biology and Biomedical Sciences, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Dmitri A. Nusinow
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Prachee Avasthi
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA; (B.M.B.); (P.A.)
| | - Kirk J. Czymmek
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Ru Zhang
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
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20
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Széles E, Nagy K, Ábrahám Á, Kovács S, Podmaniczki A, Nagy V, Kovács L, Galajda P, Tóth SZ. Microfluidic Platforms Designed for Morphological and Photosynthetic Investigations of Chlamydomonas reinhardtii on a Single-Cell Level. Cells 2022; 11:cells11020285. [PMID: 35053401 PMCID: PMC8774182 DOI: 10.3390/cells11020285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 11/16/2022] Open
Abstract
Chlamydomonas reinhardtii is a model organism of increasing biotechnological importance, yet, the evaluation of its life cycle processes and photosynthesis on a single-cell level is largely unresolved. To facilitate the study of the relationship between morphology and photochemistry, we established microfluidics in combination with chlorophyll a fluorescence induction measurements. We developed two types of microfluidic platforms for single-cell investigations: (i) The traps of the “Tulip” device are suitable for capturing and immobilizing single cells, enabling the assessment of their photosynthesis for several hours without binding to a solid support surface. Using this “Tulip” platform, we performed high-quality non-photochemical quenching measurements and confirmed our earlier results on bulk cultures that non-photochemical quenching is higher in ascorbate-deficient mutants (Crvtc2-1) than in the wild-type. (ii) The traps of the “Pot” device were designed for capturing single cells and allowing the growth of the daughter cells within the traps. Using our most performant “Pot” device, we could demonstrate that the FV/FM parameter, an indicator of photosynthetic efficiency, varies considerably during the cell cycle. Our microfluidic devices, therefore, represent versatile platforms for the simultaneous morphological and photosynthetic investigations of C. reinhardtii on a single-cell level.
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Affiliation(s)
- Eszter Széles
- Institute of Plant Biology, Biological Research Centre, H-6726 Szeged, Hungary; (E.S.); (S.K.); (A.P.); (V.N.); (L.K.)
- Doctoral School of Biology, University of Szeged, H-6722 Szeged, Hungary
| | - Krisztina Nagy
- Institute of Biophysics, Biological Research Centre, H-6726 Szeged, Hungary; (K.N.); (Á.Á.); (P.G.)
| | - Ágnes Ábrahám
- Institute of Biophysics, Biological Research Centre, H-6726 Szeged, Hungary; (K.N.); (Á.Á.); (P.G.)
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, H-6720 Szeged, Hungary
| | - Sándor Kovács
- Institute of Plant Biology, Biological Research Centre, H-6726 Szeged, Hungary; (E.S.); (S.K.); (A.P.); (V.N.); (L.K.)
| | - Anna Podmaniczki
- Institute of Plant Biology, Biological Research Centre, H-6726 Szeged, Hungary; (E.S.); (S.K.); (A.P.); (V.N.); (L.K.)
- Doctoral School of Biology, University of Szeged, H-6722 Szeged, Hungary
| | - Valéria Nagy
- Institute of Plant Biology, Biological Research Centre, H-6726 Szeged, Hungary; (E.S.); (S.K.); (A.P.); (V.N.); (L.K.)
| | - László Kovács
- Institute of Plant Biology, Biological Research Centre, H-6726 Szeged, Hungary; (E.S.); (S.K.); (A.P.); (V.N.); (L.K.)
| | - Péter Galajda
- Institute of Biophysics, Biological Research Centre, H-6726 Szeged, Hungary; (K.N.); (Á.Á.); (P.G.)
| | - Szilvia Z. Tóth
- Institute of Plant Biology, Biological Research Centre, H-6726 Szeged, Hungary; (E.S.); (S.K.); (A.P.); (V.N.); (L.K.)
- Correspondence:
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21
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McQuillan JL, Berndt AJ, Sproles AE, Mayfield SP, Pandhal J. Novel cis-regulatory elements as synthetic promoters to drive recombinant protein expression from the Chlamydomonas reinhardtii nuclear genome. N Biotechnol 2022; 68:9-18. [PMID: 34990855 DOI: 10.1016/j.nbt.2022.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/29/2021] [Accepted: 01/01/2022] [Indexed: 12/17/2022]
Abstract
Eukaryotic green microalgae represent a sustainable, photosynthetic biotechnology platform for generating high-value products. The model green alga Chlamydomonas reinhardtii has already been used to generate high value bioproducts such as recombinant proteins and terpenoids. However, low, unstable, and variable nuclear transgene expression has limited the ease and speed of metabolic engineering and recombinant protein expression in this system. Here, novel genetic devices for transgene expression in C. reinhardtii have been developed by identifying cis-regulatory DNA elements capable of driving high transgene expression in C. reinhardtii promoters using de novo motif discovery informatics approaches. Thirteen putative motifs were synthesized as concatemers, linked to a common minimal basal promoter, and assayed for their activity to drive expression of a yellow fluorescent protein reporter gene. Following transformation of the vectors into C. reinhardtii by electroporation, in vivo measurements of yellow fluorescent protein expression by flow cytometry revealed that five of the DNA motifs analyzed displayed significantly higher reporter expression compared to the basal promoter control. Two of the concatemerized motifs, despite being much smaller minimal cis-regulatory elements, drove reporter expression at levels approaching that of the conventionally-used AR1 promoter. This analysis provides insight into C. reinhardtii promoter structure and gene regulation, and provides a new toolbox of cis-regulatory elements that can be used to drive transgene expression at a variety of expression levels.
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Affiliation(s)
- Josie L McQuillan
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - Anthony J Berndt
- California Center for Algae Biotechnology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, United States
| | - Ashley E Sproles
- California Center for Algae Biotechnology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, United States
| | - Stephen P Mayfield
- California Center for Algae Biotechnology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, United States
| | - Jagroop Pandhal
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK.
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22
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Treves H, Küken A, Arrivault S, Ishihara H, Hoppe I, Erban A, Höhne M, Moraes TA, Kopka J, Szymanski J, Nikoloski Z, Stitt M. Carbon flux through photosynthesis and central carbon metabolism show distinct patterns between algae, C 3 and C 4 plants. NATURE PLANTS 2022; 8:78-91. [PMID: 34949804 PMCID: PMC8786664 DOI: 10.1038/s41477-021-01042-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 11/09/2021] [Indexed: 05/26/2023]
Abstract
Photosynthesis-related pathways are regarded as a promising avenue for crop improvement. Whilst empirical studies have shown that photosynthetic efficiency is higher in microalgae than in C3 or C4 crops, the underlying reasons remain unclear. Using a tailor-made microfluidics labelling system to supply 13CO2 at steady state, we investigated in vivo labelling kinetics in intermediates of the Calvin Benson cycle and sugar, starch, organic acid and amino acid synthesis pathways, and in protein and lipids, in Chlamydomonas reinhardtii, Chlorella sorokiniana and Chlorella ohadii, which is the fastest growing green alga on record. We estimated flux patterns in these algae and compared them with published and new data from C3 and C4 plants. Our analyses identify distinct flux patterns supporting faster growth in photosynthetic cells, with some of the algae exhibiting faster ribulose 1,5-bisphosphate regeneration and increased fluxes through the lower glycolysis and anaplerotic pathways towards the tricarboxylic acid cycle, amino acid synthesis and lipid synthesis than in higher plants.
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Affiliation(s)
- Haim Treves
- Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany.
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.
| | - Anika Küken
- Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany
- Bioinformatics group, University of Potsdam, Potsdam, Germany
| | | | - Hirofumi Ishihara
- Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Ines Hoppe
- Bioinformatics group, University of Potsdam, Potsdam, Germany
| | - Alexander Erban
- Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Melanie Höhne
- Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Thiago Alexandre Moraes
- Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany
- Crop Science Centre, University of Cambridge, Cambridge, UK
| | - Joachim Kopka
- Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Jedrzej Szymanski
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, OT Gatersleben, Germany
| | - Zoran Nikoloski
- Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany
- Bioinformatics group, University of Potsdam, Potsdam, Germany
| | - Mark Stitt
- Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany
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23
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Stitt M, Luca Borghi G, Arrivault S. Targeted metabolite profiling as a top-down approach to uncover interspecies diversity and identify key conserved operational features in the Calvin-Benson cycle. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5961-5986. [PMID: 34473300 PMCID: PMC8411860 DOI: 10.1093/jxb/erab291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/21/2021] [Indexed: 05/02/2023]
Abstract
Improving photosynthesis is a promising avenue to increase crop yield. This will be aided by better understanding of natural variance in photosynthesis. Profiling of Calvin-Benson cycle (CBC) metabolites provides a top-down strategy to uncover interspecies diversity in CBC operation. In a study of four C4 and five C3 species, principal components analysis separated C4 species from C3 species and also separated different C4 species. These separations were driven by metabolites that reflect known species differences in their biochemistry and pathways. Unexpectedly, there was also considerable diversity between the C3 species. Falling atmospheric CO2 and changing temperature, nitrogen, and water availability have driven evolution of C4 photosynthesis in multiple lineages. We propose that analogous selective pressures drove lineage-dependent evolution of the CBC in C3 species. Examples of species-dependent variation include differences in the balance between the CBC and the light reactions, and in the balance between regulated steps in the CBC. Metabolite profiles also reveal conserved features including inactivation of enzymes in low irradiance, and maintenance of CBC metabolites at relatively high levels in the absence of net CO2 fixation. These features may be important for photosynthetic efficiency in low light, fluctuating irradiance, and when stomata close due to low water availability.
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Affiliation(s)
- Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Gian Luca Borghi
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Stéphanie Arrivault
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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24
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Stephens TG, Gabr A, Calatrava V, Grossman AR, Bhattacharya D. Why is primary endosymbiosis so rare? THE NEW PHYTOLOGIST 2021; 231:1693-1699. [PMID: 34018613 PMCID: PMC8711089 DOI: 10.1111/nph.17478] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/05/2021] [Indexed: 05/05/2023]
Abstract
Endosymbiosis is a relationship between two organisms wherein one cell resides inside the other. This affiliation, when stable and beneficial for the 'host' cell, can result in massive genetic innovation with the foremost examples being the evolution of eukaryotic organelles, the mitochondria and plastids. Despite its critical evolutionary role, there is limited knowledge about how endosymbiosis is initially established and how host-endosymbiont biology is integrated. Here, we explore this issue, using as our model the rhizarian amoeba Paulinella, which represents an independent case of primary plastid origin that occurred c. 120 million yr ago. We propose the 'chassis and engine' model that provides a theoretical framework for understanding primary plastid endosymbiosis, potentially explaining why it is so rare.
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Affiliation(s)
- Timothy G. Stephens
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Arwa Gabr
- Graduate Program in Molecular Bioscience and Program in Microbiology and Molecular Genetics, Rutgers University, Piscataway, NJ 08854, USA
| | - Victoria Calatrava
- Department of Plant Biology, The Carnegie Institution, Stanford, CA 94305, USA
| | - Arthur R. Grossman
- Department of Plant Biology, The Carnegie Institution, Stanford, CA 94305, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
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25
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Oren N, Timm S, Frank M, Mantovani O, Murik O, Hagemann M. Red/far-red light signals regulate the activity of the carbon-concentrating mechanism in cyanobacteria. SCIENCE ADVANCES 2021; 7:7/34/eabg0435. [PMID: 34407941 PMCID: PMC8373116 DOI: 10.1126/sciadv.abg0435] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 06/28/2021] [Indexed: 05/11/2023]
Abstract
Desiccation-tolerant cyanobacteria can survive frequent hydration/dehydration cycles likely affecting inorganic carbon (Ci) levels. It was recently shown that red/far-red light serves as signal-preparing cells toward dehydration. Here, the effects of desiccation on Ci assimilation by Leptolyngbya ohadii isolated from Israel's Negev desert were investigated. Metabolomic investigations indicated a decline in ribulose-1,5-bisphosphate carboxylase/oxygenase carboxylation activity, and this was accelerated by far-red light. Far-red light negatively affected the Ci affinity of L. ohadii during desiccation and in liquid cultures. Similar effects were evident in the non-desiccation-tolerant cyanobacterium Synechocystis The Synechocystis Δcph1 mutant lacking the major phytochrome exhibited reduced photosynthetic Ci affinity when exposed to far-red light, whereas the mutant ΔsbtB lacking a Ci uptake inhibitory protein lost the far-red light inhibition. Collectively, these results suggest that red/far-red light perception likely via phytochromes regulates Ci uptake by cyanobacteria and that this mechanism contributes to desiccation tolerance in strains such as L. ohadii.
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Affiliation(s)
- Nadav Oren
- Plant Physiology Department, University of Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany.
| | - Stefan Timm
- Plant Physiology Department, University of Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany
| | - Marcus Frank
- Medical Biology and Electron Microscopy Centre, Medical Faculty, University of Rostock, Strempelstr. 14, 18057 Rostock, Germany
- Department of Life, Light, and Matter, University of Rostock, Albert-Einstein-Str. 25, 18059 Rostock, Germany
| | - Oliver Mantovani
- Plant Physiology Department, University of Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany
| | - Omer Murik
- Medical Genetics Institute, Shaare Zedek Medical Center, 9103102 Jerusalem, Israel
| | - Martin Hagemann
- Plant Physiology Department, University of Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany
- Department of Life, Light, and Matter, University of Rostock, Albert-Einstein-Str. 25, 18059 Rostock, Germany
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26
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Emrich-Mills TZ, Yates G, Barrett J, Girr P, Grouneva I, Lau CS, Walker CE, Kwok TK, Davey JW, Johnson MP, Mackinder LCM. A recombineering pipeline to clone large and complex genes in Chlamydomonas. THE PLANT CELL 2021; 33:1161-1181. [PMID: 33723601 PMCID: PMC8633747 DOI: 10.1093/plcell/koab024] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 01/18/2021] [Indexed: 05/10/2023]
Abstract
The ability to clone genes has greatly advanced cell and molecular biology research, enabling researchers to generate fluorescent protein fusions for localization and confirm genetic causation by mutant complementation. Most gene cloning is polymerase chain reaction (PCR)�or DNA synthesis-dependent, which can become costly and technically challenging as genes increase in size, particularly if they contain complex regions. This has been a long-standing challenge for the Chlamydomonas reinhardtii research community, as this alga has a high percentage of genes containing complex sequence structures. Here we overcame these challenges by developing a recombineering pipeline for the rapid parallel cloning of genes from a Chlamydomonas bacterial artificial chromosome collection. To generate fluorescent protein fusions for localization, we applied the pipeline at both batch and high-throughput scales to 203 genes related to the Chlamydomonas CO2 concentrating mechanism (CCM), with an overall cloning success rate of 77%. Cloning success was independent of gene size and complexity, with cloned genes as large as 23 kb. Localization of a subset of CCM targets confirmed previous mass spectrometry data, identified new pyrenoid components, and enabled complementation of mutants. We provide vectors and detailed protocols to facilitate easy adoption of this technology, which we envision will open up new possibilities in algal and plant research.
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Affiliation(s)
- Tom Z Emrich-Mills
- Department of Biology, University of York, York YO10 5DD, UK
- Department Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Gary Yates
- Department of Biology, University of York, York YO10 5DD, UK
| | - James Barrett
- Department of Biology, University of York, York YO10 5DD, UK
| | - Philipp Girr
- Department of Biology, University of York, York YO10 5DD, UK
| | - Irina Grouneva
- Department of Biology, University of York, York YO10 5DD, UK
| | - Chun Sing Lau
- Department of Biology, University of York, York YO10 5DD, UK
| | | | - Tsz Kam Kwok
- Department of Biology, University of York, York YO10 5DD, UK
| | - John W Davey
- Department of Biology, University of York, York YO10 5DD, UK
| | - Matthew P Johnson
- Department Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Luke C M Mackinder
- Department of Biology, University of York, York YO10 5DD, UK
- Author for correspondence: (L.C.M.M.)
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27
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Rees TAV, Raven JA. The maximum growth rate hypothesis is correct for eukaryotic photosynthetic organisms, but not cyanobacteria. THE NEW PHYTOLOGIST 2021; 230:601-611. [PMID: 33449358 PMCID: PMC8048539 DOI: 10.1111/nph.17190] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/23/2020] [Indexed: 05/12/2023]
Abstract
The (maximum) growth rate (µmax ) hypothesis predicts that cellular and tissue phosphorus (P) concentrations should increase with increasing growth rate, and RNA should also increase as most of the P is required to make ribosomes. Using published data, we show that though there is a strong positive relationship between the µmax of all photosynthetic organisms and their P content (% dry weight), leading to a relatively constant P productivity, the relationship with RNA content is more complex. In eukaryotes there is a strong positive relationship between µmax and RNA content expressed as % dry weight, and RNA constitutes a relatively constant 25% of total P. In prokaryotes the rRNA operon copy number is the important determinant of the amount of RNA present in the cell. The amount of phospholipid expressed as % dry weight increases with increasing µmax in microalgae. The relative proportions of each of the five major P-containing constituents is remarkably constant, except that the proportion of RNA is greater and phospholipids smaller in prokaryotic than eukaryotic photosynthetic organisms. The effect of temperature differences between studies was minor. The evidence for and against P-containing constituents other than RNA being involved with ribosome synthesis and functioning is discussed.
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Affiliation(s)
- T. A. V. Rees
- Leigh Marine LaboratoryInstitute of Marine ScienceUniversity of AucklandAuckland1142New Zealand
| | - John A. Raven
- Division of Plant ScienceUniversity of Dundee at the James Hutton InstituteInvergowrie, Dundee,DD2 5DAUK
- Climate Change ClusterFaculty of ScienceUniversity of TechnologySydney, UltimoNSW2007Australia
- School of Biological SciencesUniversity of Western AustraliaCrawleyWA6009Australia
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28
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Kleine T, Nägele T, Neuhaus HE, Schmitz-Linneweber C, Fernie AR, Geigenberger P, Grimm B, Kaufmann K, Klipp E, Meurer J, Möhlmann T, Mühlhaus T, Naranjo B, Nickelsen J, Richter A, Ruwe H, Schroda M, Schwenkert S, Trentmann O, Willmund F, Zoschke R, Leister D. Acclimation in plants - the Green Hub consortium. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:23-40. [PMID: 33368770 DOI: 10.1111/tpj.15144] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/08/2020] [Accepted: 12/14/2020] [Indexed: 05/04/2023]
Abstract
Acclimation is the capacity to adapt to environmental changes within the lifetime of an individual. This ability allows plants to cope with the continuous variation in ambient conditions to which they are exposed as sessile organisms. Because environmental changes and extremes are becoming even more pronounced due to the current period of climate change, enhancing the efficacy of plant acclimation is a promising strategy for mitigating the consequences of global warming on crop yields. At the cellular level, the chloroplast plays a central role in many acclimation responses, acting both as a sensor of environmental change and as a target of cellular acclimation responses. In this Perspective article, we outline the activities of the Green Hub consortium funded by the German Science Foundation. The main aim of this research collaboration is to understand and strategically modify the cellular networks that mediate plant acclimation to adverse environments, employing Arabidopsis, tobacco (Nicotiana tabacum) and Chlamydomonas as model organisms. These efforts will contribute to 'smart breeding' methods designed to create crop plants with improved acclimation properties. To this end, the model oilseed crop Camelina sativa is being used to test modulators of acclimation for their potential to enhance crop yield under adverse environmental conditions. Here we highlight the current state of research on the role of gene expression, metabolism and signalling in acclimation, with a focus on chloroplast-related processes. In addition, further approaches to uncovering acclimation mechanisms derived from systems and computational biology, as well as adaptive laboratory evolution with photosynthetic microbes, are highlighted.
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Affiliation(s)
- Tatjana Kleine
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Thomas Nägele
- Plant Evolutionary Cell Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Munich, 82152, Germany
| | - H Ekkehard Neuhaus
- Plant Physiology, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | | | - Alisdair R Fernie
- Central Metabolism, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, 14476, Germany
| | - Peter Geigenberger
- Plant Metabolism, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Munich, 82152, Germany
| | - Bernhard Grimm
- Plant Physiology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Kerstin Kaufmann
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Edda Klipp
- Theoretical Biophysics, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Jörg Meurer
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Torsten Möhlmann
- Plant Physiology, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Timo Mühlhaus
- Computational Systems Biology, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Belen Naranjo
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Jörg Nickelsen
- Molecular Plant Science, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Munich, 82152, Germany
| | - Andreas Richter
- Physiology of Plant Organelles, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Hannes Ruwe
- Molecular Genetics, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Michael Schroda
- Molecular Biotechnology & Systems Biology, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Serena Schwenkert
- Plant Biochemistry and Physiology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Munich, 82152, Germany
| | - Oliver Trentmann
- Plant Physiology, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Reimo Zoschke
- Translational Regulation in Plants, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, 14476, Germany
| | - Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
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29
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Plant Proteomics and Systems Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1346:51-66. [DOI: 10.1007/978-3-030-80352-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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30
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Winck FV, Monteiro LDFR, Souza GM. Introduction: Advances in Plant Omics and Systems Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1346:1-9. [DOI: 10.1007/978-3-030-80352-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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31
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Martins MCM, Mafra V, Monte-Bello CC, Caldana C. The Contribution of Metabolomics to Systems Biology: Current Applications Bridging Genotype and Phenotype in Plant Science. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1346:91-105. [DOI: 10.1007/978-3-030-80352-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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32
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High-Resolution Crystal Structure of Chloroplastic Ribose-5-Phosphate Isomerase from Chlamydomonas reinhardtii-An Enzyme Involved in the Photosynthetic Calvin-Benson Cycle. Int J Mol Sci 2020; 21:ijms21207787. [PMID: 33096784 PMCID: PMC7589169 DOI: 10.3390/ijms21207787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/16/2020] [Accepted: 10/19/2020] [Indexed: 01/01/2023] Open
Abstract
The Calvin–Benson cycle is the key metabolic pathway of photosynthesis responsible for carbon fixation and relies on eleven conserved enzymes. Ribose-5-phosphate isomerase (RPI) isomerizes ribose-5-phosphate into ribulose-5-phosphate and contributes to the regeneration of the Rubisco substrate. Plant RPI is the target of diverse post-translational modifications including phosphorylation and thiol-based modifications to presumably adjust its activity to the photosynthetic electron flow. Here, we describe the first experimental structure of a photosynthetic RPI at 1.4 Å resolution. Our structure confirms the composition of the catalytic pocket of the enzyme. We describe the homo-dimeric state of the protein that we observed in the crystal and in solution. We also map the positions of previously reported post-translational modifications and propose mechanisms by which they may impact the catalytic parameters. The structural data will inform the biochemical modeling of photosynthesis.
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33
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Schneider K, Venn B, Mühlhaus T. TMEA: A Thermodynamically Motivated Framework for Functional Characterization of Biological Responses to System Acclimation. ENTROPY 2020; 22:e22091030. [PMID: 33286800 PMCID: PMC7597090 DOI: 10.3390/e22091030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/07/2020] [Accepted: 09/11/2020] [Indexed: 12/16/2022]
Abstract
The objective of gene set enrichment analysis (GSEA) in modern biological studies is to identify functional profiles in huge sets of biomolecules generated by high-throughput measurements of genes, transcripts, metabolites, and proteins. GSEA is based on a two-stage process using classical statistical analysis to score the input data and subsequent testing for overrepresentation of the enrichment score within a given functional coherent set. However, enrichment scores computed by different methods are merely statistically motivated and often elusive to direct biological interpretation. Here, we propose a novel approach, called Thermodynamically Motivated Enrichment Analysis (TMEA), to account for the energy investment in biological relevant processes. Therefore, TMEA is based on surprisal analysis, which offers a thermodynamic-free energy-based representation of the biological steady state and of the biological change. The contribution of each biomolecule underlying the changes in free energy is used in a Monte Carlo resampling procedure resulting in a functional characterization directly coupled to the thermodynamic characterization of biological responses to system perturbations. To illustrate the utility of our method on real experimental data, we benchmark our approach on plant acclimation to high light and compare the performance of TMEA with the most frequently used method for GSEA.
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34
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Küken A, Gennermann K, Nikoloski Z. Characterization of maximal enzyme catalytic rates in central metabolism of Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:2168-2177. [PMID: 32656814 DOI: 10.1111/tpj.14890] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 05/06/2020] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
Availability of plant-specific enzyme kinetic data is scarce, limiting the predictive power of metabolic models and precluding identification of genetic factors of enzyme properties. Enzyme kinetic data are measured in vitro, often under non-physiological conditions, and conclusions elicited from modeling warrant caution. Here we estimate maximal in vivo catalytic rates for 168 plant enzymes, including photosystems I and II, cytochrome-b6f complex, ATP-citrate synthase, sucrose-phosphate synthase as well as enzymes from amino acid synthesis with previously undocumented enzyme kinetic data in BRENDA. The estimations are obtained by integrating condition-specific quantitative proteomics data, maximal rates of selected enzymes, growth measurements from Arabidopsis thaliana rosette with and fluxes through canonical pathways in a constraint-based model of leaf metabolism. In comparison to findings in Escherichia coli, we demonstrate weaker concordance between the plant-specific in vitro and in vivo enzyme catalytic rates due to a low degree of enzyme saturation. This is supported by the finding that concentrations of nicotinamide adenine dinucleotide (phosphate), adenosine triphosphate and uridine triphosphate, calculated based on our maximal in vivo catalytic rates, and available quantitative metabolomics data are below reported KM values and, therefore, indicate undersaturation of respective enzymes. Our findings show that genome-wide profiling of enzyme kinetic properties is feasible in plants, paving the way for understanding resource allocation.
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Affiliation(s)
- Anika Küken
- System Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, Germany
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam-Golm, Germany
| | - Kristin Gennermann
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam-Golm, Germany
| | - Zoran Nikoloski
- System Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, Germany
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam-Golm, Germany
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Puzanskiy RK, Romanyuk DA, Kirpichnikova AA, Shishova MF. Alteration in the Expression of Genes Encoding Primary Metabolism Enzymes and Plastid Transporters during the Culture Growth of Chlamydomonas reinhardtii. Mol Biol 2020. [DOI: 10.1134/s0026893320040147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Treves H, Siemiatkowska B, Luzarowska U, Murik O, Fernandez-Pozo N, Moraes TA, Erban A, Armbruster U, Brotman Y, Kopka J, Rensing SA, Szymanski J, Stitt M. Multi-omics reveals mechanisms of total resistance to extreme illumination of a desert alga. NATURE PLANTS 2020; 6:1031-1043. [PMID: 32719473 DOI: 10.1038/s41477-020-0729-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 06/24/2020] [Indexed: 05/25/2023]
Abstract
The unparalleled performance of Chlorella ohadii under irradiances of twice full sunlight underlines the gaps in our understanding of how the photosynthetic machinery operates, and what sets its upper functional limit. Rather than succumbing to photodamage under extreme irradiance, unique features of photosystem II function allow C. ohadii to maintain high rates of photosynthesis and growth, accompanied by major changes in composition and cellular structure. This remarkable resilience allowed us to investigate the systems response of photosynthesis and growth to extreme illumination in a metabolically active cell. Using redox proteomics, transcriptomics, metabolomics and lipidomics, we explored the cellular mechanisms that promote dissipation of excess redox energy, protein S-glutathionylation, inorganic carbon concentration, lipid and starch accumulation, and thylakoid stacking. C. ohadii possesses a readily available capacity to utilize a sudden excess of reducing power and carbon for growth and reserve formation, and post-translational redox regulation plays a pivotal role in this rapid response. Frequently the response in C. ohadii deviated from that of model species, reflecting its life history in desert sand crusts. Comparative global and case-specific analyses provided insights into the potential evolutionary role of effective reductant utilization in this extreme resistance of C. ohadii to extreme irradiation.
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Affiliation(s)
- Haim Treves
- Max Planck Institute for Molecular Plant Physiology, Potsdam, Germany.
| | | | | | - Omer Murik
- Department of Plant & Environmental Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Noe Fernandez-Pozo
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | | | - Alexander Erban
- Max Planck Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Ute Armbruster
- Max Planck Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Yariv Brotman
- Max Planck Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Joachim Kopka
- Max Planck Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Stefan Andreas Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Jedrzej Szymanski
- Department of Network Analysis and Modelling, IPK, Gatersleben, Germany
| | - Mark Stitt
- Max Planck Institute for Molecular Plant Physiology, Potsdam, Germany
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Sarkar D, Maranas CD. SNPeffect: identifying functional roles of SNPs using metabolic networks. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:512-531. [PMID: 32167625 PMCID: PMC9328443 DOI: 10.1111/tpj.14746] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/20/2020] [Indexed: 05/04/2023]
Abstract
Genetic sources of phenotypic variation have been a focus of plant studies aimed at improving agricultural yield and understanding adaptive processes. Genome-wide association studies identify the genetic background behind a trait by examining associations between phenotypes and single-nucleotide polymorphisms (SNPs). Although such studies are common, biological interpretation of the results remains a challenge; especially due to the confounding nature of population structure and the systematic biases thus introduced. Here, we propose a complementary analysis (SNPeffect) that offers putative genotype-to-phenotype mechanistic interpretations by integrating biochemical knowledge encoded in metabolic models. SNPeffect is used to explain differential growth rate and metabolite accumulation in A. thaliana and P. trichocarpa accessions as the outcome of SNPs in enzyme-coding genes. To this end, we also constructed a genome-scale metabolic model for Populus trichocarpa, the first for a perennial woody tree. As expected, our results indicate that growth is a complex polygenic trait governed by carbon and energy partitioning. The predicted set of functional SNPs in both species are associated with experimentally characterized growth-determining genes and also suggest putative ones. Functional SNPs were found in pathways such as amino acid metabolism, nucleotide biosynthesis, and cellulose and lignin biosynthesis, in line with breeding strategies that target pathways governing carbon and energy partition.
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Affiliation(s)
- Debolina Sarkar
- Department of Chemical EngineeringPennsylvania State UniversityUniversity ParkPAUSA
| | - Costas D. Maranas
- Department of Chemical EngineeringPennsylvania State UniversityUniversity ParkPAUSA
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Hammel A, Sommer F, Zimmer D, Stitt M, Mühlhaus T, Schroda M. Overexpression of Sedoheptulose-1,7-Bisphosphatase Enhances Photosynthesis in Chlamydomonas reinhardtii and Has No Effect on the Abundance of Other Calvin-Benson Cycle Enzymes. FRONTIERS IN PLANT SCIENCE 2020; 11:868. [PMID: 32655601 PMCID: PMC7324757 DOI: 10.3389/fpls.2020.00868] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/27/2020] [Indexed: 05/18/2023]
Abstract
The productivity of plants and microalgae needs to be increased to feed the growing world population and to promote the development of a low-carbon economy. This goal can be achieved by improving photosynthesis via genetic engineering. In this study, we have employed the Modular Cloning strategy to overexpress the Calvin-Benson cycle (CBC) enzyme sedoheptulose-1,7-bisphosphatase (SBP1) up to threefold in the unicellular green alga Chlamydomonas reinhardtii. The protein derived from the nuclear transgene represented ∼0.3% of total cell protein. Photosynthetic rate and growth were significantly increased in SBP1-overexpressing lines under high-light and elevated CO2 conditions. Absolute quantification of the abundance of all other CBC enzymes by the QconCAT approach revealed no consistent differences between SBP1-overexpressing lines and the recipient strain. This analysis also revealed that the 11 CBC enzymes represent 11.9% of total cell protein in Chlamydomonas. Here, the range of concentrations of CBC enzymes turned out to be much larger than estimated earlier, with a 128-fold difference between the most abundant CBC protein (rbcL) and the least abundant (triose phosphate isomerase). Accordingly, the concentrations of the CBC intermediates are often but not always higher than the binding site concentrations of the enzymes for which they act as substrates. The enzymes with highest substrate to binding site ratios might represent good candidates for overexpression in subsequent engineering steps.
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Affiliation(s)
- Alexander Hammel
- Molecular Biotechnology & Systems Biology, TU Kaiserslautern, Kaiserslautern, Germany
| | - Frederik Sommer
- Molecular Biotechnology & Systems Biology, TU Kaiserslautern, Kaiserslautern, Germany
| | - David Zimmer
- Computational Systems Biology, TU Kaiserslautern, Kaiserslautern, Germany
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Timo Mühlhaus
- Computational Systems Biology, TU Kaiserslautern, Kaiserslautern, Germany
| | - Michael Schroda
- Molecular Biotechnology & Systems Biology, TU Kaiserslautern, Kaiserslautern, Germany
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Vecchi V, Barera S, Bassi R, Dall’Osto L. Potential and Challenges of Improving Photosynthesis in Algae. PLANTS 2020; 9:plants9010067. [PMID: 31947868 PMCID: PMC7020468 DOI: 10.3390/plants9010067] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/24/2019] [Accepted: 12/30/2019] [Indexed: 11/16/2022]
Abstract
Sunlight energy largely exceeds the energy required by anthropic activities, and therefore its exploitation represents a major target in the field of renewable energies. The interest in the mass cultivation of green microalgae has grown in the last decades, as algal biomass could be employed to cover a significant portion of global energy demand. Advantages of microalgal vs. plant biomass production include higher light-use efficiency, efficient carbon capture and the valorization of marginal lands and wastewaters. Realization of this potential requires a decrease of the current production costs, which can be obtained by increasing the productivity of the most common industrial strains, by the identification of factors limiting biomass yield, and by removing bottlenecks, namely through domestication strategies aimed to fill the gap between the theoretical and real productivity of algal cultures. In particular, the light-to-biomass conversion efficiency represents one of the major constraints for achieving a significant improvement of algal cell lines. This review outlines the molecular events of photosynthesis, which regulate the conversion of light into biomass, and discusses how these can be targeted to enhance productivity through mutagenesis, strain selection or genetic engineering. This review highlights the most recent results in the manipulation of the fundamental mechanisms of algal photosynthesis, which revealed that a significant yield enhancement is feasible. Moreover, metabolic engineering of microalgae, focused upon the development of renewable fuel biorefineries, has also drawn attention and resulted in efforts for enhancing productivity of oil or isoprenoids.
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Affiliation(s)
| | | | | | - Luca Dall’Osto
- Correspondence: ; Tel.: +39-045-8027806; Fax: +39-045-8027929
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40
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Schuster M, Gao Y, Schöttler MA, Bock R, Zoschke R. Limited Responsiveness of Chloroplast Gene Expression during Acclimation to High Light in Tobacco. PLANT PHYSIOLOGY 2020; 182:424-435. [PMID: 31636102 PMCID: PMC6945831 DOI: 10.1104/pp.19.00953] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/08/2019] [Indexed: 05/21/2023]
Abstract
Acclimation to changing light intensities poses major challenges to plant metabolism and has been shown to involve regulatory adjustments in chloroplast gene expression. However, this regulation has not been examined at a plastid genome-wide level and for many genes, it is unknown whether their expression responds to altered light intensities. Here, we applied comparative ribosome profiling and transcriptomic experiments to analyze changes in chloroplast transcript accumulation and translation in leaves of tobacco (Nicotiana tabacum) seedlings after transfer from moderate light to physiological high light. Our time-course data revealed almost unaltered chloroplast transcript levels and only mild changes in ribosome occupancy during 2 d of high light exposure. Ribosome occupancy on the psbA mRNA (encoding the D1 reaction center protein of PSII) increased and that on the petG transcript decreased slightly after high light treatment. Transfer from moderate light to high light did not induce substantial alterations in ribosome pausing. Transfer experiments from low light to high light conditions resulted in strong PSII photoinhibition and revealed the distinct light-induced activation of psbA translation, which was further confirmed by reciprocal shift experiments. In low-light-to-high-light shift experiments, as well as reciprocal treatments, the expression of all other chloroplast genes remained virtually unaltered. Altogether, our data suggest that low light-acclimated plants upregulate the translation of a single chloroplast gene, psbA, during acclimation to high light. Our results indicate that psbA translation activation occurs already at moderate light intensities. Possible reasons for the otherwise mild effects of light intensity changes on gene expression in differentiated chloroplasts are discussed.
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Affiliation(s)
- Maja Schuster
- Department III, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Yang Gao
- Department III, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Mark Aurel Schöttler
- Department III, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Department III, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Reimo Zoschke
- Department III, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
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Borghi GL, Moraes TA, Günther M, Feil R, Mengin V, Lunn JE, Stitt M, Arrivault S. Relationship between irradiance and levels of Calvin-Benson cycle and other intermediates in the model eudicot Arabidopsis and the model monocot rice. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5809-5825. [PMID: 31353406 PMCID: PMC6812724 DOI: 10.1093/jxb/erz346] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/22/2019] [Indexed: 05/02/2023]
Abstract
Metabolite profiles provide a top-down overview of the balance between the reactions in a pathway. We compared Calvin-Benson cycle (CBC) intermediate profiles in different conditions in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) to learn which features of CBC regulation differ and which are shared between these model eudicot and monocot C3 species. Principal component analysis revealed that CBC intermediate profiles follow different trajectories in Arabidopsis and rice as irradiance increases. The balance between subprocesses or reactions differed, with 3-phosphoglycerate reduction being favoured in Arabidopsis and ribulose 1,5-bisphosphate regeneration in rice, and sedoheptulose-1,7-bisphosphatase being favoured in Arabidopsis compared with fructose-1,6-bisphosphatase in rice. Photosynthesis rates rose in parallel with ribulose 1,5-bisphosphate levels in Arabidopsis, but not in rice. Nevertheless, some responses were shared between Arabidopsis and rice. Fructose 1,6-bisphosphate and sedoheptulose-1,7-bisphosphate were high or peaked at very low irradiance in both species. Incomplete activation of fructose-1,6-bisphosphatase and sedoheptulose-1,7-bisphosphatase may prevent wasteful futile cycles in low irradiance. End-product synthesis is inhibited and high levels of CBC intermediates are maintained in low light or in low CO2 in both species. This may improve photosynthetic efficiency in fluctuating irradiance, and facilitate rapid CBC flux to support photorespiration and energy dissipation in low CO2.
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Affiliation(s)
- Gian Luca Borghi
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Manuela Günther
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Regina Feil
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Virginie Mengin
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - John E Lunn
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Stéphanie Arrivault
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Correspondence:
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Yang B, Zhong Z, Wang T, Ou Y, Tian J, Komatsu S, Zhang L. Integrative omics of Lonicera japonica Thunb. Flower development unravels molecular changes regulating secondary metabolites. J Proteomics 2019; 208:103470. [PMID: 31374363 PMCID: PMC7102679 DOI: 10.1016/j.jprot.2019.103470] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 07/12/2019] [Accepted: 07/24/2019] [Indexed: 12/26/2022]
Abstract
Lonicera japonica Thunb. is an important medicinal plant. The secondary metabolites in L. japonica are diverse and vary in levels during development, leading to the ambiguous evaluation for its medical value. In order to reveal the regulatory mechanism of secondary metabolites during the flowering stages, transcriptomic, proteomic, and metabolomic analyses were performed. The integration analysis of omic-data illustrated that the metabolic changes over the flower developmental stages were mainly involved in sugar metabolism, lipopolysaccharide biosynthesis, carbon conversion, and secondary metabolism. Further proteomic analysis revealed that uniquely identified proteins were mainly involved in glycolysis/phenylpropanoids and tricarboxylic acid cycle/terpenoid backbone pathways in early and late stages, respectively. Transketolase was commonly identified in the 5 developmental stages and 2-fold increase in gold flowering stage compared with juvenile bud stage. Simple phenylpropanoids/flavonoids and 1-deoxy-D-xylulose-5-phosphate were accumulated in early stages and upregulated in late stages, respectively. These results indicate that phenylpropanoids were accumulated attributing to the activated glycolysis process in the early stages, while the terpenoids biosynthetic pathways might be promoted by the transketolase-contained regulatory circuit in the late stages of L. japonica flower development. Biological Significance Lonicera japonica Thunb. is a native species in the East Asian and used in traditional Chinese medicine. In order to reveal the regulatory mechanism of secondary metabolites during the flowering stages, transcriptomic, proteomic, and metabolomic analyses were performed. The integration analysis of omic-data illustrated that the metabolic changes over the flower developmental stages were mainly involved in sugar metabolism, lipopolysaccharide biosynthesis, carbon conversion, and secondary metabolism. Our results indicate that phenylpropanoids were accumulated attributing to the activated glycolysis process in the early stages, while the terpenoids biosynthetic pathways might be promoted by the transketolase-contained regulatory circuit in the late stages of L. japonica flower development. Metabolic changes were mainly involved in sugar metabolism, lipopolysaccharide biosynthesis, and carbon conversion. The unique DAPs were mainly involved in glycolysis and tricarboxylic acid cycle in early and late stages, respectively. Transketolase was commonly identified and 2-fold increase in gold flowering stage compared with juvenile bud stage. Simple phenylpropanoids/flavonoids and DXPS were accumulated in early stages and upregulated in late stages, respectively.
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Affiliation(s)
- Bingxian Yang
- College of Life Science, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Zhuoheng Zhong
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China
| | - Tantan Wang
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China
| | - Yuting Ou
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China
| | - Jingkui Tian
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China
| | - Setsuko Komatsu
- Faculty of Environmental and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
| | - Lin Zhang
- College of Life Science, Zhejiang Sci-Tech University, Hangzhou 310018, China.
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Werner A, Broeckling CD, Prasad A, Peebles CAM. A comprehensive time-course metabolite profiling of the model cyanobacterium Synechocystis sp. PCC 6803 under diurnal light:dark cycles. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:379-388. [PMID: 30889309 DOI: 10.1111/tpj.14320] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/06/2019] [Accepted: 03/12/2019] [Indexed: 05/07/2023]
Abstract
Cyanobacteria are a model photoautotroph and a chassis for the sustainable production of fuels and chemicals. Knowledge of photoautotrophic metabolism in the natural environment of day/night cycles is lacking, yet has implications for improved yield from plants, algae and cyanobacteria. Here, a thorough approach to characterizing diverse metabolites-including carbohydrates, lipids, amino acids, pigments, cofactors, nucleic acids and polysaccharides-in the model cyanobacterium Synechocystis sp. PCC 6803 (S. 6803) under sinusoidal diurnal light:dark cycles was developed and applied. A custom photobioreactor and multi-platform mass spectrometry workflow enabled metabolite profiling every 30-120 min across a 24-h diurnal sinusoidal LD ('sinLD') cycle peaking at 1600 μmol photons m-2 sec-1 . We report widespread oscillations across the sinLD cycle with 90%, 94% and 40% of the identified polar/semi-polar, non-polar and polymeric metabolites displaying statistically significant oscillations, respectively. Microbial growth displayed distinct lag, biomass accumulation and cell division phases of growth. During the lag phase, amino acids and nucleic acids accumulated to high levels per cell followed by decreased levels during the biomass accumulation phase, presumably due to protein and DNA synthesis. Insoluble carbohydrates displayed sharp oscillations per cell at the day-to-night transition. Potential bottlenecks in central carbon metabolism are highlighted. Together, this report provides a comprehensive view of photosynthetic metabolite behavior with high temporal resolution, offering insight into the impact of growth synchronization to light cycles via circadian rhythms. Incorporation into computational modeling and metabolic engineering efforts promises to improve industrially relevant strain design.
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Affiliation(s)
- Allison Werner
- Cell and Molecular Biology Program, Colorado State University, 1005 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Corey D Broeckling
- Proteomics and Metabolomics Facility, Colorado State University, 2021 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Ashok Prasad
- Cell and Molecular Biology Program, Colorado State University, 1005 Campus Delivery, Fort Collins, CO, 80523, USA
- Department of Chemical and Biological Engineering, Colorado State University, 1370 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Christie A M Peebles
- Cell and Molecular Biology Program, Colorado State University, 1005 Campus Delivery, Fort Collins, CO, 80523, USA
- Department of Chemical and Biological Engineering, Colorado State University, 1370 Campus Delivery, Fort Collins, CO, 80523, USA
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Arrivault S, Alexandre Moraes T, Obata T, Medeiros DB, Fernie AR, Boulouis A, Ludwig M, Lunn JE, Borghi GL, Schlereth A, Guenther M, Stitt M. Metabolite profiles reveal interspecific variation in operation of the Calvin-Benson cycle in both C4 and C3 plants. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1843-1858. [PMID: 30773587 PMCID: PMC6436152 DOI: 10.1093/jxb/erz051] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/29/2019] [Indexed: 05/18/2023]
Abstract
Low atmospheric CO2 in recent geological time led to the evolution of carbon-concentrating mechanisms (CCMs) such as C4 photosynthesis in >65 terrestrial plant lineages. We know little about the impact of low CO2 on the Calvin-Benson cycle (CBC) in C3 species that did not evolve CCMs, representing >90% of terrestrial plant species. Metabolite profiling provides a top-down strategy to investigate the operational balance in a pathway. We profiled CBC intermediates in a panel of C4 (Zea mays, Setaria viridis, Flaveria bidentis, and F. trinervia) and C3 species (Oryza sativa, Triticium aestivum, Arabidopsis thaliana, Nicotiana tabacum, and Manihot esculenta). Principal component analysis revealed differences between C4 and C3 species that were driven by many metabolites, including lower ribulose 1,5-bisphosphate in C4 species. Strikingly, there was also considerable variation between C3 species. This was partly due to different chlorophyll and protein contents, but mainly to differences in relative levels of metabolites. Correlation analysis indicated that one contributory factor was the balance between fructose-1,6-bisphosphatase, sedoheptulose-1,7-bisphosphatase, phosphoribulokinase, and Rubisco. Our results point to the CBC having experienced different evolutionary trajectories in C3 species since the ancestors of modern plant lineages diverged. They underline the need to understand CBC operation in a wide range of species.
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Affiliation(s)
- Stéphanie Arrivault
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam-Golm, Germany
| | | | - Toshihiro Obata
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam-Golm, Germany
- Present address: Department of Biochemistry, Center for Plant Science Innovation, University of Nebraska-Lincoln, 1901 Vine Str, Lincoln, NE 68588, USA
| | - David B Medeiros
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam-Golm, Germany
| | - Alix Boulouis
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam-Golm, Germany
- Present address: Institut de Biologie Physico-Chimique, CNRS - Sorbonne Université, Paris, France
| | - Martha Ludwig
- School of Molecular Sciences, The University of Western Australia, Crawley WA, Australia
| | - John E Lunn
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam-Golm, Germany
| | - Gian Luca Borghi
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam-Golm, Germany
| | - Armin Schlereth
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam-Golm, Germany
| | - Manuela Guenther
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam-Golm, Germany
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam-Golm, Germany
- Correspondence:
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Rohr M, Ries F, Herkt C, Gotsmann VL, Westrich LD, Gries K, Trösch R, Christmann J, Chaux-Jukic F, Jung M, Zimmer D, Mühlhaus T, Sommer F, Schroda M, Keller S, Möhlmann T, Willmund F. The Role of Plastidic Trigger Factor Serving Protein Biogenesis in Green Algae and Land Plants. PLANT PHYSIOLOGY 2019; 179:1093-1110. [PMID: 30651302 PMCID: PMC6393800 DOI: 10.1104/pp.18.01252] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/07/2019] [Indexed: 05/07/2023]
Abstract
Biochemical processes in chloroplasts are important for virtually all life forms. Tight regulation of protein homeostasis and the coordinated assembly of protein complexes, composed of both imported and locally synthesized subunits, are vital to plastid functionality. Protein biogenesis requires the action of cotranslationally acting molecular chaperones. One such chaperone is trigger factor (TF), which is known to cotranslationally bind most newly synthesized proteins in bacteria, thereby assisting their correct folding and maturation. However, how these processes are regulated in chloroplasts remains poorly understood. We report here functional investigation of chloroplast-localized TF (TIG1) in the green alga (Chlamydomonas reinhardtii) and the vascular land plant Arabidopsis (Arabidopsis thaliana). We show that chloroplastic TIG1 evolved as a specialized chaperone. Unlike other plastidic chaperones that are functionally interchangeable with their prokaryotic counterpart, TIG1 was not able to complement the broadly acting ortholog in Escherichia coli. Whereas general chaperone properties such as the prevention of aggregates or substrate recognition seems to be conserved between bacterial and plastidic TFs, plant TIG1s differed by associating with only a relatively small population of translating ribosomes. Furthermore, a reduction of plastidic TIG1 levels leads to deregulated protein biogenesis at the expense of increased translation, thereby disrupting the chloroplast energy household. This suggests a central role of TIG1 in protein biogenesis in the chloroplast.
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Affiliation(s)
- Marina Rohr
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
| | - Fabian Ries
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
| | - Claudia Herkt
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
| | - Vincent Leon Gotsmann
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
| | - Lisa Désirée Westrich
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
| | - Karin Gries
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
| | - Raphael Trösch
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
| | - Jens Christmann
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
| | | | - Martin Jung
- Medical Biochemistry and Molecular Biology, Building 44, Saarland University, 66421 Homburg, Germany
| | - David Zimmer
- Computational Systems Biology, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
| | - Timo Mühlhaus
- Computational Systems Biology, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
| | - Frederik Sommer
- Molecular Biotechnology and Systems Biology, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
| | - Michael Schroda
- Molecular Biotechnology and Systems Biology, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
| | - Torsten Möhlmann
- Plant Physiology, University of Kaiserslautern, Paul-Ehrlich Strasse 22, 67663 Kaiserslautern, Germany
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
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46
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Nama S, Madireddi SK, Yadav RM, Subramanyam R. Non-photochemical quenching-dependent acclimation and thylakoid organization of Chlamydomonas reinhardtii to high light stress. PHOTOSYNTHESIS RESEARCH 2019; 139:387-400. [PMID: 29982908 DOI: 10.1007/s11120-018-0551-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/30/2018] [Indexed: 05/19/2023]
Abstract
Light is essential for all photosynthetic organisms while an excess of it can lead to damage mainly the photosystems of the thylakoid membrane. In this study, we have grown Chlamydomonas reinhardtii cells in different intensities of high light to understand the photosynthetic process with reference to thylakoid membrane organization during its acclimation process. We observed, the cells acclimatized to long-term response to high light intensities of 500 and 1000 µmol m-2 s-1 with faster growth and more biomass production when compared to cells at 50 µmol m-2 s-1 light intensity. The ratio of Chl a/b was marginally decreased from the mid-log phase of growth at the high light intensity. Increased level of zeaxanthin and LHCSR3 expression was also found which is known to play a key role in non-photochemical quenching (NPQ) mechanism for photoprotection. Changes in photosynthetic parameters were observed such as increased levels of NPQ, marginal change in electron transport rate, and many other changes which demonstrate that cells were acclimatized to high light which is an adaptive mechanism. Surprisingly, PSII core protein contents have marginally reduced when compared to peripherally arranged LHCII in high light-grown cells. Further, we also observed alterations in stromal subunits of PSI and low levels of PsaG, probably due to disruption of PSI assembly and also its association with LHCI. During the process of acclimation, changes in thylakoid organization occurred in high light intensities with reduction of PSII supercomplex formation. This change may be attributed to alteration of protein-pigment complexes which are in agreement with circular dichoism spectra of high light-acclimatized cells, where decrease in the magnitude of psi-type bands indicates changes in ordered arrays of PSII-LHCII supercomplexes. These results specify that acclimation to high light stress through NPQ mechanism by expression of LHCSR3 and also observed changes in thylakoid protein profile/supercomplex formation lead to low photochemical yield and more biomass production in high light condition.
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Affiliation(s)
- Srilatha Nama
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India
| | - Sai Kiran Madireddi
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India
| | - Ranay Mohan Yadav
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India
| | - Rajagopal Subramanyam
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India.
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47
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Lachmann SC, Mettler‐Altmann T, Wacker A, Spijkerman E. Nitrate or ammonium: Influences of nitrogen source on the physiology of a green alga. Ecol Evol 2019; 9:1070-1082. [PMID: 30805141 PMCID: PMC6374670 DOI: 10.1002/ece3.4790] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 10/19/2018] [Accepted: 10/30/2018] [Indexed: 11/25/2022] Open
Abstract
In freshwaters, algal species are exposed to different inorganic nitrogen (Ni) sources whose incorporation varies in biochemical energy demand. We hypothesized that due to the lesser energy requirement of ammonium ( NH 4 + )-use, in contrast to nitrate ( NO 3 - )-use, more energy remains for other metabolic processes, especially under CO2- and phosphorus (Pi) limiting conditions. Therefore, we tested differences in cell characteristics of the green alga Chlamydomonas acidophila grown on NH 4 + or NO 3 - under covariation of CO2 and Pi-supply in order to determine limitations, in a full-factorial design. As expected, results revealed higher carbon fixation rates for NH 4 + -grown cells compared to growth with NO 3 - under low CO2 conditions. NO 3 - -grown cells accumulated more of the nine analyzed amino acids, especially under Pi-limited conditions, compared to cells provided with NH 4 + . This is probably due to a slower protein synthesis in cells provided with NO 3 - . In contrast to our expectations, compared to NH 4 + -grown cells NO 3 - -grown cells had higher photosynthetic efficiency under Pi-limitation. In conclusion, growth on the Ni-source NH 4 + did not result in a clearly enhanced Ci-assimilation, as it was highly dependent on Pi and CO2 conditions (replete or limited). Results are potentially connected to the fact that C. acidophila is able to use only CO2 as its inorganic carbon (Ci) source.
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Affiliation(s)
| | - Tabea Mettler‐Altmann
- Cluster of Excellence on Plant Sciences and Institute of Plant BiochemistryHeinrich‐Heine UniversityDüsseldorfGermany
| | - Alexander Wacker
- Heisenberg‐Group: Theoretical Aquatic Ecology and Ecophysiology, Institute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
| | - Elly Spijkerman
- Institute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
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48
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Kaye Y, Huang W, Clowez S, Saroussi S, Idoine A, Sanz-Luque E, Grossman AR. The mitochondrial alternative oxidase from Chlamydomonas reinhardtii enables survival in high light. J Biol Chem 2018; 294:1380-1395. [PMID: 30510139 DOI: 10.1074/jbc.ra118.004667] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 10/24/2018] [Indexed: 01/07/2023] Open
Abstract
Photosynthetic organisms often experience extreme light conditions that can cause hyper-reduction of the chloroplast electron transport chain, resulting in oxidative damage. Accumulating evidence suggests that mitochondrial respiration and chloroplast photosynthesis are coupled when cells are absorbing high levels of excitation energy. This coupling helps protect the cells from hyper-reduction of photosynthetic electron carriers and diminishes the production of reactive oxygen species (ROS). To examine this cooperative protection, here we characterized Chlamydomonas reinhardtii mutants lacking the mitochondrial alternative terminal respiratory oxidases, CrAOX1 and CrAOX2. Using fluorescent fusion proteins, we experimentally demonstrated that both enzymes localize to mitochondria. We also observed that the mutant strains were more sensitive than WT cells to high light under mixotrophic and photoautotrophic conditions, with the aox1 strain being more sensitive than aox2 Additionally, the lack of CrAOX1 increased ROS accumulation, especially in very high light, and damaged the photosynthetic machinery, ultimately resulting in cell death. These findings indicate that the Chlamydomonas AOX proteins can participate in acclimation of C. reinhardtii cells to excess absorbed light energy. They suggest that when photosynthetic electron carriers are highly reduced, a chloroplast-mitochondria coupling allows safe dissipation of photosynthetically derived electrons via the reduction of O2 through AOX (especially AOX1)-dependent mitochondrial respiration.
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Affiliation(s)
- Yuval Kaye
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305.
| | - Weichao Huang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Sophie Clowez
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Shai Saroussi
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Adam Idoine
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Emanuel Sanz-Luque
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
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49
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Zimmer D, Schneider K, Sommer F, Schroda M, Mühlhaus T. Artificial Intelligence Understands Peptide Observability and Assists With Absolute Protein Quantification. FRONTIERS IN PLANT SCIENCE 2018; 9:1559. [PMID: 30483279 PMCID: PMC6242780 DOI: 10.3389/fpls.2018.01559] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/04/2018] [Indexed: 05/20/2023]
Abstract
Targeted mass spectrometry has become the method of choice to gain absolute quantification information of high quality, which is essential for a quantitative understanding of biological systems. However, the design of absolute protein quantification assays remains challenging due to variations in peptide observability and incomplete knowledge about factors influencing peptide detectability. Here, we present a deep learning algorithm for peptide detectability prediction, d::pPop, which allows the informed selection of synthetic proteotypic peptides for the successful design of targeted proteomics quantification assays. The deep neural network is able to learn a regression model that relates the physicochemical properties of a peptide to its ion intensity detected by mass spectrometry. The approach makes use of experimentally detected deviations from the assumed equimolar abundance of all peptides derived from a given protein. Trained on extensive proteomics datasets, d::pPop's plant and non-plant specific models can predict the quality of proteotypic peptides for not yet experimentally identified proteins. Interrogating the deep neural network after learning from ~76,000 peptides per model organism allows to investigate the impact of different physicochemical properties on the observability of a peptide, thus providing insights into peptide observability as a multifaceted process. Empirical evaluation with rank accuracy metrics showed that our prediction approach outperforms existing algorithms. We circumvent the delicate step of selecting positive and negative training sets and at the same time also more closely reflect the need for selecting the top most promising peptides for targeting a protein of interest. Further, we used an artificial QconCAT protein to experimentally validate the observability prediction. Our proteotypic peptide prediction approach not only facilitates the design of absolute protein quantification assays via a user-friendly web interface but also enables the selection of proteotypic peptides for not yet observed proteins, hence rendering the tool especially useful for plant research.
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Affiliation(s)
- David Zimmer
- Computational Systems BiologyTU Kaiserslautern, Kaiserslautern, Germany
| | - Kevin Schneider
- Computational Systems BiologyTU Kaiserslautern, Kaiserslautern, Germany
| | - Frederik Sommer
- Molekulare Biotechnologie & SystembiologieTU Kaiserslautern, Kaiserslautern, Germany
| | - Michael Schroda
- Molekulare Biotechnologie & SystembiologieTU Kaiserslautern, Kaiserslautern, Germany
| | - Timo Mühlhaus
- Computational Systems BiologyTU Kaiserslautern, Kaiserslautern, Germany
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50
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Krüsemann JL, Lindner SN, Dempfle M, Widmer J, Arrivault S, Debacker M, He H, Kubis A, Chayot R, Anissimova M, Marlière P, Cotton CAR, Bar‐Even A. Artificial pathway emergence in central metabolism from three recursive phosphoketolase reactions. FEBS J 2018; 285:4367-4377. [DOI: 10.1111/febs.14682] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/11/2018] [Accepted: 10/17/2018] [Indexed: 01/17/2023]
Affiliation(s)
- Jan L. Krüsemann
- Max Planck Institute of Molecular Plant Physiology Potsdam‐Golm Germany
| | | | - Marian Dempfle
- Max Planck Institute of Molecular Plant Physiology Potsdam‐Golm Germany
| | - Julian Widmer
- Max Planck Institute of Molecular Plant Physiology Potsdam‐Golm Germany
| | | | | | - Hai He
- Max Planck Institute of Molecular Plant Physiology Potsdam‐Golm Germany
| | - Armin Kubis
- Max Planck Institute of Molecular Plant Physiology Potsdam‐Golm Germany
| | | | | | - Philippe Marlière
- Altar Evry France
- TESSSI The European Syndicate of Synthetic Scientists and Industrialists Paris France
| | | | - Arren Bar‐Even
- Max Planck Institute of Molecular Plant Physiology Potsdam‐Golm Germany
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