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Zhang J, Zhang F, Dong Z, Zhang W, Sun T, Chen L. Response and acclimation of cyanobacteria to acidification: A comprehensive review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 945:173978. [PMID: 38897479 DOI: 10.1016/j.scitotenv.2024.173978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/08/2024] [Accepted: 06/11/2024] [Indexed: 06/21/2024]
Abstract
Cyanobacteria, as vital components of aquatic ecosystems, face increasing challenges due to acidification driven by various anthropogenic and natural factors. Understanding how cyanobacteria adapt and respond to acidification is crucial for predicting their ecological dynamics and potential impacts on ecosystem health. This comprehensive review synthesizes current knowledge on the acclimation mechanisms and responses of cyanobacteria to acidification stress. Detailly, ecological roles of cyanobacteria were firstly briefly concluded, followed by the effects of acidification on aquatic ecosystems and cyanobacteria. Then the review focuses on the physiological, biochemical, and molecular strategies employed by cyanobacteria to cope with acidification stress, highlighting key adaptive mechanisms and their ecological implications. Finally, a summary of strategies to enhance acid resistance in cyanobacteria and future directions was discussed. Utilizing omics data and machine learning technology to build a cyanobacterial acid regulatory network allows for predicting the impact of acidification on cyanobacteria and inferring its broader effects on ecosystems. Additionally, acquiring acid-tolerant chassis cells of cyanobacteria through innovative techniques facilitates the advancement of environmentally friendly production of acidic chemicals. By synthesizing empirical evidence and theoretical frameworks, this review aims to elucidate the complex interplay between cyanobacteria and acidification stressors, providing insights for future research directions and ecosystem management strategies.
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Affiliation(s)
- Jie Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China
| | - Fenfang Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China
| | - Zhengxin Dong
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China; Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, PR China
| | - Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China; Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, PR China..
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China.
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2
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Turnsek JB, Oltrogge LM, Savage DF. Conserved and repetitive motifs in an intrinsically disordered protein drive ⍺-carboxysome assembly. J Biol Chem 2024:107532. [PMID: 38971311 DOI: 10.1016/j.jbc.2024.107532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 05/30/2024] [Accepted: 06/06/2024] [Indexed: 07/08/2024] Open
Abstract
All cyanobacteria and some chemoautotrophic bacteria fix CO2 into sugars using specialized proteinaceous compartments called carboxysomes. Carboxysomes enclose the enzymes Rubisco and carbonic anhydrase inside a layer of shell proteins to increase the CO2 concentration for efficient carbon fixation by Rubisco. In the ⍺-carboxysome lineage, a disordered and highly repetitive protein named CsoS2 is essential for carboxysome formation and function. Without it, the bacteria require high CO2 to grow. How does a protein predicted to be lacking structure serve as the architectural scaffold for such a vital cellular compartment? In this study, we identify key residues present in the repeats of CsoS2, VTG and Y, which are necessary for building functional ⍺-carboxysomes in vivo. These highly conserved and repetitive residues contribute to the multivalent binding interaction and phase separation behavior between CsoS2 and shell proteins. We also demonstrate 3-component reconstitution of CsoS2, Rubisco, and shell proteins into spherical condensates, and show the utility of reconstitution as a biochemical tool to study carboxysome biogenesis. The precise self-assembly of thousands of proteins is crucial for carboxysome formation, and understanding this process could enable their use in alternative biological hosts or industrial processes as effective tools to fix carbon.
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Affiliation(s)
- Julia B Turnsek
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Luke M Oltrogge
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA; Howard Hughes Medical Institute, University of California, Berkeley, California, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA; Howard Hughes Medical Institute, University of California, Berkeley, California, USA; Innovative Genomics Institute, University of California, Berkeley, California, USA.
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3
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de Pins B, Greenspoon L, Bar-On YM, Shamshoum M, Ben-Nissan R, Milshtein E, Davidi D, Sharon I, Mueller-Cajar O, Noor E, Milo R. A systematic exploration of bacterial form I rubisco maximal carboxylation rates. EMBO J 2024; 43:3072-3083. [PMID: 38806660 PMCID: PMC11251275 DOI: 10.1038/s44318-024-00119-z] [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: 02/01/2024] [Revised: 03/26/2024] [Accepted: 04/22/2024] [Indexed: 05/30/2024] Open
Abstract
Autotrophy is the basis for complex life on Earth. Central to this process is rubisco-the enzyme that catalyzes almost all carbon fixation on the planet. Yet, with only a small fraction of rubisco diversity kinetically characterized so far, the underlying biological factors driving the evolution of fast rubiscos in nature remain unclear. We conducted a high-throughput kinetic characterization of over 100 bacterial form I rubiscos, the most ubiquitous group of rubisco sequences in nature, to uncover the determinants of rubisco's carboxylation velocity. We show that the presence of a carboxysome CO2 concentrating mechanism correlates with faster rubiscos with a median fivefold higher rate. In contrast to prior studies, we find that rubiscos originating from α-cyanobacteria exhibit the highest carboxylation rates among form I enzymes (≈10 s-1 median versus <7 s-1 in other groups). Our study systematically reveals biological and environmental properties associated with kinetic variation across rubiscos from nature.
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Affiliation(s)
- Benoit de Pins
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Lior Greenspoon
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yinon M Bar-On
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Melina Shamshoum
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Roee Ben-Nissan
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Eliya Milshtein
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Dan Davidi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
- Aleph, Tel Aviv-Yafo, 6688210, Israel
| | - Itai Sharon
- Migal Galilee Research Institute, Kiryat Shmona, 11016, Israel
| | - Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel.
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4
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Kunz HH, Armbruster U, Mühlbauer S, de Vries J, Davis GA. Chloroplast ion homeostasis - what do we know and where should we go? THE NEW PHYTOLOGIST 2024; 243:543-559. [PMID: 38515227 DOI: 10.1111/nph.19661] [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: 07/01/2023] [Accepted: 02/01/2024] [Indexed: 03/23/2024]
Abstract
Plant yields heavily depend on proper macro- and micronutrient supply from the soil. In the leaf cells, nutrient ions fulfill specific roles in biochemical reactions, especially photosynthesis housed in the chloroplast. Here, a well-balanced ion homeostasis is maintained by a number of ion transport proteins embedded in the envelope and thylakoid membranes. Ten years ago, the first alkali metal transporters from the K+ EFFLUX ANTIPORTER family were discovered in the model plant Arabidopsis. Since then, our knowledge about the physiological importance of these carriers and their substrates has greatly expanded. New insights into the role of alkali ions in plastid gene expression and photoprotective mechanisms, both prerequisites for plant productivity in natural environments, were gained. The discovery of a Cl- channel in the thylakoid and several additional plastid alkali and alkali metal transport proteins have advanced the field further. Nevertheless, scientists still have long ways to go before a complete systemic understanding of the chloroplast's ion transportome will emerge. In this Tansley review, we highlight and discuss the achievements of the last decade. More importantly, we make recommendations on what areas to prioritize, so the field can reach the next milestones. One area, laid bare by our similarity-based comparisons among phototrophs is our lack of knowledge what ion transporters are used by cyanobacteria to buffer photosynthesis fluctuations.
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Affiliation(s)
- Hans-Henning Kunz
- Plant Biochemistry, Biology, LMU Munich, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Ute Armbruster
- Institute of Molecular Photosynthesis, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
- CEPLAS - Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Susanne Mühlbauer
- Plant Biochemistry, Biology, LMU Munich, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, Goettingen Center for Molecular Biosciences (GZMB), Campus Institute Data Science (CIDAS), University of Goettingen, Goldschmidtstr. 1, D-37077, Göttingen, Germany
| | - Geoffry A Davis
- Plant Biochemistry, Biology, LMU Munich, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
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5
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Karikomi M, Katayama N, Osanai T. Pyruvate kinase 2 from Synechocystis sp. PCC 6803 increased substrate affinity via glucose-6-phosphate and ribose-5-phosphate for phosphoenolpyruvate consumption. PLANT MOLECULAR BIOLOGY 2024; 114:60. [PMID: 38758412 PMCID: PMC11101554 DOI: 10.1007/s11103-023-01401-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 11/30/2023] [Indexed: 05/18/2024]
Abstract
Pyruvate kinase (Pyk, EC 2.7.1.40) is a glycolytic enzyme that generates pyruvate and adenosine triphosphate (ATP) from phosphoenolpyruvate (PEP) and adenosine diphosphate (ADP), respectively. Pyk couples pyruvate and tricarboxylic acid metabolisms. Synechocystis sp. PCC 6803 possesses two pyk genes (encoded pyk1, sll0587 and pyk2, sll1275). A previous study suggested that pyk2 and not pyk1 is essential for cell viability; however, its biochemical analysis is yet to be performed. Herein, we biochemically analyzed Synechocystis Pyk2 (hereafter, SyPyk2). The optimum pH and temperature of SyPyk2 were 7.0 and 55 °C, respectively, and the Km values for PEP and ADP under optimal conditions were 1.5 and 0.053 mM, respectively. SyPyk2 is activated in the presence of glucose-6-phosphate (G6P) and ribose-5-phosphate (R5P); however, it remains unaltered in the presence of adenosine monophosphate (AMP) or fructose-1,6-bisphosphate. These results indicate that SyPyk2 is classified as PykA type rather than PykF, stimulated by sugar monophosphates, such as G6P and R5P, but not by AMP. SyPyk2, considering substrate affinity and effectors, can play pivotal roles in sugar catabolism under nonphotosynthetic conditions.
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Affiliation(s)
- Masahiro Karikomi
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-Ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Noriaki Katayama
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-Ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Takashi Osanai
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-Ku, Kawasaki, Kanagawa, 214-8571, Japan.
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6
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Pulsford SB, Outram MA, Förster B, Rhodes T, Williams SJ, Badger MR, Price GD, Jackson CJ, Long BM. Cyanobacterial α-carboxysome carbonic anhydrase is allosterically regulated by the Rubisco substrate RuBP. SCIENCE ADVANCES 2024; 10:eadk7283. [PMID: 38728392 PMCID: PMC11086599 DOI: 10.1126/sciadv.adk7283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 04/08/2024] [Indexed: 05/12/2024]
Abstract
Cyanobacterial CO2 concentrating mechanisms (CCMs) sequester a globally consequential proportion of carbon into the biosphere. Proteinaceous microcompartments, called carboxysomes, play a critical role in CCM function, housing two enzymes to enhance CO2 fixation: carbonic anhydrase (CA) and Rubisco. Despite its importance, our current understanding of the carboxysomal CAs found in α-cyanobacteria, CsoSCA, remains limited, particularly regarding the regulation of its activity. Here, we present a structural and biochemical study of CsoSCA from the cyanobacterium Cyanobium sp. PCC7001. Our results show that the Cyanobium CsoSCA is allosterically activated by the Rubisco substrate ribulose-1,5-bisphosphate and forms a hexameric trimer of dimers. Comprehensive phylogenetic and mutational analyses are consistent with this regulation appearing exclusively in cyanobacterial α-carboxysome CAs. These findings clarify the biologically relevant oligomeric state of α-carboxysomal CAs and advance our understanding of the regulation of photosynthesis in this globally dominant lineage.
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Affiliation(s)
- Sacha B. Pulsford
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW, Australia
- Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - Megan A. Outram
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Britta Förster
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Timothy Rhodes
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Simon J. Williams
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Murray R. Badger
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - G. Dean Price
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Colin J. Jackson
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW, Australia
- Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - Benedict M. Long
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW, Australia
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
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7
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Nguyen ND, Pulsford SB, Förster B, Rottet S, Rourke L, Long BM, Price GD. A carboxysome-based CO 2 concentrating mechanism for C 3 crop chloroplasts: advances and the road ahead. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:940-952. [PMID: 38321620 DOI: 10.1111/tpj.16667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/17/2024] [Accepted: 01/24/2024] [Indexed: 02/08/2024]
Abstract
The introduction of the carboxysome-based CO2 concentrating mechanism (CCM) into crop plants has been modelled to significantly increase crop yields. This projection serves as motivation for pursuing this strategy to contribute to global food security. The successful implementation of this engineering challenge is reliant upon the transfer of a microcompartment that encapsulates cyanobacterial Rubisco, known as the carboxysome, alongside active bicarbonate transporters. To date, significant progress has been achieved with respect to understanding various aspects of the cyanobacterial CCM, and more recently, different components of the carboxysome have been successfully introduced into plant chloroplasts. In this Perspective piece, we summarise recent findings and offer new research avenues that will accelerate research in this field to ultimately and successfully introduce the carboxysome into crop plants for increased crop yields.
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Affiliation(s)
- Nghiem D Nguyen
- Plant Science Division, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory, 2601, Australia
| | - Sacha B Pulsford
- Research School of Chemistry, Australian National University, 137 Sullivan's Ck Rd, Acton, Australian Capital Territory, 2601, Australia
| | - Britta Förster
- Plant Science Division, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory, 2601, Australia
| | - Sarah Rottet
- Plant Science Division, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory, 2601, Australia
| | - Loraine Rourke
- Plant Science Division, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory, 2601, Australia
| | - Benedict M Long
- Discipline of Biological Sciences, School of Environmental and Life Sciences, ARC Centre of Excellence in Synthetic Biology, The University of Newcastle, University Drive, Callaghan, New South Wales, 2308, Australia
| | - G Dean Price
- Plant Science Division, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory, 2601, Australia
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8
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Gómez F, Rodríguez N, Rodríguez-Manfredi JA, Escudero C, Carrasco-Ropero I, Martínez JM, Ferrari M, De Angelis S, Frigeri A, Fernández-Sampedro M, Amils R. Association of Acidotolerant Cyanobacteria to Microbial Mats below pH 1 in Acidic Mineral Precipitates in Río Tinto River in Spain. Microorganisms 2024; 12:829. [PMID: 38674771 PMCID: PMC11052175 DOI: 10.3390/microorganisms12040829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/04/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
This report describes acidic microbial mats containing cyanobacteria that are strongly associated to precipitated minerals in the source area of Río Tinto. Río Tinto (Huelva, Southwestern Spain) is an extreme acidic environment where iron and sulfur cycles play a fundamental role in sustaining the extremely low pH and the high concentration of heavy metals, while maintaining a high level of microbial diversity. These multi-layered mineral deposits are stable all year round and are characterized by a succession of thick greenish-blue and brownish layers mainly composed of natrojarosite. The temperature and absorbance above and below the mineral precipitates were followed and stable conditions were detected inside the mineral precipitates. Different methodologies, scanning and transmission electron microscopy, immunological detection, fluorescence in situ hybridization, and metagenomic analysis were used to describe the biodiversity existing in these microbial mats, demonstrating, for the first time, the existence of acid-tolerant cyanobacteria in a hyperacidic environment of below pH 1. Up to 0.46% of the classified sequences belong to cyanobacterial microorganisms, and 1.47% of the aligned DNA reads belong to the Cyanobacteria clade.
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Affiliation(s)
- Felipe Gómez
- Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Nuria Rodríguez
- Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | | | - Cristina Escudero
- Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | | | - José M. Martínez
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Cantoblanco, 28049 Madrid, Spain
| | - Marco Ferrari
- Istituto di Astrofisica e Planetologia Spaziali (INAF), via del Fosso del Cavaliere 100, 00133 Rome, Italy
| | - Simone De Angelis
- Istituto di Astrofisica e Planetologia Spaziali (INAF), via del Fosso del Cavaliere 100, 00133 Rome, Italy
| | - Alessandro Frigeri
- Istituto di Astrofisica e Planetologia Spaziali (INAF), via del Fosso del Cavaliere 100, 00133 Rome, Italy
| | - Maite Fernández-Sampedro
- Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Ricardo Amils
- Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir km 4, Torrejón de Ardoz, 28850 Madrid, Spain
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Cantoblanco, 28049 Madrid, Spain
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9
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Sendker FL, Lo YK, Heimerl T, Bohn S, Persson LJ, Mais CN, Sadowska W, Paczia N, Nußbaum E, Del Carmen Sánchez Olmos M, Forchhammer K, Schindler D, Erb TJ, Benesch JLP, Marklund EG, Bange G, Schuller JM, Hochberg GKA. Emergence of fractal geometries in the evolution of a metabolic enzyme. Nature 2024; 628:894-900. [PMID: 38600380 PMCID: PMC11041685 DOI: 10.1038/s41586-024-07287-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 03/08/2024] [Indexed: 04/12/2024]
Abstract
Fractals are patterns that are self-similar across multiple length-scales1. Macroscopic fractals are common in nature2-4; however, so far, molecular assembly into fractals is restricted to synthetic systems5-12. Here we report the discovery of a natural protein, citrate synthase from the cyanobacterium Synechococcus elongatus, which self-assembles into Sierpiński triangles. Using cryo-electron microscopy, we reveal how the fractal assembles from a hexameric building block. Although different stimuli modulate the formation of fractal complexes and these complexes can regulate the enzymatic activity of citrate synthase in vitro, the fractal may not serve a physiological function in vivo. We use ancestral sequence reconstruction to retrace how the citrate synthase fractal evolved from non-fractal precursors, and the results suggest it may have emerged as a harmless evolutionary accident. Our findings expand the space of possible protein complexes and demonstrate that intricate and regulatable assemblies can evolve in a single substitution.
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Affiliation(s)
- Franziska L Sendker
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Yat Kei Lo
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Thomas Heimerl
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Stefan Bohn
- Cryo-EM Platform and Institute of Structural Biology, Helmholtz Munich, Neuherberg, Germany
| | - Louise J Persson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | - Wiktoria Sadowska
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Nicole Paczia
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Eva Nußbaum
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, Tübingen, Germany
| | | | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, Tübingen, Germany
| | - Daniel Schindler
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
- MaxGENESYS Biofoundry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Tobias J Erb
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Justin L P Benesch
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Max Planck Fellow Group Molecular Physiology of Microbes, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jan M Schuller
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany.
| | - Georg K A Hochberg
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany.
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10
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Usai G, Cordara A, Mazzocchi E, Re A, Fino D, Pirri CF, Menin B. Coupling dairy wastewaters for nutritional balancing and water recycling: sustainable heterologous 2-phenylethanol production by engineered cyanobacteria. Front Bioeng Biotechnol 2024; 12:1359032. [PMID: 38497052 PMCID: PMC10940361 DOI: 10.3389/fbioe.2024.1359032] [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: 12/20/2023] [Accepted: 02/12/2024] [Indexed: 03/19/2024] Open
Abstract
Microalgae biotechnology is hampered by the high production costs and the massive usage of water during large-volume cultivations. These drawbacks can be softened by the production of high-value compounds and by adopting metabolic engineering strategies to improve their performances and productivity. Today, the most sustainable approach is the exploitation of industrial wastewaters for microalgae cultivation, which couples valuable biomass production with water resource recovery. Among the food processing sectors, the dairy industry generates the largest volume of wastewaters through the manufacturing process. These effluents are typically rich in dissolved organic matter and nutrients, which make it a challenging and expensive waste stream for companies to manage. Nevertheless, these rich wastewaters represent an appealing resource for microalgal biotechnology. In this study, we propose a sustainable approach for high-value compound production from dairy wastewaters through cyanobacteria. This strategy is based on a metabolically engineered strain of the model cyanobacterium Synechococcus elongatus PCC 7942 (already published elsewhere) for 2-phenylethanol (2-PE). 2-PE is a high-value aromatic compound that is widely employed as a fragrance in the food and cosmetics industry thanks to its pleasant floral scent. First, we qualitatively assessed the impact of four dairy effluents on cyanobacterial growth to identify the most promising substrates. Both tank-washing water and the liquid effluent of exhausted sludge resulted as suitable nutrient sources. Thus, we created an ideal buffer system by combining the two wastewaters while simultaneously providing balanced nutrition and completely avoiding the need for fresh water. The combination of 75% liquid effluent of exhausted sludge and 25% tank-washing water with a fine-tuning ammonium supplementation yielded 180 mg L-1 of 2-PE and a biomass concentration of 0.6 gDW L-1 within 10 days. The mixture of 90% exhausted sludge and 10% washing water produced the highest yield of 2-PE (205 mg L-1) and biomass accumulation (0.7 gDW L-1), although in 16 days. Through these treatments, the phosphates were completely consumed, and nitrogen was removed in a range of 74%-77%. Overall, our approach significantly valorized water recycling and the exploitation of valuable wastewaters to circularly produce marketable compounds via microalgae biotechnology, laying a promising groundwork for subsequent implementation and scale-up.
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Affiliation(s)
- Giulia Usai
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- Department of Applied Science and Technology—DISAT, Politecnico di Torino, Turin, Italy
| | - Alessandro Cordara
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- Department of Environment, Land and Infrastructure Engineering—DIATI, Politecnico di Torino, Turin, Italy
| | - Elena Mazzocchi
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- Department of Applied Science and Technology—DISAT, Politecnico di Torino, Turin, Italy
| | - Angela Re
- Department of Applied Science and Technology—DISAT, Politecnico di Torino, Turin, Italy
| | - Debora Fino
- Department of Applied Science and Technology—DISAT, Politecnico di Torino, Turin, Italy
| | - Candido Fabrizio Pirri
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- Department of Applied Science and Technology—DISAT, Politecnico di Torino, Turin, Italy
| | - Barbara Menin
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche IBBA-CNR, Milan, Italy
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11
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Oltrogge LM, Chen AW, Chaijarasphong T, Turnšek JB, Savage DF. α-Carboxysome Size Is Controlled by the Disordered Scaffold Protein CsoS2. Biochemistry 2024; 63:219-229. [PMID: 38085650 PMCID: PMC10795168 DOI: 10.1021/acs.biochem.3c00403] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 01/17/2024]
Abstract
Carboxysomes are protein microcompartments that function in the bacterial CO2 concentrating mechanism (CCM) to facilitate CO2 assimilation. To do so, carboxysomes assemble from thousands of constituent proteins into an icosahedral shell, which encapsulates the enzymes Rubisco and carbonic anhydrase to form structures typically > 100 nm and > 300 megadaltons. Although many of the protein interactions driving the assembly process have been determined, it remains unknown how size and composition are precisely controlled. Here, we show that the size of α-carboxysomes is controlled by the disordered scaffolding protein CsoS2. CsoS2 contains two classes of related peptide repeats that bind to the shell in a distinct fashion, and our data indicate that size is controlled by the relative number of these interactions. We propose an energetic and structural model wherein the two repeat classes bind at the junction of shell hexamers but differ in their preferences for the shell contact angles, and thus the local curvature. In total, this model suggests that a set of specific and repeated interactions between CsoS2 and shell proteins collectively achieve the large size and monodispersity of α-carboxysomes.
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Affiliation(s)
- Luke M. Oltrogge
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
- Howard
Hughes Medical Institute, University of California, Berkeley, California 94720, United States
| | - Allen W. Chen
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | | | - Julia B. Turnšek
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
| | - David F. Savage
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
- Howard
Hughes Medical Institute, University of California, Berkeley, California 94720, United States
- Innovative
Genomics Institute, University of California, Berkeley, California 94720, United States
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12
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Jiang HW, Wu HY, Wang CH, Yang CH, Ko JT, Ho HC, Tsai MD, Bryant DA, Li FW, Ho MC, Ho MY. A structure of the relict phycobilisome from a thylakoid-free cyanobacterium. Nat Commun 2023; 14:8009. [PMID: 38049400 PMCID: PMC10696076 DOI: 10.1038/s41467-023-43646-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 11/15/2023] [Indexed: 12/06/2023] Open
Abstract
Phycobilisomes (PBS) are antenna megacomplexes that transfer energy to photosystems II and I in thylakoids. PBS likely evolved from a basic, inefficient form into the predominant hemidiscoidal shape with radiating peripheral rods. However, it has been challenging to test this hypothesis because ancestral species are generally inaccessible. Here we use spectroscopy and cryo-electron microscopy to reveal a structure of a "paddle-shaped" PBS from a thylakoid-free cyanobacterium that likely retains ancestral traits. This PBS lacks rods and specialized ApcD and ApcF subunits, indicating relict characteristics. Other features include linkers connecting two chains of five phycocyanin hexamers (CpcN) and two core subdomains (ApcH), resulting in a paddle-shaped configuration. Energy transfer calculations demonstrate that chains are less efficient than rods. These features may nevertheless have increased light absorption by elongating PBS before multilayered thylakoids with hemidiscoidal PBS evolved. Our results provide insights into the evolution and diversification of light-harvesting strategies before the origin of thylakoids.
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Affiliation(s)
- Han-Wei Jiang
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Hsiang-Yi Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chun-Hsiung Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Cheng-Han Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Jui-Tse Ko
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Han-Chen Ho
- Department of Anatomy, Tzu Chi University, Hualien, Taiwan
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.
- Graduate Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei, Taiwan.
| | - Ming-Yang Ho
- Department of Life Science, National Taiwan University, Taipei, Taiwan.
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan.
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13
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Zafar AM, Aly Hassan A. Seawater biodesalination treatment using Phormidium keutzingianum in attached growth-packed bed continuous flow stirred tank reactor. ENVIRONMENTAL RESEARCH 2023; 236:116784. [PMID: 37517498 DOI: 10.1016/j.envres.2023.116784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/13/2023] [Accepted: 07/27/2023] [Indexed: 08/01/2023]
Abstract
Water scarcity is increasing worldwide due to rising population which is creating opportunities to unlock alternative green desalination techniques for seawater, such as biodesalination. Therefore, this study presents the utilization of the Phormidium keutzingianum strain in an attached growth-packed bed reactor to treat seawater in real-time in a continuous-flow stirred tank reactor for biodesalination. Two reactors were designed and developed, in which zeolites were used as the support media for the attached growth. The experiment was conducted in an open outdoor environment with a continuous air flow rate of 3 mL/min and two hydraulic retention times (HRT) of 7 and 15 d. Parameters such as the pH, chloride ion concentration, total organic carbon (TOC), and optical density were monitored regularly. The pH change was not significant in either reactor and remained within the range of 7.25-8.0. Chloride ion removal was the most crucial component of biodesalination efficiency, with d 7 removal efficiencies of approximately 40% and 32% for reactors 1 and 2, respectively. Reactor 1 exhibited a TOC reduction of 36% within the first 10 d at a HRT of 7, and when the HRT was set to 15 d, a TOC removal efficiency of 89% was achieved on d 53. For reactor 2, a TOC removal efficiency of approximately 81% was achieved on d 11 at HRT 7, and it reduced to less than 50% at an HRT of 15. The chloride ion and TOC removal phenomena were similar in both reactors. The optical density (OD) showed low measurement recordings, ranging from 0.005 to 0.01, indicating low cell detachment in the seawater effluent. Therefore, using the attached growth method for the biodesalination of seawater is feasible. Furthermore, biomass harvesting in attached growth systems is easier than that in suspension growth systems.
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Affiliation(s)
- Abdul Mannan Zafar
- Civil and Environmental Engineering Department, United Arab Emirates University, Al-Ain, 15551, Abu Dhabi, United Arab Emirates.
| | - Ashraf Aly Hassan
- Civil and Environmental Engineering Department, United Arab Emirates University, Al-Ain, 15551, Abu Dhabi, United Arab Emirates; National Water and Energy Center (NWEC), United Arab Emirates University, Al-Ain, 15551, Abu Dhabi, United Arab Emirates.
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14
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Blikstad C, Dugan EJ, Laughlin TG, Turnšek JB, Liu MD, Shoemaker SR, Vogiatzi N, Remis JP, Savage DF. Identification of a carbonic anhydrase-Rubisco complex within the alpha-carboxysome. Proc Natl Acad Sci U S A 2023; 120:e2308600120. [PMID: 37862384 PMCID: PMC10614612 DOI: 10.1073/pnas.2308600120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/28/2023] [Indexed: 10/22/2023] Open
Abstract
Carboxysomes are proteinaceous organelles that encapsulate key enzymes of CO2 fixation-Rubisco and carbonic anhydrase-and are the centerpiece of the bacterial CO2 concentrating mechanism (CCM). In the CCM, actively accumulated cytosolic bicarbonate diffuses into the carboxysome and is converted to CO2 by carbonic anhydrase, producing a high CO2 concentration near Rubisco and ensuring efficient carboxylation. Self-assembly of the α-carboxysome is orchestrated by the intrinsically disordered scaffolding protein, CsoS2, which interacts with both Rubisco and carboxysomal shell proteins, but it is unknown how the carbonic anhydrase, CsoSCA, is incorporated into the α-carboxysome. Here, we present the structural basis of carbonic anhydrase encapsulation into α-carboxysomes from Halothiobacillus neapolitanus. We find that CsoSCA interacts directly with Rubisco via an intrinsically disordered N-terminal domain. A 1.98 Å single-particle cryoelectron microscopy structure of Rubisco in complex with this peptide reveals that CsoSCA binding is predominantly mediated by a network of hydrogen bonds. CsoSCA's binding site overlaps with that of CsoS2, but the two proteins utilize substantially different motifs and modes of binding, revealing a plasticity of the Rubisco binding site. Our results advance the understanding of carboxysome biogenesis and highlight the importance of Rubisco, not only as an enzyme but also as a central hub for mediating assembly through protein interactions.
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Affiliation(s)
- Cecilia Blikstad
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala75120, Sweden
| | - Eli J. Dugan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Thomas G. Laughlin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Julia B. Turnšek
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Mira D. Liu
- Department of Chemistry, University of California, Berkeley, CA94720
| | - Sophie R. Shoemaker
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Nikoleta Vogiatzi
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala75120, Sweden
| | - Jonathan P. Remis
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
| | - David F. Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- HHMI, University of California, Berkeley, CA94720
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15
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Basalla JL, Mak CA, Byrne JA, Ghalmi M, Hoang Y, Vecchiarelli AG. Dissecting the phase separation and oligomerization activities of the carboxysome positioning protein McdB. eLife 2023; 12:e81362. [PMID: 37668016 PMCID: PMC10554743 DOI: 10.7554/elife.81362] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/01/2023] [Indexed: 09/06/2023] Open
Abstract
Across bacteria, protein-based organelles called bacterial microcompartments (BMCs) encapsulate key enzymes to regulate their activities. The model BMC is the carboxysome that encapsulates enzymes for CO2 fixation to increase efficiency and is found in many autotrophic bacteria, such as cyanobacteria. Despite their importance in the global carbon cycle, little is known about how carboxysomes are spatially regulated. We recently identified the two-factor system required for the maintenance of carboxysome distribution (McdAB). McdA drives the equal spacing of carboxysomes via interactions with McdB, which associates with carboxysomes. McdA is a ParA/MinD ATPase, a protein family well studied in positioning diverse cellular structures in bacteria. However, the adaptor proteins like McdB that connect these ATPases to their cargos are extremely diverse. In fact, McdB represents a completely unstudied class of proteins. Despite the diversity, many adaptor proteins undergo phase separation, but functional roles remain unclear. Here, we define the domain architecture of McdB from the model cyanobacterium Synechococcus elongatus PCC 7942, and dissect its mode of biomolecular condensate formation. We identify an N-terminal intrinsically disordered region (IDR) that modulates condensate solubility, a central coiled-coil dimerizing domain that drives condensate formation, and a C-terminal domain that trimerizes McdB dimers and provides increased valency for condensate formation. We then identify critical basic residues in the IDR, which we mutate to glutamines to solubilize condensates. Finally, we find that a condensate-defective mutant of McdB has altered association with carboxysomes and influences carboxysome enzyme content. The results have broad implications for understanding spatial organization of BMCs and the molecular grammar of protein condensates.
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Affiliation(s)
- Joseph L Basalla
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Claudia A Mak
- Department of Biological Chemistry, University of Michigan-Ann ArborAnn ArborUnited States
| | - Jordan A Byrne
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Maria Ghalmi
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Y Hoang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Anthony G Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan-Ann ArborAnn ArborUnited States
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16
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He S, Crans VL, Jonikas MC. The pyrenoid: the eukaryotic CO2-concentrating organelle. THE PLANT CELL 2023; 35:3236-3259. [PMID: 37279536 PMCID: PMC10473226 DOI: 10.1093/plcell/koad157] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/09/2023] [Accepted: 05/17/2023] [Indexed: 06/08/2023]
Abstract
The pyrenoid is a phase-separated organelle that enhances photosynthetic carbon assimilation in most eukaryotic algae and the land plant hornwort lineage. Pyrenoids mediate approximately one-third of global CO2 fixation, and engineering a pyrenoid into C3 crops is predicted to boost CO2 uptake and increase yields. Pyrenoids enhance the activity of the CO2-fixing enzyme Rubisco by supplying it with concentrated CO2. All pyrenoids have a dense matrix of Rubisco associated with photosynthetic thylakoid membranes that are thought to supply concentrated CO2. Many pyrenoids are also surrounded by polysaccharide structures that may slow CO2 leakage. Phylogenetic analysis and pyrenoid morphological diversity support a convergent evolutionary origin for pyrenoids. Most of the molecular understanding of pyrenoids comes from the model green alga Chlamydomonas (Chlamydomonas reinhardtii). The Chlamydomonas pyrenoid exhibits multiple liquid-like behaviors, including internal mixing, division by fission, and dissolution and condensation in response to environmental cues and during the cell cycle. Pyrenoid assembly and function are induced by CO2 availability and light, and although transcriptional regulators have been identified, posttranslational regulation remains to be characterized. Here, we summarize the current knowledge of pyrenoid function, structure, components, and dynamic regulation in Chlamydomonas and extrapolate to pyrenoids in other species.
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Affiliation(s)
- Shan He
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08540, USA
| | - Victoria L Crans
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08540, USA
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17
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Treece TR, Tessman M, Pomeroy RS, Mayfield SP, Simkovsky R, Atsumi S. Fluctuating pH for efficient photomixotrophic succinate production. Metab Eng 2023; 79:118-129. [PMID: 37499856 DOI: 10.1016/j.ymben.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/15/2023] [Accepted: 07/23/2023] [Indexed: 07/29/2023]
Abstract
Cyanobacteria are attracting increasing attention as a photosynthetic chassis organism for diverse biochemical production, however, photoautotrophic production remains inefficient. Photomixotrophy, a method where sugar is used to supplement baseline autotrophic metabolism in photosynthetic hosts, is becoming increasingly popular for enhancing sustainable bioproduction with multiple input energy streams. In this study, the commercially relevant diacid, succinate, was produced photomixotrophically. Succinate is an important industrial chemical that can be used for the production of a wide array of products, from pharmaceuticals to biopolymers. In this system, the substrate, glucose, is transported by a proton symporter and the product, succinate, is hypothesized to be transported by another proton symporter, but in the opposite direction. Thus, low pH is required for the import of glucose and high pH is required for the export of succinate. Succinate production was initiated in a pH 7 medium containing bicarbonate. Glucose was efficiently imported at around neutral pH. Utilization of bicarbonate by CO2 fixation raised the pH of the medium. As succinate, a diacid, was produced, the pH of the medium dropped. By repeating this cycle with additional pH adjustment, those contradictory requirements for transport were overcome. pH affects a variety of biological factors and by cycling from high pH to neutral pH processes such as CO2 fixation rates and CO2 solubility can vary. In this study the engineered strains produced succinate during fluctuating pH conditions, achieving a titer of 5.0 g L-1 after 10 days under shake flask conditions. These results demonstrate the potential for photomixotrophic production as a viable option for the large-scale production of succinate.
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Affiliation(s)
- Tanner R Treece
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA
| | | | - Robert S Pomeroy
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Stephen P Mayfield
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA; California Center for Algae Biotechnology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ryan Simkovsky
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA; California Center for Algae Biotechnology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Shota Atsumi
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA.
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18
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Cobb SJ, Dharani AM, Oliveira AR, Pereira IAC, Reisner E. Carboxysome-Inspired Electrocatalysis using Enzymes for the Reduction of CO 2 at Low Concentrations. Angew Chem Int Ed Engl 2023; 62:e202218782. [PMID: 37078435 DOI: 10.1002/anie.202218782] [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: 12/19/2022] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 04/21/2023]
Abstract
The electrolysis of dilute CO2 streams suffers from low concentrations of dissolved substrate and its rapid depletion at the electrolyte-electrocatalyst interface. These limitations require first energy-intensive CO2 capture and concentration, before electrolyzers can achieve acceptable performances. For direct electrocatalytic CO2 reduction from low-concentration sources, we introduce a strategy that mimics the carboxysome in cyanobacteria by utilizing microcompartments with nanoconfined enzymes in a porous electrode. A carbonic anhydrase accelerates CO2 hydration kinetics and minimizes substrate depletion by making all dissolved carbon available for utilization, while a highly efficient formate dehydrogenase reduces CO2 cleanly to formate; down to even atmospheric concentrations of CO2 . This bio-inspired concept demonstrates that the carboxysome provides a viable blueprint for the reduction of low-concentration CO2 streams to chemicals by using all forms of dissolved carbon.
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Affiliation(s)
- Samuel J Cobb
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Azim M Dharani
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Ana Rita Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Erwin Reisner
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
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19
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Li R, He Y, Chen J, Zheng S, Zhuang C. Research Progress in Improving Photosynthetic Efficiency. Int J Mol Sci 2023; 24:ijms24119286. [PMID: 37298238 DOI: 10.3390/ijms24119286] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Photosynthesis is the largest mass- and energy-conversion process on Earth, and it is the material basis for almost all biological activities. The efficiency of converting absorbed light energy into energy substances during photosynthesis is very low compared to theoretical values. Based on the importance of photosynthesis, this article summarizes the latest progress in improving photosynthesis efficiency from various perspectives. The main way to improve photosynthetic efficiency is to optimize the light reactions, including increasing light absorption and conversion, accelerating the recovery of non-photochemical quenching, modifying enzymes in the Calvin cycle, introducing carbon concentration mechanisms into C3 plants, rebuilding the photorespiration pathway, de novo synthesis, and changing stomatal conductance. These developments indicate that there is significant room for improvement in photosynthesis, providing support for improving crop yields and mitigating changes in climate conditions.
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Affiliation(s)
- Ruiqi Li
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Ying He
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Junyu Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Shaoyan Zheng
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Chuxiong Zhuang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
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20
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Steensma AK, Shachar-Hill Y, Walker BJ. The carbon-concentrating mechanism of the extremophilic red microalga Cyanidioschyzon merolae. PHOTOSYNTHESIS RESEARCH 2023; 156:247-264. [PMID: 36780115 PMCID: PMC10154280 DOI: 10.1007/s11120-023-01000-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 01/27/2023] [Indexed: 05/03/2023]
Abstract
Cyanidioschyzon merolae is an extremophilic red microalga which grows in low-pH, high-temperature environments. The basis of C. merolae's environmental resilience is not fully characterized, including whether this alga uses a carbon-concentrating mechanism (CCM). To determine if C. merolae uses a CCM, we measured CO2 uptake parameters using an open-path infra-red gas analyzer and compared them to values expected in the absence of a CCM. These measurements and analysis indicated that C. merolae had the gas-exchange characteristics of a CCM-operating organism: low CO2 compensation point, high affinity for external CO2, and minimized rubisco oxygenation. The biomass δ13C of C. merolae was also consistent with a CCM. The apparent presence of a CCM in C. merolae suggests the use of an unusual mechanism for carbon concentration, as C. merolae is thought to lack a pyrenoid and gas-exchange measurements indicated that C. merolae primarily takes up inorganic carbon as carbon dioxide, rather than bicarbonate. We use homology to known CCM components to propose a model of a pH-gradient-based CCM, and we discuss how this CCM can be further investigated.
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Affiliation(s)
- Anne K Steensma
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Michigan State University - Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
| | - Yair Shachar-Hill
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Berkley J Walker
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
- Michigan State University - Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, USA.
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21
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Aguiló-Nicolau P, Galmés J, Fais G, Capó-Bauçà S, Cao G, Iñiguez C. Singular adaptations in the carbon assimilation mechanism of the polyextremophile cyanobacterium Chroococcidiopsis thermalis. PHOTOSYNTHESIS RESEARCH 2023; 156:231-245. [PMID: 36941458 PMCID: PMC10154277 DOI: 10.1007/s11120-023-01008-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/16/2023] [Indexed: 05/03/2023]
Abstract
Cyanobacteria largely contribute to the biogeochemical carbon cycle fixing ~ 25% of the inorganic carbon on Earth. However, the carbon acquisition and assimilation mechanisms in Cyanobacteria are still underexplored regardless of being of great importance for shedding light on the origins of autotropism on Earth and providing new bioengineering tools for crop yield improvement. Here, we fully characterized these mechanisms from the polyextremophile cyanobacterium Chroococcidiopsis thermalis KOMAREK 1964/111 in comparison with the model cyanobacterial strain, Synechococcus sp. PCC6301. In particular, we analyzed the Rubisco kinetics along with the in vivo photosynthetic CO2 assimilation in response to external dissolved inorganic carbon, the effect of CO2 concentrating mechanism (CCM) inhibitors on net photosynthesis and the anatomical particularities of their carboxysomes when grown under either ambient air (0.04% CO2) or 2.5% CO2-enriched air. Our results show that Rubisco from C. thermalis possess the highest specificity factor and carboxylation efficiency ever reported for Cyanobacteria, which were accompanied by a highly effective CCM, concentrating CO2 around Rubisco more than 140-times the external CO2 levels, when grown under ambient CO2 conditions. Our findings provide new insights into the Rubisco kinetics of Cyanobacteria, suggesting that improved Sc/o values can still be compatible with a fast-catalyzing enzyme. The combination of Rubisco kinetics and CCM effectiveness in C. thermalis relative to other cyanobacterial species might indicate that the co-evolution between Rubisco and CCMs in Cyanobacteria is not as constrained as in other phylogenetic groups.
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Affiliation(s)
- Pere Aguiló-Nicolau
- Research Group on Plant Biology Under Mediterranean Conditions, Universitat de les Illes Balears, INAGEA, Ctra. Valldemossa km. 7.5, 07122, Palma, Balearic Islands, Spain
| | - Jeroni Galmés
- Research Group on Plant Biology Under Mediterranean Conditions, Universitat de les Illes Balears, INAGEA, Ctra. Valldemossa km. 7.5, 07122, Palma, Balearic Islands, Spain.
| | - Giacomo Fais
- Interdepartmental Centre of Environmental Science and Engineering, University of Cagliari, Via San Giorgio 12, 09124, Cagliari, Italy
| | - Sebastià Capó-Bauçà
- Research Group on Plant Biology Under Mediterranean Conditions, Universitat de les Illes Balears, INAGEA, Ctra. Valldemossa km. 7.5, 07122, Palma, Balearic Islands, Spain
| | - Giacomo Cao
- Interdepartmental Centre of Environmental Science and Engineering, University of Cagliari, Via San Giorgio 12, 09124, Cagliari, Italy
- Department of Mechanical, Chemical and Materials Engineering, University of Cagliari, Via Marengo 2, 09123, Cagliari, Italy
| | - Concepción Iñiguez
- Research Group on Plant Biology Under Mediterranean Conditions, Universitat de les Illes Balears, INAGEA, Ctra. Valldemossa km. 7.5, 07122, Palma, Balearic Islands, Spain
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22
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Li M, Young JN. Temperature sensitivity of carbon concentrating mechanisms in the diatom Phaeodactylum tricornutum. PHOTOSYNTHESIS RESEARCH 2023; 156:205-215. [PMID: 36881356 PMCID: PMC10154264 DOI: 10.1007/s11120-023-01004-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/10/2023] [Indexed: 05/03/2023]
Abstract
Marine diatoms are key primary producers across diverse habitats in the global ocean. Diatoms rely on a biophysical carbon concentrating mechanism (CCM) to supply high concentrations of CO2 around their carboxylating enzyme, RuBisCO. The necessity and energetic cost of the CCM are likely to be highly sensitive to temperature, as temperature impacts CO2 concentration, diffusivity, and the kinetics of CCM components. Here, we used membrane inlet mass spectrometry (MIMS) and modeling to capture temperature regulation of the CCM in the diatom Phaeodactylum tricornutum (Pt). We found that enhanced carbon fixation rates by Pt at elevated temperatures were accompanied by increased CCM activity capable of maintaining RuBisCO close to CO2 saturation but that the mechanism varied. At 10 and 18 °C, diffusion of CO2 into the cell, driven by Pt's 'chloroplast pump' was the major inorganic carbon source. However, at 18 °C, upregulation of the chloroplast pump enhanced (while retaining the proportion of) both diffusive CO2 and active HCO3- uptake into the cytosol, and significantly increased chloroplast HCO3- concentrations. In contrast, at 25 °C, compared to 18 °C, the chloroplast pump had only a slight increase in activity. While diffusive uptake of CO2 into the cell remained constant, active HCO3- uptake across the cell membrane increased resulting in Pt depending equally on both CO2 and HCO3- as inorganic carbon sources. Despite changes in the CCM, the overall rate of active carbon transport remained double that of carbon fixation across all temperatures tested. The implication of the energetic cost of the Pt CCM in response to increasing temperatures was discussed.
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Affiliation(s)
- Meng Li
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Jodi N Young
- School of Oceanography, University of Washington, Seattle, WA, USA.
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23
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Kupriyanova EV, Pronina NA, Los DA. Adapting from Low to High: An Update to CO 2-Concentrating Mechanisms of Cyanobacteria and Microalgae. PLANTS (BASEL, SWITZERLAND) 2023; 12:1569. [PMID: 37050194 PMCID: PMC10096703 DOI: 10.3390/plants12071569] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
The intracellular accumulation of inorganic carbon (Ci) by microalgae and cyanobacteria under ambient atmospheric CO2 levels was first documented in the 80s of the 20th Century. Hence, a third variety of the CO2-concentrating mechanism (CCM), acting in aquatic photoautotrophs with the C3 photosynthetic pathway, was revealed in addition to the then-known schemes of CCM, functioning in CAM and C4 higher plants. Despite the low affinity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) of microalgae and cyanobacteria for the CO2 substrate and low CO2/O2 specificity, CCM allows them to perform efficient CO2 fixation in the reductive pentose phosphate (RPP) cycle. CCM is based on the coordinated operation of strategically located carbonic anhydrases and CO2/HCO3- uptake systems. This cooperation enables the intracellular accumulation of HCO3-, which is then employed to generate a high concentration of CO2 molecules in the vicinity of Rubisco's active centers compensating up for the shortcomings of enzyme features. CCM functions as an add-on to the RPP cycle while also acting as an important regulatory link in the interaction of dark and light reactions of photosynthesis. This review summarizes recent advances in the study of CCM molecular and cellular organization in microalgae and cyanobacteria, as well as the fundamental principles of its functioning and regulation.
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24
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Gao S, Pittman K, Edmundson S, Huesemann M, Greer M, Louie W, Chen P, Nobles D, Benemann J, Crowe B. A newly isolated alkaliphilic cyanobacterium for biomass production with direct air CO2 capture. J CO2 UTIL 2023. [DOI: 10.1016/j.jcou.2023.102399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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25
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Two-stage cultivation of Spirulina sp. LEB 18: a strategy to increase biomass productivity and synthesis of macromolecules. BRAZILIAN JOURNAL OF CHEMICAL ENGINEERING 2023. [DOI: 10.1007/s43153-022-00279-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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26
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Optimized culture conditions facilitate the estrone biodegradation ability and laccase activity of Spirulina CPCC-695. Biodegradation 2023; 34:43-51. [PMID: 36396827 DOI: 10.1007/s10532-022-10005-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 11/01/2022] [Indexed: 11/19/2022]
Abstract
Endocrine disrupting compounds (EDCs) are emerging contaminants that persist and contaminate the environment. They mimic hormones, block hormones, or modulate their synthesis, metabolism, transport, and action, affecting living organisms and their progeny. Steroid hormones from exogenous sources like water bodies are important EDCs. Their biodegradation is an urgent global need. The present study is a preliminary work to maximize the estrone degradation potential of Spirulina CPCC-695 and study the effect of optimized conditions on its laccase activity. It was observed that the exponential phase culture at pH 10.0, 30 ℃, and 200 rpm of agitation speed resulted in the maximum growth, estrone degradation efficiency (93.12%), and highest laccase activity (74%) of Spirulina CPCC-695.
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27
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Ang WSL, How JA, How JB, Mueller-Cajar O. The stickers and spacers of Rubiscondensation: assembling the centrepiece of biophysical CO2-concentrating mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:612-626. [PMID: 35903998 DOI: 10.1093/jxb/erac321] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Aquatic autotrophs that fix carbon using ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) frequently expend metabolic energy to pump inorganic carbon towards the enzyme's active site. A central requirement of this strategy is the formation of highly concentrated Rubisco condensates (or Rubiscondensates) known as carboxysomes and pyrenoids, which have convergently evolved multiple times in prokaryotes and eukaryotes, respectively. Recent data indicate that these condensates form by the mechanism of liquid-liquid phase separation. This mechanism requires networks of weak multivalent interactions typically mediated by intrinsically disordered scaffold proteins. Here we comparatively review recent rapid developments that detail the determinants and precise interactions that underlie diverse Rubisco condensates. The burgeoning field of biomolecular condensates has few examples where liquid-liquid phase separation can be linked to clear phenotypic outcomes. When present, Rubisco condensates are essential for photosynthesis and growth, and they are thus emerging as powerful and tractable models to investigate the structure-function relationship of phase separation in biology.
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Affiliation(s)
- Warren Shou Leong Ang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Jian Ann How
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Jian Boon How
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
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28
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Strandberg U, Hiltunen M, Creed IF, Arts MT, Kankaala P. Browning-induced changes in trophic functioning of planktonic food webs in temperate and boreal lakes: insights from fatty acids. Oecologia 2023; 201:183-197. [PMID: 36520221 PMCID: PMC9813244 DOI: 10.1007/s00442-022-05301-w] [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: 03/14/2022] [Accepted: 12/05/2022] [Indexed: 12/16/2022]
Abstract
The effects of lake browning on trophic functioning of planktonic food webs are not fully understood. We studied the effects of browning on the response patterns of polyunsaturated fatty acids and n-3/n-6 ratio in seston and compared them between boreal and temperate lakes. We also compared the regional differences and the effects of lake browning on the reliance of zooplankton on heterotrophic microbial pathways and the mass fractions of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) in zooplankton. Lake browning was associated with increasing phytoplankton biomass and concentrations of EPA and DHA in both temperate and boreal lakes, but the seston n-3/n-6 ratio was lower in temperate than boreal lakes, most likely due the differences in phytoplankton community composition. The browning-induced increase in phytoplankton biomass was associated with increased reliance of zooplankton on a heterotrophic microbial pathway for both cladocerans and copepods in boreal and temperate lakes. This increased reliance on the heterotrophic microbial diet was correlated with a decrease in the EPA and DHA mass fractions in temperate copepods and a decrease in the n-3/n-6 ratio in boreal cladocerans and copepods. Our results indicate that although phytoplankton responses to lake browning were similar across regions, this did not directly cascade to the next trophic level, where zooplankton responses were highly taxa- and region-specific. These results indicate that lake browning should be considered as an overarching moderator that is linked to, e.g., nutrient increases, which have more immediate consequences on trophic interactions at the phytoplankton-zooplankton interface.
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Affiliation(s)
- Ursula Strandberg
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Minna Hiltunen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland ,Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | | | - Michael T. Arts
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Canada
| | - Paula Kankaala
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
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29
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Abstract
Cyanobacteria rely on CO2-concentrating mechanisms (CCMs) to grow in today's atmosphere (0.04% CO2). These complex physiological adaptations require ≈15 genes to produce two types of protein complexes: inorganic carbon (Ci) transporters and 100+ nm carboxysome compartments that encapsulate rubisco with a carbonic anhydrase (CA) enzyme. Mutations disrupting any of these genes prohibit growth in ambient air. If any plausible ancestral form-i.e., lacking a single gene-cannot grow, how did the CCM evolve? Here, we test the hypothesis that evolution of the bacterial CCM was "catalyzed" by historically high CO2 levels that decreased over geologic time. Using an E. coli reconstitution of a bacterial CCM, we constructed strains lacking one or more CCM components and evaluated their growth across CO2 concentrations. We expected these experiments to demonstrate the importance of the carboxysome. Instead, we found that partial CCMs expressing CA or Ci uptake genes grew better than controls in intermediate CO2 levels (≈1%) and observed similar phenotypes in two autotrophic bacteria, Halothiobacillus neapolitanus and Cupriavidus necator. To understand how CA and Ci uptake improve growth, we model autotrophy as colimited by CO2 and HCO3-, as both are required to produce biomass. Our experiments and model delineated a viable trajectory for CCM evolution where decreasing atmospheric CO2 induces an HCO3- deficiency that is alleviated by acquisition of CA or Ci uptake, thereby enabling the emergence of a modern CCM. This work underscores the importance of considering physiology and environmental context when studying the evolution of biological complexity.
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30
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Sawant KR, Sarnaik AP, Savvashe P, Hajinajaf N, Poole P, Varman AM, Lali A, Pandit R. One cell-two wells bio-refinery: Demonstrating cyanobacterial chassis for co-production of heterologous and natural hydrocarbons. BIORESOURCE TECHNOLOGY 2022; 363:127921. [PMID: 36089131 DOI: 10.1016/j.biortech.2022.127921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/04/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
In order to improve the potential of cyanobacterial cell factories, Synechococcus sp. PCC7002 was engineered as 'one cell-two wells bio-refinery', for ethylene ('heterologous' hydrocarbon) and carotenoids ('natural' metabolites) production, and demonstrating its outdoor performance. Although the cultures showed better production outdoor, they experienced multiple collapses during scale-up. Hence, flux balance analysis was performed which predicted higher ethylene production with increase in carbon input under outdoor light conditions. Furthermore, FBA predicted that ethylene production will not increase beyond a threshold carbon input flux, owing to limitations on ribulose-1,5-bisphosphate regeneration. Hence, a bicarbonate-supplementation strategy was devised. Cultures grown outdoor at optimal bicarbonate concentration (20 g/L) resulted in improved growth (0.141/h) and ethylene productivity (1.88 mL/L.h) for > 10 days, with enhanced carotenoid titres (40.4 mg/L). In a 100 L air-lift photo-bioreactor; cultures exhibited efficient ethylene (2.464 mL/L.h) and biomass (0.3 g/L.d) productivities, and carotenoids titres (64.4 mg/L), establishing a significant step towards commercialization.
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Affiliation(s)
- Kaustubh R Sawant
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Matunga, Mumbai 400019, India
| | - Aditya P Sarnaik
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Matunga, Mumbai 400019, India; Chemical Engineering Department, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA
| | - Prashant Savvashe
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Matunga, Mumbai 400019, India; Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai 400019, India
| | - Nima Hajinajaf
- Chemical Engineering Department, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA
| | - Parker Poole
- Chemical Engineering Department, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA
| | - Arul M Varman
- Chemical Engineering Department, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA
| | - Arvind Lali
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai 400019, India
| | - Reena Pandit
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Matunga, Mumbai 400019, India.
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31
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Cabello-Yeves PJ, Scanlan DJ, Callieri C, Picazo A, Schallenberg L, Huber P, Roda-Garcia JJ, Bartosiewicz M, Belykh OI, Tikhonova IV, Torcello-Requena A, De Prado PM, Millard AD, Camacho A, Rodriguez-Valera F, Puxty RJ. α-cyanobacteria possessing form IA RuBisCO globally dominate aquatic habitats. THE ISME JOURNAL 2022; 16:2421-2432. [PMID: 35851323 PMCID: PMC9477826 DOI: 10.1038/s41396-022-01282-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/21/2022] [Accepted: 06/28/2022] [Indexed: 11/24/2022]
Abstract
RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) is one the most abundant enzymes on Earth. Virtually all food webs depend on its activity to supply fixed carbon. In aerobic environments, RuBisCO struggles to distinguish efficiently between CO2 and O2. To compensate, organisms have evolved convergent solutions to concentrate CO2 around the active site. The genetic engineering of such inorganic carbon concentrating mechanisms (CCMs) into plants could help facilitate future global food security for humankind. In bacteria, the carboxysome represents one such CCM component, of which two independent forms exist: α and β. Cyanobacteria are important players in the planet's carbon cycle and the vast majority of the phylum possess a β-carboxysome, including most cyanobacteria used as laboratory models. The exceptions are the exclusively marine Prochlorococcus and Synechococcus that numerically dominate open ocean systems. However, the reason why marine systems favor an α-form is currently unknown. Here, we report the genomes of 58 cyanobacteria, closely related to marine Synechococcus that were isolated from freshwater lakes across the globe. We find all these isolates possess α-carboxysomes accompanied by a form 1A RuBisCO. Moreover, we demonstrate α-cyanobacteria dominate freshwater lakes worldwide. Hence, the paradigm of a separation in carboxysome type across the salinity divide does not hold true, and instead the α-form dominates all aquatic systems. We thus question the relevance of β-cyanobacteria as models for aquatic systems at large and pose a hypothesis for the reason for the success of the α-form in nature.
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Affiliation(s)
- Pedro J Cabello-Yeves
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain.
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Cristiana Callieri
- National Research Council (CNR), Institute of Water Research (IRSA), Verbania, Italy
| | - Antonio Picazo
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, E-46980 Paterna, Valencia, Spain
| | | | - Paula Huber
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET., Av. Intendente Marino Km 8,200, 7130, Chascomús, Buenos Aires, Argentina
- Instituto Nacional de Limnología (INALI), CONICET-UNL., Ciudad Universitaria-Paraje el Pozo s/n, 3000, Santa Fé, Argentina
| | - Juan J Roda-Garcia
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Maciej Bartosiewicz
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Olga I Belykh
- Limnological Institute, Russian Academy of Sciences, P.O. Box 278, 664033, Irkutsk, Russia
| | - Irina V Tikhonova
- Limnological Institute, Russian Academy of Sciences, P.O. Box 278, 664033, Irkutsk, Russia
| | | | | | - Andrew D Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Antonio Camacho
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, E-46980 Paterna, Valencia, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Richard J Puxty
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
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32
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Huang J, Jiang Q, Yang M, Dykes GF, Weetman SL, Xin W, He HL, Liu LN. Probing the Internal pH and Permeability of a Carboxysome Shell. Biomacromolecules 2022; 23:4339-4348. [PMID: 36054822 PMCID: PMC9554877 DOI: 10.1021/acs.biomac.2c00781] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The carboxysome is a protein-based nanoscale organelle
in cyanobacteria
and many proteobacteria, which encapsulates the key CO2-fixing enzymes ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco)
and carbonic anhydrase (CA) within a polyhedral protein shell. The
intrinsic self-assembly and architectural features of carboxysomes
and the semipermeability of the protein shell provide the foundation
for the accumulation of CO2 within carboxysomes and enhanced
carboxylation. Here, we develop an approach to determine the interior
pH conditions and inorganic carbon accumulation within an α-carboxysome
shell derived from a chemoautotrophic proteobacterium Halothiobacillus neapolitanus and evaluate the shell
permeability. By incorporating a pH reporter, pHluorin2, within empty
α-carboxysome shells produced in Escherichia
coli, we probe the interior pH of the protein shells
with and without CA. Our in vivo and in vitro results demonstrate a lower interior pH of α-carboxysome shells
than the cytoplasmic pH and buffer pH, as well as the modulation of
the interior pH in response to changes in external environments, indicating
the shell permeability to bicarbonate ions and protons. We further
determine the saturated HCO3– concentration
of 15 mM within α-carboxysome shells and show the CA-mediated
increase in the interior CO2 level. Uncovering the interior
physiochemical microenvironment of carboxysomes is crucial for understanding
the mechanisms underlying carboxysomal shell permeability and enhancement
of Rubisco carboxylation within carboxysomes. Such fundamental knowledge
may inform reprogramming carboxysomes to improve metabolism and recruit
foreign enzymes for enhanced catalytical performance.
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Affiliation(s)
- Jiafeng Huang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.,School of Life Sciences, Central South University, Changsha 410017, China
| | - Qiuyao Jiang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.,Department of Central Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China
| | - Mengru Yang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Gregory F Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Samantha L Weetman
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Wei Xin
- Department of Central Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China.,Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 271000, China
| | - Hai-Lun He
- School of Life Sciences, Central South University, Changsha 410017, China
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.,College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
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33
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Abstract
Despite the importance of microcompartments in prokaryotic biology and bioengineering, structural heterogeneity has prevented a complete understanding of their architecture, ultrastructure, and spatial organization. Here, we employ cryo-electron tomography to image α-carboxysomes, a pseudo-icosahedral microcompartment responsible for carbon fixation. We have solved a high-resolution subtomogram average of the Rubisco cargo inside the carboxysome, and determined the arrangement of the enzyme. We find that the H. neapolitanus Rubisco polymerizes in vivo, mediated by the small Rubisco subunit. These fibrils can further pack to form a lattice with six-fold pseudo-symmetry. This arrangement preserves freedom of motion and accessibility around the Rubisco active site and the binding sites for two other carboxysome proteins, CsoSCA (a carbonic anhydrase) and the disordered CsoS2, even at Rubisco concentrations exceeding 800 μM. This characterization of Rubisco cargo inside the α-carboxysome provides insight into the balance between order and disorder in microcompartment organization.
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Liu J, Yin W, Zhang X, Xie X, Dong G, Lu Y, Tao B, Gong Q, Chen X, Shi C, Qin Y, Zeng R, Li D, Li H, Zhao C, Zhang H. RNA-seq analysis reveals genes related to photosynthetic carbon partitioning and lipid production in Phaeodactylum tricornutum under alkaline conditions. Front Microbiol 2022; 13:969639. [PMID: 36051763 PMCID: PMC9425035 DOI: 10.3389/fmicb.2022.969639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Alkaline pH can induce triacylglyceride accumulation in microalgae, however its molecular mechanism remains elusive. Here, we investigated the effect of 2-[N-cyclohexylamino]-ethane-sulfonic acid (CHES) -induced intracellular alkalization on the lipid production in Phaeodactylum tricornutum. Intracellular pH was increased upon CHES treatment, displaying a high BCECF fluorescence ratio. CHES treatment significantly induced lipid accumulation but had no change in cell density and biomass. The expression of genes involved in photoreaction, carbon fixation, glycolysis, pentose phosphate pathway, amino acid catabolism, GS/GOGAT cycle, TCA cycle, triacylglyceride assembly, de novo fatty acid synthesis were up-regulated, while that in amino acid biosynthesis were down-regulated under CHES conditions. Correspondingly, the activity of phosphoribulokinase, carbonic anhydrase, pyruvate dehydrogenase and acetaldehyde dehydrogenase were enhanced by CHES treatment. Chloroplast-specific biological processes were activated by CHES treatment in P. tricornutum, which redirects the flux of carbon into lipid biosynthesis, meanwhile stimulates de novo fatty acid biosynthesis, leading to lipid accumulation under CHES conditions. These indicate an enhancement of intermediate metabolism, resulting in lipid accumulation by CHES.
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Affiliation(s)
- Jian Liu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weihua Yin
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xinya Zhang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuan Xie
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guanghui Dong
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yao Lu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Baoxiang Tao
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qiangbin Gong
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xinyan Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chao Shi
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan Qin
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Pingtan Science and Technology Research Institute of Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rensen Zeng
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dawei Li
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institute, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Hongye Li
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institute, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Chao Zhao
- College of Marine Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huiying Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Huiying Zhang,
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35
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King DT, Zhu S, Hardie DB, Serrano-Negrón JE, Madden Z, Kolappan S, Vocadlo DJ. Chemoproteomic identification of CO 2-dependent lysine carboxylation in proteins. Nat Chem Biol 2022; 18:782-791. [PMID: 35710617 DOI: 10.1038/s41589-022-01043-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 04/15/2022] [Indexed: 01/09/2023]
Abstract
Carbon dioxide is an omnipresent gas that drives adaptive responses within organisms from all domains of life. The molecular mechanisms by which proteins serve as sensors of CO2 are, accordingly, of great interest. Because CO2 is electrophilic, one way it can modulate protein biochemistry is by carboxylation of the amine group of lysine residues. However, the resulting CO2-carboxylated lysines spontaneously decompose, giving off CO2, which makes studying this modification difficult. Here we describe a method to stably mimic CO2-carboxylated lysine residues in proteins. We leverage this method to develop a quantitative approach to identify CO2-carboxylated lysines of proteins and explore the lysine 'carboxylome' of the CO2-responsive cyanobacterium Synechocystis sp. We uncover one CO2-carboxylated lysine within the effector binding pocket of the metabolic signaling protein PII. CO2-carboxylatation of this lysine markedly lowers the affinity of PII for its regulatory effector ligand ATP, illuminating a negative molecular control mechanism mediated by CO2.
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Affiliation(s)
- Dustin T King
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Sha Zhu
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Darryl B Hardie
- University of Victoria-Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada
| | - Jesús E Serrano-Negrón
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Zarina Madden
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Subramania Kolappan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - David J Vocadlo
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada. .,Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
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Song K, Hagemann M, Georg J, Maaß S, Becher D, Hess WR. Expression of the Cyanobacterial F oF 1 ATP Synthase Regulator AtpΘ Depends on Small DNA-Binding Proteins and Differential mRNA Stability. Microbiol Spectr 2022; 10:e0256221. [PMID: 35446123 PMCID: PMC9241938 DOI: 10.1128/spectrum.02562-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/19/2022] [Indexed: 11/20/2022] Open
Abstract
FoF1 ATP synthases produce ATP, the universal biological energy source. ATP synthase complexes on cyanobacterial thylakoid membranes use proton gradients generated either by photosynthesis or respiration. AtpΘ is an ATP synthase regulator in cyanobacteria which is encoded by the gene atpT. AtpΘ prevents the hydrolysis of ATP (reverse reaction) that otherwise would occur under unfavorable conditions. In the cyanobacterium Synechocystis sp. PCC 6803, AtpΘ is expressed maximum in darkness but at very low levels under optimum phototrophic growth conditions or in the presence of glucose. DNA coimmunoprecipitation experiments followed by mass spectrometry identified the binding of the two transcriptional regulators cyAbrB1 and cyAbrB2 to the promoter and the histone-like protein HU to the 5'UTR of atpT. Analyses of nucleotide substitutions in the promoter and GFP reporter assays identified a functionally relevant sequence motif resembling the HLR1 element bound by the RpaB transcription factor. Electrophoretic mobility shift assays confirmed interaction of cyAbrB1, cyAbrB2, and RpaB with the promoter DNA. However, overall the effect of transcriptional regulation was comparatively low. In contrast, atpT transcript stabilities differed dramatically, half-lives were 1.6 min in the light, 33 min in the dark and substantial changes were observed if glucose or DCMU were added. These findings show that transcriptional control of atpT involves nucleoid-associated DNA-binding proteins, positive regulation through RpaB, while the major effect on the condition-dependent regulation of atpT expression is mediated by controlling mRNA stability, which is related to the cellular redox and energy status. IMPORTANCE FoF1 ATP synthases produce ATP, the universal biological energy source. Under unfavorable conditions, ATP synthases can operate in a futile reverse reaction, pumping protons while ATP is used up. Cyanobacteria perform plant-like photosynthesis, but they cannot use the same mechanism as plant chloroplasts to inhibit ATP synthases during the night because respiratory and photosynthetic complexes are both located in the same membrane system. AtpΘ is a small protein encoded by the gene atpT in cyanobacteria that can prevent the ATP synthase reverse reaction (ATPase activity). Here we found that three transcription factors contribute to the regulation of atpT expression. However, the control of mRNA stability was identified as the major regulatory process governing atpT expression. Thus, it is the interplay between transcriptional and posttranscriptional regulation that position the AtpΘ-based regulatory mechanism within the context of the cellular redox and energy balance.
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Affiliation(s)
- Kuo Song
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Martin Hagemann
- Plant Physiology Department, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Jens Georg
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Sandra Maaß
- Department of Microbial Proteomics, Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Wolfgang R. Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany
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Getting Closer to Decrypting the Phase Transitions of Bacterial Biomolecules. Biomolecules 2022; 12:biom12070907. [PMID: 35883463 PMCID: PMC9312465 DOI: 10.3390/biom12070907] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/24/2022] [Accepted: 06/26/2022] [Indexed: 12/31/2022] Open
Abstract
Liquid–liquid phase separation (LLPS) of biomolecules has emerged as a new paradigm in cell biology, and the process is one proposed mechanism for the formation of membraneless organelles (MLOs). Bacterial cells have only recently drawn strong interest in terms of studies on both liquid-to-liquid and liquid-to-solid phase transitions. It seems that these processes drive the formation of prokaryotic cellular condensates that resemble eukaryotic MLOs. In this review, we present an overview of the key microbial biomolecules that undergo LLPS, as well as the formation and organization of biomacromolecular condensates within the intracellular space. We also discuss the current challenges in investigating bacterial biomacromolecular condensates. Additionally, we highlight a summary of recent knowledge about the participation of bacterial biomolecules in a phase transition and provide some new in silico analyses that can be helpful for further investigations.
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38
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A Review of Cyanophage–Host Relationships: Highlighting Cyanophages as a Potential Cyanobacteria Control Strategy. Toxins (Basel) 2022; 14:toxins14060385. [PMID: 35737046 PMCID: PMC9229316 DOI: 10.3390/toxins14060385] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 11/16/2022] Open
Abstract
Harmful algal blooms (HABs) are naturally occurring phenomena, and cyanobacteria are the most commonly occurring HABs in freshwater systems. Cyanobacteria HABs (cyanoHABs) negatively affect ecosystems and drinking water resources through the production of potent toxins. Furthermore, the frequency, duration, and distribution of cyanoHABs are increasing, and conditions that favor cyanobacteria growth are predicted to increase in the coming years. Current methods for mitigating cyanoHABs are generally short-lived and resource-intensive, and have negative impacts on non-target species. Cyanophages (viruses that specifically target cyanobacteria) have the potential to provide a highly specific control strategy with minimal impacts on non-target species and propagation in the environment. A detailed review (primarily up to 2020) of cyanophage lifecycle, diversity, and factors influencing infectivity is provided in this paper, along with a discussion of cyanophage and host cyanobacteria relationships for seven prominent cyanoHAB-forming genera in North America, including: Synechococcus, Microcystis, Dolichospermum, Aphanizomenon, Cylindrospermopsis, Planktothrix, and Lyngbya. Lastly, factors affecting the potential application of cyanophages as a cyanoHAB control strategy are discussed, including efficacy considerations, optimization, and scalability for large-scale applications.
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Tang J, Zhou H, Yao D, Riaz S, You D, Klepacz-Smółka A, Daroch M. Comparative Genomic Analysis Revealed Distinct Molecular Components and Organization of CO 2-Concentrating Mechanism in Thermophilic Cyanobacteria. Front Microbiol 2022; 13:876272. [PMID: 35602029 PMCID: PMC9120777 DOI: 10.3389/fmicb.2022.876272] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/04/2022] [Indexed: 12/30/2022] Open
Abstract
Cyanobacteria evolved an inorganic carbon-concentrating mechanism (CCM) to perform effective oxygenic photosynthesis and prevent photorespiratory carbon losses. This process facilitates the acclimation of cyanobacteria to various habitats, particularly in CO2-limited environments. To date, there is limited information on the CCM of thermophilic cyanobacteria whose habitats limit the solubility of inorganic carbon. Here, genome-based approaches were used to identify the molecular components of CCM in 17 well-described thermophilic cyanobacteria. These cyanobacteria were from the genus Leptodesmis, Leptolyngbya, Leptothermofonsia, Thermoleptolyngbya, Thermostichus, and Thermosynechococcus. All the strains belong to β-cyanobacteria based on their β-carboxysome shell proteins with 1B form of Rubisco. The diversity in the Ci uptake systems and carboxysome composition of these thermophiles were analyzed based on their genomic information. For Ci uptake systems, two CO2 uptake systems (NDH-13 and NDH-14) and BicA for HCO3– transport were present in all the thermophilic cyanobacteria, while most strains did not have the Na+/HCO3– Sbt symporter and HCO3– transporter BCT1 were absent in four strains. As for carboxysome, the β-carboxysomal shell protein, ccmK2, was absent only in Thermoleptolyngbya strains, whereas ccmK3/K4 were absent in all Thermostichus and Thermosynechococcus strains. Besides, all Thermostichus and Thermosynechococcus strains lacked carboxysomal β-CA, ccaA, the carbonic anhydrase activity of which may be replaced by ccmM proteins as indicated by comparative domain analysis. The genomic distribution of CCM-related genes was different among the thermophiles, suggesting probably distinct expression regulation. Overall, the comparative genomic analysis revealed distinct molecular components and organization of CCM in thermophilic cyanobacteria. These findings provided insights into the CCM components of thermophilic cyanobacteria and fundamental knowledge for further research regarding photosynthetic improvement and biomass yield of thermophilic cyanobacteria with biotechnological potentials.
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Affiliation(s)
- Jie Tang
- School of Food and Bioengineering, Chengdu University, Chengdu, China
| | - Huizhen Zhou
- School of Food and Bioengineering, Chengdu University, Chengdu, China
| | - Dan Yao
- School of Food and Bioengineering, Chengdu University, Chengdu, China
| | - Sadaf Riaz
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Dawei You
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Anna Klepacz-Smółka
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Łódź University of Technology, Łódź, Poland
| | - Maurycy Daroch
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
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40
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Fei C, Wilson AT, Mangan NM, Wingreen NS, Jonikas MC. Modelling the pyrenoid-based CO 2-concentrating mechanism provides insights into its operating principles and a roadmap for its engineering into crops. NATURE PLANTS 2022; 8:583-595. [PMID: 35596080 PMCID: PMC9122830 DOI: 10.1038/s41477-022-01153-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 04/11/2022] [Indexed: 05/19/2023]
Abstract
Many eukaryotic photosynthetic organisms enhance their carbon uptake by supplying concentrated CO2 to the CO2-fixing enzyme Rubisco in an organelle called the pyrenoid. Ongoing efforts seek to engineer this pyrenoid-based CO2-concentrating mechanism (PCCM) into crops to increase yields. Here we develop a computational model for a PCCM on the basis of the postulated mechanism in the green alga Chlamydomonas reinhardtii. Our model recapitulates all Chlamydomonas PCCM-deficient mutant phenotypes and yields general biophysical principles underlying the PCCM. We show that an effective and energetically efficient PCCM requires a physical barrier to reduce pyrenoid CO2 leakage, as well as proper enzyme localization to reduce futile cycling between CO2 and HCO3-. Importantly, our model demonstrates the feasibility of a purely passive CO2 uptake strategy at air-level CO2, while active HCO3- uptake proves advantageous at lower CO2 levels. We propose a four-step engineering path to increase the rate of CO2 fixation in the plant chloroplast up to threefold at a theoretical cost of only 1.3 ATP per CO2 fixed, thereby offering a framework to guide the engineering of a PCCM into land plants.
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Affiliation(s)
- Chenyi Fei
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Alexandra T Wilson
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Niall M Mangan
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, USA.
| | - Ned S Wingreen
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Howard Hughes Medical Institute, Princeton University, Princeton, NJ, USA.
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Park J, Lee H, Dinh TB, Choi S, De Saeger J, Depuydt S, Brown MT, Han T. Commercial Potential of the Cyanobacterium Arthrospira maxima: Physiological and Biochemical Traits and the Purification of Phycocyanin. BIOLOGY 2022; 11:biology11050628. [PMID: 35625356 PMCID: PMC9138259 DOI: 10.3390/biology11050628] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 12/11/2022]
Abstract
Simple Summary Arthrospira maxima is an unbranched, filamentous cyanobacterium rich in important cellular products such as vitamins, minerals, iron, essential amino acids, essential fatty acids, and protein, which has made it one of the most important commercial photoautotrophs. To optimize the growth conditions for the production of target compounds and to ensure profitability in commercial applications, the effects of pH and temperature were investigated. A. maxima has been shown to be tolerant to a range of pH conditions and to exhibit hyper-accumulation of phycoerythrin and allophycocyanin at low temperatures. These traits may offer significant advantages for future exploitation, especially in outdoor cultivation with fluctuating pH and temperature. Our study also demonstrated a new method for the purification of phycocyanin from A. maxima by using by ultrafiltration, ion-exchange chromatography, and gel filtration, producing PC at 1.0 mg·mL−1 with 97.6% purity. Abstract Arthrospira maxima is a natural source of fine chemicals for multiple biotechnological applications. We determined the optimal environmental conditions for A. maxima by measuring its relative growth rate (RGR), pigment yield, and photosynthetic performance under different pH and temperature conditions. RGR was highest at pH 7–9 and 30 °C. Chlorophyll a, phycocyanin, maximal quantum yield (Fv/Fm), relative maximal electron transport rate (rETRmax), and effective quantum yield (ΦPSII) were highest at pH 7–8 and 25 °C. Interestingly, phycoerythrin and allophycocyanin content was highest at 15 °C, which may be the lowest optimum temperature reported for phycobiliprotein production in the Arthrospira species. A threestep purification of phycocyanin (PC) by ultrafiltration, ion-exchange chromatography, and gel filtration resulted in a 97.6% purity of PC.
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Affiliation(s)
- Jihae Park
- Development & Planning Office, Ghent University Global Campus, 119-5, Songdomunhwa-ro, Incheon 21985, Korea; (J.P.); (H.L.)
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, 119-5, Songdomunhwa-ro, Incheon 21985, Korea;
| | - Hojun Lee
- Development & Planning Office, Ghent University Global Campus, 119-5, Songdomunhwa-ro, Incheon 21985, Korea; (J.P.); (H.L.)
| | - Thai Binh Dinh
- Department of Cosmetic Science and Management, Incheon National University, 119, Academy-ro, Incheon 22012, Korea;
| | - Soyeon Choi
- Department of Marine Science, Incheon National University, 119, Academy-ro, Incheon 22012, Korea;
| | - Jonas De Saeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium;
| | - Stephen Depuydt
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, 119-5, Songdomunhwa-ro, Incheon 21985, Korea;
| | - Murray T. Brown
- School of Marine Science & Engineering, Plymouth University, Plymouth PL4 8AA, Devon, UK;
| | - Taejun Han
- Development & Planning Office, Ghent University Global Campus, 119-5, Songdomunhwa-ro, Incheon 21985, Korea; (J.P.); (H.L.)
- Department of Marine Science, Incheon National University, 119, Academy-ro, Incheon 22012, Korea;
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Coupure Links 653-Block F, 9000 Ghent, Belgium
- Correspondence:
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42
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Wei S, Zhuang G, Cheng L, Wang S. The proliferation rule of Microcystis aeruginosa under different initial pH conditions and its influence on the pH value of the environment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:13835-13844. [PMID: 34599447 DOI: 10.1007/s11356-021-16719-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
This study investigated the characteristics of the proliferation process of Microcystis aeruginosa and its changes to environmental pH values under different initial pH values and different initial inoculation densities. The results showed that although the initial pH value or the initial inoculation density was different, the pH values of the culture systems fluctuated up and down throughout the proliferation of M. aeruginosa, both on a daily and hourly time scale, and then tended to stabilize around the same value of 10.0 at the end of proliferation. The optimal pH value for the proliferation of M. aeruginosa was 9.55. This study creatively proposes that the period when the environmental pH value starts to rise rapidly toward 9.0 could be selected as an early warning period for a cyanobacterial outbreak, and the environmental pH value could be adjusted to below 8.0 to delay the outbreak. These results provide a scientific basis for further understanding the mechanism of cyanobacterial blooms and formulating pH-based control strategies.
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Affiliation(s)
- Sijie Wei
- Department of Environmental Science and Engineering, Fudan University, 2005 Songhu Road, Shanghai, 200433, People's Republic of China
| | - Guanjie Zhuang
- Department of Environmental Science and Engineering, Fudan University, 2005 Songhu Road, Shanghai, 200433, People's Republic of China
| | - Lirijian Cheng
- Department of Environmental Science and Engineering, Fudan University, 2005 Songhu Road, Shanghai, 200433, People's Republic of China
| | - Shoubing Wang
- Department of Environmental Science and Engineering, Fudan University, 2005 Songhu Road, Shanghai, 200433, People's Republic of China.
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Abstract
A small subset of marine microbial enzymes and surface transporters have a disproportionately important influence on the cycling of carbon and nutrients in the global ocean. As a result, they largely determine marine biological productivity and have been the focus of considerable research attention from microbial oceanographers. Like all biological catalysts, the activity of these keystone biomolecules is subject to control by temperature and pH, leaving the crucial ecosystem functions they support potentially vulnerable to anthropogenic environmental change. We summarize and discuss both consensus and conflicting evidence on the effects of sea surface warming and ocean acidification for five of these critical enzymes [carbonic anhydrase, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), nitrogenase, nitrate reductase, and ammonia monooxygenase] and one important transporter (proteorhodopsin). Finally, we forecast how the responses of these few but essential biocatalysts to ongoing global change processes may ultimately help to shape the microbial communities and biogeochemical cycles of the future greenhouse ocean.
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Affiliation(s)
- David A Hutchins
- Marine and Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA;
| | - Sergio A Sañudo-Wilhelmy
- Marine and Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA;
- Department of Earth Sciences, University of Southern California, Los Angeles, California 90089, USA;
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44
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Artier J, Walker RM, Miller NT, Zhang M, Price GD, Burnap RL. Modeling and mutagenesis of amino acid residues critical for CO 2 hydration by specialized NDH-1 complexes in cyanobacteria. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148503. [PMID: 34610280 DOI: 10.1016/j.bbabio.2021.148503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/24/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
The uptake of inorganic carbon in cyanobacteria is facilitated by an energetically intensive CO2-concentrating mechanism (CCM). This includes specialized Type-1 NDH complexes that function to couple photosynthetic redox energy to CO2 hydration forming the bicarbonate that accumulates to high cytoplasmic concentrations during the operation of the CCM, required for effective carbon fixation. Here we used a Synechococcus PCC7942 expression system to investigate the role of conserved histidine and cysteine residues in the CupB (also designated, ChpX) protein, which has been hypothesized to participate in a vectoral CO2 hydration reaction near the interface between CupB protein and the proton-pumping subunits of the NDH-1 complex. A homology model has been constructed and most of the targeted conserved residues are in the vicinity of a Zn ion modeled to form the catalytic site of deprotonation and CO2 hydration. Growth and CO2 uptake assays show that the most severe defects in activity among the targeted residues are due to a substitution of the predicted Zn ligand, CupB-His86. Mutations at other sites produced intermediate effects. Proteomic analysis revealed that some amino acid substitution mutations of CupB caused the induction of bicarbonate uptake proteins to a greater extent than complete deletion of CupB, despite growth under CO2-enriched conditions. The results are discussed in terms of hypotheses on the catalytic function of this unusual enzyme.
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Affiliation(s)
- Juliana Artier
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Ross M Walker
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Neil T Miller
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Minquan Zhang
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - G Dean Price
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Robert L Burnap
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA.
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Figures of Merit for Photocatalysis: Comparison of NiO/La-NaTaO3 and Synechocystis sp. PCC 6803 as a Semiconductor and a Bio-Photocatalyst for Water Splitting. Catalysts 2021. [DOI: 10.3390/catal11111415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
While photocatalysis is considered a promising sustainable technology in the field of heterogeneous catalysis as well as biocatalysis, figures of merit (FOM) for comparing catalytic performance, especially between disciplines, are not well established. Here, photocatalytic water splitting was conducted using a semiconductor (NiO/La-NaTaO3) and a bio-photocatalyst (Synechocystis sp. PCC 6803) in the same setup under similar reaction conditions, eliminating the often ill-defined influence of the setup on the FOMs obtained. Comparing the results enables the critical evaluation of existing FOMs and a quantitative comparison of both photocatalytic systems. A single FOM is insufficient to compare the photocatalysts, instead a combination of multiple FOMs (reaction rate, photocatalytic space time yield and a redefined apparent quantum yield) is superior for assessing a variety of photocatalytic systems.
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Iñiguez C, Aguiló-Nicolau P, Galmés J. Improving photosynthesis through the enhancement of Rubisco carboxylation capacity. Biochem Soc Trans 2021; 49:2007-2019. [PMID: 34623388 DOI: 10.1042/bst20201056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/07/2021] [Accepted: 09/09/2021] [Indexed: 12/14/2022]
Abstract
Rising human population, along with the reduction in arable land and the impacts of global change, sets out the need for continuously improving agricultural resource use efficiency and crop yield (CY). Bioengineering approaches for photosynthesis optimization have largely demonstrated the potential for enhancing CY. This review is focused on the improvement of Rubisco functioning, which catalyzes the rate-limiting step of CO2 fixation required for plant growth, but also catalyzes the ribulose-bisphosphate oxygenation initiating the carbon and energy wasteful photorespiration pathway. Rubisco carboxylation capacity can be enhanced by engineering the Rubisco large and/or small subunit genes to improve its catalytic traits, or by engineering the mechanisms that provide enhanced Rubisco expression, activation and/or elevated [CO2] around the active sites to favor carboxylation over oxygenation. Recent advances have been made in the expression, assembly and activation of foreign (either natural or mutant) faster and/or more CO2-specific Rubisco versions. Some components of CO2 concentrating mechanisms (CCMs) from bacteria, algae and C4 plants has been successfully expressed in tobacco and rice. Still, none of the transformed plant lines expressing foreign Rubisco versions and/or simplified CCM components were able to grow faster than wild type plants under present atmospheric [CO2] and optimum conditions. However, the results obtained up to date suggest that it might be achievable in the near future. In addition, photosynthetic and yield improvements have already been observed when manipulating Rubisco quantity and activation degree in crops. Therefore, engineering Rubisco carboxylation capacity continues being a promising target for the improvement in photosynthesis and yield.
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Affiliation(s)
- Concepción Iñiguez
- Research Group on Plant Biology Under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
- Department of Ecology, Faculty of Sciences, University of Málaga, Málaga, Spain
| | - Pere Aguiló-Nicolau
- Research Group on Plant Biology Under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
| | - Jeroni Galmés
- Research Group on Plant Biology Under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
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Huffine CA, Wheeler LC, Wing B, Cameron JC. Computational modeling and evolutionary implications of biochemical reactions in bacterial microcompartments. Curr Opin Microbiol 2021; 65:15-23. [PMID: 34717259 DOI: 10.1016/j.mib.2021.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/02/2021] [Indexed: 11/19/2022]
Abstract
Bacterial microcompartments (BMCs) are protein-encapsulated compartments found across at least 23 bacterial phyla. BMCs contain a variety of metabolic processes that share the commonality of toxic or volatile intermediates, oxygen-sensitive enzymes and cofactors, or increased substrate concentration for magnified reaction rates. These compartmentalized reactions have been computationally modeled to explore the encapsulated dynamics, ask evolutionary-based questions, and develop a more systematic understanding required for the engineering of novel BMCs. Many crucial aspects of these systems remain unknown or unmeasured, such as substrate permeabilities across the protein shell, feasibility of pH gradients, and transport rates of associated substrates into the cell. This review explores existing BMC models, dominated in the literature by cyanobacterial carboxysomes, and highlights potentially important areas for exploration.
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Affiliation(s)
- Clair A Huffine
- BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80309, USA; Department of Biochemistry, University of Colorado, Boulder, CO 80309, USA; Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO 80309, USA; Interdisciplinary Quantitative Biology Program (IQ Biology), BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Lucas C Wheeler
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
| | - Boswell Wing
- Department of Geological Sciences, Boulder, CO 80309, USA
| | - Jeffrey C Cameron
- Department of Biochemistry, University of Colorado, Boulder, CO 80309, USA; Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO 80309, USA; National Renewable Energy Laboratory, Golden, CO 80401, USA.
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Choi HI, Hwang SW, Kim J, Park B, Jin E, Choi IG, Sim SJ. Augmented CO 2 tolerance by expressing a single H +-pump enables microalgal valorization of industrial flue gas. Nat Commun 2021; 12:6049. [PMID: 34663809 PMCID: PMC8523702 DOI: 10.1038/s41467-021-26325-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 10/01/2021] [Indexed: 12/02/2022] Open
Abstract
Microalgae can accumulate various carbon-neutral products, but their real-world applications are hindered by their CO2 susceptibility. Herein, the transcriptomic changes in a model microalga, Chlamydomonas reinhardtii, in a high-CO2 milieu (20%) are evaluated. The primary toxicity mechanism consists of aberrantly low expression of plasma membrane H+-ATPases (PMAs) accompanied by intracellular acidification. Our results demonstrate that the expression of a universally expressible PMA in wild-type strains makes them capable of not only thriving in acidity levels that they usually cannot survive but also exhibiting 3.2-fold increased photoautotrophic production against high CO2 via maintenance of a higher cytoplasmic pH. A proof-of-concept experiment involving cultivation with toxic flue gas (13 vol% CO2, 20 ppm NOX, and 32 ppm SOX) shows that the production of CO2-based bioproducts by the strain is doubled compared with that by the wild-type, implying that this strategy potentially enables the microalgal valorization of CO2 in industrial exhaust.
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Affiliation(s)
- Hong Il Choi
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Sung-Won Hwang
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Jongrae Kim
- Department of Life Science, Hanyang University, 206, Wangsimni-ro, Seongbuk-gu, Seoul, 04763, Republic of Korea
| | - Byeonghyeok Park
- Department of Biotechnology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - EonSeon Jin
- Department of Life Science, Hanyang University, 206, Wangsimni-ro, Seongbuk-gu, Seoul, 04763, Republic of Korea
| | - In-Geol Choi
- Department of Biotechnology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Sang Jun Sim
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea.
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González-Resendiz L, Sánchez-García L, Hernández-Martínez I, Vigueras-Ramírez G, Jiménez-García LF, Lara-Martínez R, Morales-Ibarría M. Photoautotrophic poly(3-hydroxybutyrate) production by a wild-type Synechococcus elongatus isolated from an extreme environment. BIORESOURCE TECHNOLOGY 2021; 337:125508. [PMID: 34320776 DOI: 10.1016/j.biortech.2021.125508] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
Abstract
The photoautotrophic poly(3-hydroxybutyrate) (PHB) production by cyanobacteria is an attractive option as it only requires CO2 and light. In this work, a new wild-type strain producing PHB, Synechococcus elongatus UAM-C/S03, was identified using a polyphasic approach. The strain was cultured in a photobioreactor operated under N-sufficiency conditions at different pH values (7 to 11) and fed with CO2 on demand. We also evaluated the production of PHB under N-starving conditions. Highest biomass productivity, 324 mg L-1 d-1, and CO2 capture, 674 mg L-1 d-1, were obtained at pH 7 and under N-sufficiency conditions. The strain accumulated 29.42% of PHB in dry cell weight (DCW) under N-starvation conditions without pH control, and highest PHB productivity was 58.10 mg L-1 d-1. The highest carbohydrate content registered at pH 8, 50.84% in DCW, along with a release of carbon-based organic compounds, suggested the presence of exopolysaccharides in the culture medium.
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Affiliation(s)
- Laura González-Resendiz
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Av. Vasco de Quiroga 4871, Santa Fe Cuajimalpa, Cd. de México C.P. 05348, Mexico
| | - León Sánchez-García
- Doctorado en Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Cd. de México C.P. 09340, Mexico
| | - Ingrid Hernández-Martínez
- Doctorado en Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana-Cuajimalpa, Av. Vasco de Quiroga 4871, Santa Fe Cuajimalpa, Cd. de México C.P. 05348, Mexico
| | - Gabriel Vigueras-Ramírez
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Av. Vasco de Quiroga 4871, Santa Fe Cuajimalpa, Cd. de México C.P. 05348, Mexico
| | - Luis Felipe Jiménez-García
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Circuito Exterior Ciudad Universitaria, Cd. de México C.P. 04510, Mexico
| | - Reyna Lara-Martínez
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Circuito Exterior Ciudad Universitaria, Cd. de México C.P. 04510, Mexico
| | - Marcia Morales-Ibarría
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Av. Vasco de Quiroga 4871, Santa Fe Cuajimalpa, Cd. de México C.P. 05348, Mexico.
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50
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Pareek V, Sha Z, He J, Wingreen NS, Benkovic SJ. Metabolic channeling: predictions, deductions, and evidence. Mol Cell 2021; 81:3775-3785. [PMID: 34547238 PMCID: PMC8485759 DOI: 10.1016/j.molcel.2021.08.030] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/18/2021] [Accepted: 08/21/2021] [Indexed: 12/19/2022]
Abstract
With the elucidation of myriad anabolic and catabolic enzyme-catalyzed cellular pathways crisscrossing each other, an obvious question arose: how could these networks operate with maximal catalytic efficiency and minimal interference? A logical answer was the postulate of metabolic channeling, which in its simplest embodiment assumes that the product generated by one enzyme passes directly to a second without diffusion into the surrounding medium. This tight coupling of activities might increase a pathway's metabolic flux and/or serve to sequester unstable/toxic/reactive intermediates as well as prevent their access to other networks. Here, we present evidence for this concept, commencing with enzymes that feature a physical molecular tunnel, to multi-enzyme complexes that retain pathway substrates through electrostatics or enclosures, and finally to metabolons that feature collections of enzymes assembled into clusters with variable stoichiometric composition. Lastly, we discuss the advantages of reversibly assembled metabolons in the context of the purinosome, the purine biosynthesis metabolon.
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Affiliation(s)
- Vidhi Pareek
- Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Zhou Sha
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Jingxuan He
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Ned S Wingreen
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Stephen J Benkovic
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.
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