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Zhong J, Wang Y, Chen Z, Yalikun Y, He L, Liu T, Ma G. Engineering cyanobacteria as a new platform for producing taxol precursors directly from carbon dioxide. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:99. [PMID: 39014505 DOI: 10.1186/s13068-024-02555-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 07/10/2024] [Indexed: 07/18/2024]
Abstract
Taxol serves as an efficient natural anticancer agent with extensive applications in the treatment of diverse malignancies. Although advances in synthetic biology have enabled the de novo synthesis of taxol precursors in various microbial chassis, the total biosynthesis of taxol remains challengable owing to the restricted oxidation efficiency in heterotrophic microbes. Here, we engineered Synechocystis sp. PCC 6803 with modular metabolic pathways consisting of the methylerythritol phosphate pathway enzymes and taxol biosynthetic enzymes for production of taxadiene-5α-ol (T5α-ol), the key oxygenated intermediate of taxol. The best strain DIGT-P560 produced up to 17.43 mg/L of oxygenated taxanes and 4.32 mg/L of T5α-ol. Moreover, transcriptomic analysis of DIGT-P560 revealed that establishing a oxygenated taxane flux may enhance photosynthetic electron transfer efficiency and central metabolism in the engineered strain to ameliorate the metabolic disturbances triggered by the incorporation of exogenous genes. This is the first demonstration of photosynthetic production of taxadiene-5α-ol from CO2 in cyanobacteria, highlighting the broad prospects of engineered cyanobacteria as bio-solar cell factories for valuable terpenoids production and expanding the ideas for further rational engineering and optimization.
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Affiliation(s)
- Jialing Zhong
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai, 200240, People's Republic of China
| | - Yushu Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai, 200240, People's Republic of China
| | - Zhuoyang Chen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai, 200240, People's Republic of China
| | - Yaliqin Yalikun
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai, 200240, People's Republic of China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai, 200240, People's Republic of China
| | - Tiangang Liu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Gang Ma
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai, 200240, People's Republic of China.
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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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Domínguez-Lobo MT, Roldán M, Gutiérrez-Diánez AM, Florencio FJ, Muro-Pastor MI. Double blocking of carbon metabolism causes a large increase of Calvin-Benson cycle compounds in cyanobacteria. PLANT PHYSIOLOGY 2024; 195:1491-1505. [PMID: 38377468 PMCID: PMC11142378 DOI: 10.1093/plphys/kiae083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 01/08/2024] [Accepted: 01/19/2024] [Indexed: 02/22/2024]
Abstract
Carbon-flow-regulator A (CfrA) adapts carbon flux to nitrogen conditions in nondiazotrophic cyanobacteria. Under nitrogen deficiency, CfrA leads to the storage of excess carbon, which cannot combine with nitrogen, mainly as glycogen. cfrA overexpression from the arsenite-inducible, nitrogen-independent ParsB promoter allows analysis of the metabolic effects of CfrA accumulation. Considering that the main consequence of cfrA overexpression is glycogen accumulation, we examined carbon distribution in response to cfrA expression in Synechocystis sp. PCC 6803 strains impaired in synthesizing this polymer. We carried out a comparative phenotypic analysis to evaluate cfrA overexpression in the wild-type strain and in a mutant of ADP-glucose pyrophosphorylase (ΔglgC), which is unable to synthesize glycogen. The accumulation of CfrA in the wild-type background caused a photosynthetic readjustment although growth was not affected. However, in a ΔglgC strain, growth decreased depending on CfrA accumulation and photosynthesis was severely affected. An elemental analysis of the H, C, and N content of cells revealed that cfrA expression in the wild-type caused an increase in the C/N ratio, due to decreased nitrogen assimilation. Metabolomic study indicated that these cells store sucrose and glycosylglycerol, in addition to the previously described glycogen accumulation. However, cells deficient in glycogen synthesis accumulated large amounts of Calvin-Benson cycle intermediates as cfrA was expressed. These cells also showed increased levels of some amino acids, mainly alanine, serine, valine, isoleucine, and leucine. The findings suggest that by controlling cfrA expression, in different conditions and strains, we could change the distribution of fixed carbon, with potential biotechnological benefits.
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Affiliation(s)
| | - Miguel Roldán
- Instituto de Bioquímica Vegetal y Fotosíntesis (IBVF), CSIC-Universidad de Sevilla, Sevilla 41092, Spain
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Biología, Universidad de Sevilla, Sevilla 41012, Spain
| | - Alba María Gutiérrez-Diánez
- Instituto de Bioquímica Vegetal y Fotosíntesis (IBVF), CSIC-Universidad de Sevilla, Sevilla 41092, Spain
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Biología, Universidad de Sevilla, Sevilla 41012, Spain
| | - Francisco Javier Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis (IBVF), CSIC-Universidad de Sevilla, Sevilla 41092, Spain
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Biología, Universidad de Sevilla, Sevilla 41012, Spain
| | - María Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis (IBVF), CSIC-Universidad de Sevilla, Sevilla 41092, Spain
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Katayama N, Osanai T. Arginine inhibits the arginine biosynthesis rate-limiting enzyme and leads to the accumulation of intracellular aspartate in Synechocystis sp. PCC 6803. PLANT MOLECULAR BIOLOGY 2024; 114:27. [PMID: 38478146 PMCID: PMC10937788 DOI: 10.1007/s11103-024-01416-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 01/02/2024] [Indexed: 03/17/2024]
Abstract
Cyanobacteria are oxygen-evolving photosynthetic prokaryotes that affect the global carbon and nitrogen turnover. Synechocystis sp. PCC 6803 (Synechocystis 6803) is a model cyanobacterium that has been widely studied and can utilize and uptake various nitrogen sources and amino acids from the outer environment and media. l-arginine is a nitrogen-rich amino acid used as a nitrogen reservoir in Synechocystis 6803, and its biosynthesis is strictly regulated by feedback inhibition. Argininosuccinate synthetase (ArgG; EC 6.3.4.5) is the rate-limiting enzyme in arginine biosynthesis and catalyzes the condensation of citrulline and aspartate using ATP to produce argininosuccinate, which is converted to l-arginine and fumarate through argininosuccinate lyase (ArgH). We performed a biochemical analysis of Synechocystis 6803 ArgG (SyArgG) and obtained a Synechocystis 6803 mutant overexpressing SyArgG and ArgH of Synechocystis 6803 (SyArgH). The specific activity of SyArgG was lower than that of other arginine biosynthesis enzymes and SyArgG was inhibited by arginine, especially among amino acids and organic acids. Both arginine biosynthesis enzyme-overexpressing strains grew faster than the wild-type Synechocystis 6803. Based on previous reports and our results, we suggest that SyArgG is the rate-limiting enzyme in the arginine biosynthesis pathway in cyanobacteria and that arginine biosynthesis enzymes are similarly regulated by arginine in this cyanobacterium. Our results contribute to elucidating the regulation of arginine biosynthesis during nitrogen metabolism.
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Affiliation(s)
- Noriaki Katayama
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-ku, 214-8571, Kawasaki, Kanagawa, Japan
| | - Takashi Osanai
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-ku, 214-8571, Kawasaki, Kanagawa, Japan.
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Singh PR, Gupta A, Singh AP, Jaiswal J, Sinha RP. Effects of ultraviolet radiation on cellular functions of the cyanobacterium Synechocystis sp. PCC 6803 and its recovery under photosynthetically active radiation. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2024; 252:112866. [PMID: 38364711 DOI: 10.1016/j.jphotobiol.2024.112866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/27/2024] [Accepted: 02/07/2024] [Indexed: 02/18/2024]
Abstract
Cyanobacteria are photosynthetic organisms and challenged by large number of stresses, especially by ultraviolet radiation (UVR). UVR primarily impacts lipids, proteins, DNA, photosynthetic performance, which lowers the fitness and production of cyanobacteria. UVR has a catastrophic effect on cyanobacterial cells and eventually leads to cell death. UVR tolerance in the Synechocystis was poorly studied. Therefore, we irradiated Synechocystis sp. PCC 6803 to varying hours of photosynthetically active radiations (PAR), PAR + UV-A (PA), and PAR + UV-A + UV-B (PAB) for 48 h. To study the tolerance of Synechocystis sp. PCC 6803 against different UVR. The study shows that Chl a and total carotenoids content increased up to 36 h in PAR and PA, after 36 h a decrease was observed. PC increased up to 4-fold in 48 h of PA irradiation compared to 12 h. Maximum increase in ROS was observed under 48 h PAB i.e., 5.8-fold. Flowcytometry (FCM) based analysis shows that 25% of cells do not give fluorescence of Chl a and H2DCFH. In case of cell viability 10% cells were found to be non-viable in 48 h of PAB irradiance compared to 12 h. From the above study it was found that FCM-based approaches would provide a better understanding of the variations that occurred within the Synechocystis cells compared to fluorescence microscopy-based methods.
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Affiliation(s)
- Prashant R Singh
- Laboratory of Photobiology and Molecular Microbiology, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Amit Gupta
- Laboratory of Photobiology and Molecular Microbiology, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Ashish P Singh
- Laboratory of Photobiology and Molecular Microbiology, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Jyoti Jaiswal
- Laboratory of Photobiology and Molecular Microbiology, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Rajeshwar P Sinha
- Laboratory of Photobiology and Molecular Microbiology, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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Hernández-Gómez A, Irisarri I, Fernández-Justel D, Peláez R, Jiménez A, Revuelta JL, Balsera M, Buey RM. GuaB3, an overlooked enzyme in cyanobacteria's toolbox that sheds light on IMP dehydrogenase evolution. Structure 2023; 31:1526-1534.e4. [PMID: 37875114 DOI: 10.1016/j.str.2023.09.014] [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: 07/11/2023] [Revised: 09/05/2023] [Accepted: 09/28/2023] [Indexed: 10/26/2023]
Abstract
IMP dehydrogenase and GMP reductase are enzymes from the same protein family with analogous structures and catalytic mechanisms that have gained attention because of their essential roles in nucleotide metabolism and as potential drug targets. This study focusses on GuaB3, a less-explored enzyme within this family. Phylogenetic analysis uncovers GuaB3's independent evolution from other members of the family and it predominantly occurs in Cyanobacteria. Within this group, GuaB3 functions as a unique IMP dehydrogenase, while its counterpart in Actinobacteria has a yet unknown function. Synechocystis sp. PCC6803 GuaB3 structures demonstrate differences in the active site compared to canonical IMP dehydrogenases, despite shared catalytic mechanisms. These findings highlight the essential role of GuaB3 in Cyanobacteria, provide insights into the diversity and evolution of the IMP dehydrogenase protein family, and reveal a distinctive characteristic in nucleotide metabolism, potentially aiding in combating harmful cyanobacterial blooms-a growing concern for humans and wildlife.
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Affiliation(s)
- Alejandro Hernández-Gómez
- Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Iker Irisarri
- Section Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - David Fernández-Justel
- Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Rafael Peláez
- Laboratorio de Química Orgánica y Farmacéutica, Dpto. Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Alberto Jiménez
- Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - José Luis Revuelta
- Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Mónica Balsera
- Department Abiotic Stress, Instituto de Recursos Naturales y Agrobiología (IRNASA-CSIC), Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Rubén M Buey
- Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007 Salamanca, Spain.
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Xie H, Kjellström J, Lindblad P. Sustainable production of photosynthetic isobutanol and 3-methyl-1-butanol in the cyanobacterium Synechocystis sp. PCC 6803. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:134. [PMID: 37684613 PMCID: PMC10492371 DOI: 10.1186/s13068-023-02385-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023]
Abstract
BACKGROUND Cyanobacteria are emerging as green cell factories for sustainable biofuel and chemical production, due to their photosynthetic ability to use solar energy, carbon dioxide and water in a direct process. The model cyanobacterial strain Synechocystis sp. PCC 6803 has been engineered for the isobutanol and 3-methyl-1-butanol production by introducing a synthetic 2-keto acid pathway. However, the achieved productions still remained low. In the present study, diverse metabolic engineering strategies were implemented in Synechocystis sp. PCC 6803 for further enhanced photosynthetic isobutanol and 3-methyl-1-butanol production. RESULTS Long-term cultivation was performed on two selected strains resulting in maximum cumulative isobutanol and 3-methyl-1-butanol titers of 1247 mg L-1 and 389 mg L-1, on day 58 and day 48, respectively. Novel Synechocystis strain integrated with a native 2-keto acid pathway was generated and showed a production of 98 mg isobutanol L-1 in short-term screening experiments. Enhanced isobutanol and 3-methyl-1-butanol production was observed when increasing the kivdS286T copy number from three to four. Isobutanol and 3-methyl-1-butanol production was effectively improved when overexpressing selected genes of the central carbon metabolism. Identified genes are potential metabolic engineering targets to further enhance productivity of pyruvate-derived bioproducts in cyanobacteria. CONCLUSIONS Enhanced isobutanol and 3-methyl-1-butanol production was successfully achieved in Synechocystis sp. PCC 6803 strains through diverse metabolic engineering strategies. The maximum cumulative isobutanol and 3-methyl-1-butanol titers, 1247 mg L-1 and 389 mg L-1, respectively, represent the current highest value reported. The significantly enhanced isobutanol and 3-methyl-1-butanol production in this study further pave the way for an industrial application of photosynthetic cyanobacteria-based biofuel and chemical synthesis from CO2.
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Affiliation(s)
- Hao Xie
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Jarl Kjellström
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
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Li D, Dong H, Cao X, Wang W, Li C. Enhancing photosynthetic CO 2 fixation by assembling metal-organic frameworks on Chlorella pyrenoidosa. Nat Commun 2023; 14:5337. [PMID: 37660048 PMCID: PMC10475011 DOI: 10.1038/s41467-023-40839-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 08/12/2023] [Indexed: 09/04/2023] Open
Abstract
The CO2 concentration at ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is crucial to improve photosynthetic efficiency for biomass yield. However, how to concentrate and transport atmospheric CO2 towards the Rubisco carboxylation is a big challenge. Herein, we report the self-assembly of metal-organic frameworks (MOFs) on the surface of the green alga Chlorella pyrenoidosa that can greatly enhance the photosynthetic carbon fixation. The chemical CO2 concentrating approach improves the apparent photo conversion efficiency to about 1.9 folds, which is up to 9.8% in ambient air from an intrinsic 5.1%. We find that the efficient carbon fixation lies in the conversion of the captured CO2 to the transportable HCO3- species at bio-organic interface. This work demonstrates a chemical approach of concentrating atmospheric CO2 for enhancing biomass yield of photosynthesis.
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Affiliation(s)
- Dingyi Li
- School of Materials Science and Engineering, National Institute for Advanced Materials, Nankai University, Tianjin, China
| | - Hong Dong
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian National Laboratory for Clean Energy, Dalian, China
| | - Xupeng Cao
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian National Laboratory for Clean Energy, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wangyin Wang
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian National Laboratory for Clean Energy, Dalian, China.
| | - Can Li
- School of Materials Science and Engineering, National Institute for Advanced Materials, Nankai University, Tianjin, China.
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian National Laboratory for Clean Energy, Dalian, China.
- University of Chinese Academy of Sciences, Beijing, China.
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Ge-Zhang S, Cai T, Song M. Life in biophotovoltaics systems. FRONTIERS IN PLANT SCIENCE 2023; 14:1151131. [PMID: 37615025 PMCID: PMC10444202 DOI: 10.3389/fpls.2023.1151131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/03/2023] [Indexed: 08/25/2023]
Abstract
As the most suitable potential clean energy power generation technology, biophotovoltaics (BPV) not only inherits the advantages of traditional photovoltaics, such as safety, reliability and no noise, but also solves the disadvantages of high pollution and high energy consumption in the manufacturing process, providing new functions of self-repair and natural degradation. The basic idea of BPV is to collect light energy and generate electric energy by using photosynthetic autotrophs or their parts, and the core is how these biological materials can quickly and low-loss transfer electrons to the anode through mediators after absorbing light energy and generating electrons. In this mini-review, we summarized the biological materials widely used in BPV at present, mainly cyanobacteria, green algae, biological combinations (using multiple microorganisms in the same BPV system) and isolated products (purified thylakoids, chloroplasts, photosystem I, photosystem II), introduced how researchers overcome the shortcomings of low photocurrent output of BPV, pointed out the limitations that affected the development of BPV' biological materials, and put forward reasonable assumptions accordingly.
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Affiliation(s)
| | - Taoyang Cai
- Aulin College, Northeast Forestry University, Harbin, China
| | - Mingbo Song
- College of Forestry, Northeast Forestry University, Harbin, China
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Santos-Merino M, Gargantilla-Becerra Á, de la Cruz F, Nogales J. Highlighting the potential of Synechococcus elongatus PCC 7942 as platform to produce α-linolenic acid through an updated genome-scale metabolic modeling. Front Microbiol 2023; 14:1126030. [PMID: 36998399 PMCID: PMC10043229 DOI: 10.3389/fmicb.2023.1126030] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/22/2023] [Indexed: 03/15/2023] Open
Abstract
Cyanobacteria are prokaryotic organisms that capture energy from sunlight using oxygenic photosynthesis and transform CO2 into products of interest such as fatty acids. Synechococcus elongatus PCC 7942 is a model cyanobacterium efficiently engineered to accumulate high levels of omega-3 fatty acids. However, its exploitation as a microbial cell factory requires a better knowledge of its metabolism, which can be approached by using systems biology tools. To fulfill this objective, we worked out an updated, more comprehensive, and functional genome-scale model of this freshwater cyanobacterium, which was termed iMS837. The model includes 837 genes, 887 reactions, and 801 metabolites. When compared with previous models of S. elongatus PCC 7942, iMS837 is more complete in key physiological and biotechnologically relevant metabolic hubs, such as fatty acid biosynthesis, oxidative phosphorylation, photosynthesis, and transport, among others. iMS837 shows high accuracy when predicting growth performance and gene essentiality. The validated model was further used as a test-bed for the assessment of suitable metabolic engineering strategies, yielding superior production of non-native omega-3 fatty acids such as α-linolenic acid (ALA). As previously reported, the computational analysis demonstrated that fabF overexpression is a feasible metabolic target to increase ALA production, whereas deletion and overexpression of fabH cannot be used for this purpose. Flux scanning based on enforced objective flux, a strain-design algorithm, allowed us to identify not only previously known gene overexpression targets that improve fatty acid synthesis, such as Acetyl-CoA carboxylase and β-ketoacyl-ACP synthase I, but also novel potential targets that might lead to higher ALA yields. Systematic sampling of the metabolic space contained in iMS837 identified a set of ten additional knockout metabolic targets that resulted in higher ALA productions. In silico simulations under photomixotrophic conditions with acetate or glucose as a carbon source boosted ALA production levels, indicating that photomixotrophic nutritional regimens could be potentially exploited in vivo to improve fatty acid production in cyanobacteria. Overall, we show that iMS837 is a powerful computational platform that proposes new metabolic engineering strategies to produce biotechnologically relevant compounds, using S. elongatus PCC 7942 as non-conventional microbial cell factory.
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Affiliation(s)
- María Santos-Merino
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria—CSIC, Santander, Cantabria, Spain
- *Correspondence: María Santos-Merino,
| | - Álvaro Gargantilla-Becerra
- Department of Systems Biology, Centro Nacional de Biotecnología (CSIC), Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria—CSIC, Santander, Cantabria, Spain
| | - Juan Nogales
- Department of Systems Biology, Centro Nacional de Biotecnología (CSIC), Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Juan Nogales,
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Ortega-Martínez P, Roldán M, Díaz-Troya S, Florencio FJ. Stress response requires an efficient connection between glycogen and central carbon metabolism by phosphoglucomutases in cyanobacteria. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:1532-1550. [PMID: 36454663 PMCID: PMC10010611 DOI: 10.1093/jxb/erac474] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Glycogen and starch are the main storage polysaccharides, acting as a source of carbon and energy when necessary. Interconversion of glucose-1-phosphate and glucose-6-phosphate by phosphoglucomutases connects the metabolism of these polysaccharides with central carbon metabolism. However, knowledge about how this connection affects the ability of cells to cope with environmental stresses is still scarce. The cyanobacterium Synechocystis sp. PCC 6803 has two enzymes with phosphoglucomutase activity, PGM (phosphoglucomutase) and PMM/PGM (phosphomannomutase/phosphoglucomutase). In this work, we generated a null mutant of PGM (∆PGM) that exhibits very reduced phosphoglucomutase activity (1% of wild type activity). Although this mutant accumulates moderate amounts of glycogen, its phenotype resembles that of glycogen-less mutants, including high light sensitivity and altered response to nitrogen deprivation. Using an on/off arsenite promoter, we demonstrate that PMM/PGM is essential for growth and responsible for the remaining phosphoglucomutase activity in the ∆PGM strain. Furthermore, overexpression of PMM/PGM in the ∆PGM strain is enough to revoke the phenotype of this mutant. These results emphasize the importance of an adequate flux between glycogen and central carbon metabolism to maintain cellular fitness and indicate that although PGM is the main phosphoglucomutase activity, the phosphoglucomutase activity of PMM/PGM can substitute it when expressed in sufficient amounts.
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Affiliation(s)
- Pablo Ortega-Martínez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Américo Vespucio 49, Sevilla, 41092, Spain
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Biología, Universidad de Sevilla, Profesor García González s/n, Sevilla, 41012, Spain
| | - Miguel Roldán
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Biología, Universidad de Sevilla, Profesor García González s/n, Sevilla, 41012, Spain
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12
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Jackson PJ, Hitchcock A, Brindley AA, Dickman MJ, Hunter CN. Absolute quantification of cellular levels of photosynthesis-related proteins in Synechocystis sp. PCC 6803. PHOTOSYNTHESIS RESEARCH 2023; 155:219-245. [PMID: 36542271 PMCID: PMC9958174 DOI: 10.1007/s11120-022-00990-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Quantifying cellular components is a basic and important step for understanding how a cell works, how it responds to environmental changes, and for re-engineering cells to produce valuable metabolites and increased biomass. We quantified proteins in the model cyanobacterium Synechocystis sp. PCC 6803 given the general importance of cyanobacteria for global photosynthesis, for synthetic biology and biotechnology research, and their ancestral relationship to the chloroplasts of plants. Four mass spectrometry methods were used to quantify cellular components involved in the biosynthesis of chlorophyll, carotenoid and bilin pigments, membrane assembly, the light reactions of photosynthesis, fixation of carbon dioxide and nitrogen, and hydrogen and sulfur metabolism. Components of biosynthetic pathways, such as those for chlorophyll or for photosystem II assembly, range between 1000 and 10,000 copies per cell, but can be tenfold higher for CO2 fixation enzymes. The most abundant subunits are those for photosystem I, with around 100,000 copies per cell, approximately 2 to fivefold higher than for photosystem II and ATP synthase, and 5-20 fold more than for the cytochrome b6f complex. Disparities between numbers of pathway enzymes, between components of electron transfer chains, and between subunits within complexes indicate possible control points for biosynthetic processes, bioenergetic reactions and for the assembly of multisubunit complexes.
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Affiliation(s)
- Philip J Jackson
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK.
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK.
| | - Andrew Hitchcock
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Amanda A Brindley
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK
| | - C Neil Hunter
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
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13
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Rodrigues JS, Bourgade B, Galle KR, Lindberg P. Mapping competitive pathways to terpenoid biosynthesis in Synechocystis sp. PCC 6803 using an antisense RNA synthetic tool. Microb Cell Fact 2023; 22:35. [PMID: 36823631 PMCID: PMC9951418 DOI: 10.1186/s12934-023-02040-2] [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: 11/24/2022] [Accepted: 02/10/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND Synechocystis sp. PCC 6803 utilizes pyruvate and glyceraldehyde 3-phosphate via the methylerythritol 4-phosphate (MEP) pathway for the biosynthesis of terpenoids. Considering the deep connection of the MEP pathway to the central carbon metabolism, and the low carbon partitioning towards terpenoid biosynthesis, significant changes in the metabolic network are required to increase cyanobacterial production of terpenoids. RESULTS We used the Hfq-MicC antisense RNA regulatory tool, under control of the nickel-inducible PnrsB promoter, to target 12 different genes involved in terpenoid biosynthesis, central carbon metabolism, amino acid biosynthesis and ATP production, and evaluated the changes in the performance of an isoprene-producing cyanobacterial strain. Six candidate targets showed a positive effect on isoprene production: three genes involved in terpenoid biosynthesis (crtE, chlP and thiG), two involved in amino acid biosynthesis (ilvG and ccmA) and one involved in sugar catabolism (gpi). The same strategy was applied to interfere with different parts of the terpenoid biosynthetic pathway in a bisabolene-producing strain. Increased bisabolene production was observed not only when interfering with chlorophyll a biosynthesis, but also with carotenogenesis. CONCLUSIONS We demonstrated that the Hfq-MicC synthetic tool can be used to evaluate the effects of gene knockdown on heterologous terpenoid production, despite the need for further optimization of the technique. Possible targets for future engineering of Synechocystis aiming at improved terpenoid microbial production were identified.
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Affiliation(s)
- João S. Rodrigues
- grid.8993.b0000 0004 1936 9457Department of Chemistry – Ångström, Uppsala University, Uppsala, Sweden
| | - Barbara Bourgade
- grid.8993.b0000 0004 1936 9457Department of Chemistry – Ångström, Uppsala University, Uppsala, Sweden
| | - Karen R. Galle
- grid.8993.b0000 0004 1936 9457Department of Chemistry – Ångström, Uppsala University, Uppsala, Sweden ,grid.5808.50000 0001 1503 7226Faculty of Sciences, University of Porto, Porto, Portugal
| | - Pia Lindberg
- Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden.
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14
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Sukkasam N, Leksingto J, Incharoensakdi A, Monshupanee T. Chemical Triggering Cyanobacterial Glycogen Accumulation: Methyl Viologen Treatment Increases Synechocystis sp. PCC 6803 Glycogen Storage by Enhancing Levels of Gene Transcript and Substrates in Glycogen Synthesis. PLANT & CELL PHYSIOLOGY 2023; 63:2027-2041. [PMID: 36197756 DOI: 10.1093/pcp/pcac136] [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: 07/12/2022] [Revised: 09/26/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Two-stage cultivation is effective for glycogen production by cyanobacteria. Cells were first grown under adequate nitrate supply (BG11) to increase biomass and subsequently transferred to nitrogen deprivation (-N) to stimulate glycogen accumulation. However, the two-stage method is time-consuming and requires extensive energy. Thus, one-stage cultivation that enables both cell growth and glycogen accumulation is advantageous. Such one-stage method could be achieved using a chemical triggering glycogen storage. However, there is a limited study on such chemicals. Here, nine compounds previously reported to affect cyanobacterial cellular functions were examined in Synechocystis sp. PCC 6803. 2-Phenylethanol, phenoxyethanol, 3-(3,4-dichlorophenyl)-1,1-dimethylurea and methyl viologen can stimulate glycogen accumulation. The oxidative stress agent, methyl viologen significantly increased glycogen levels up to 57% and 69% [w/w dry weight (DW)] under BG11 and -N cultivation, respectively. One-stage cultivation where methyl viologen was directly added to the pre-grown culture enhanced glycogen storage to 53% (w/w DW), compared to the 10% (w/w DW) glycogen level of the control cells without methyl viologen. Methyl viologen treatment reduced the contents of total proteins (including phycobiliproteins) but caused increased transcript levels of glycogen synthetic genes and elevated levels of metabolite substrates for glycogen synthesis. Metabolomic results suggested that upon methyl viologen treatment, proteins degraded to amino acids, some of which could be used as a carbon source for glycogen synthesis. Results of oxygen evolution and metabolomic analysis suggested that photosynthesis and carbon fixation were not completely inhibited upon methyl viologen treatment, and these two processes may partially generate upstream metabolites required for glycogen synthesis.
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Affiliation(s)
- Nannaphat Sukkasam
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Jidapa Leksingto
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Aran Incharoensakdi
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Academy of Science, Royal Society of Thailand, Bangkok 10300, Thailand
| | - Tanakarn Monshupanee
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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15
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Lindberg P, Kenkel A, Bühler K. Introduction to Cyanobacteria. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 183:1-24. [PMID: 37009973 DOI: 10.1007/10_2023_217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
Cyanobacteria are highly interesting microbes with the capacity for oxygenic photosynthesis. They fulfill an important purpose in nature but are also potent biocatalysts. This chapter gives a brief overview of this diverse phylum and shortly addresses the functions these organisms have in the natural ecosystems. Further, it introduces the main topics covered in this volume, which is dealing with the development and application of cyanobacteria as solar cell factories for the production of chemicals including potential fuels. We discuss cyanobacteria as industrial workhorses, present established chassis strains, and give an overview of the current target products. Genetic engineering strategies aiming at the photosynthetic efficiency as well as approaches to optimize carbon fluxes are summarized. Finally, main cultivation strategies are sketched.
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Affiliation(s)
- Pia Lindberg
- Department of Chemistry-Ångström, Uppsala University, Uppsala, Sweden
| | - Amelie Kenkel
- Helmholtzcenter for Environmental Research, Leipzig, Germany
| | - Katja Bühler
- Helmholtzcenter for Environmental Research, Leipzig, Germany.
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16
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Kim J, Oh EK, Kim EJ, Lee JK. Photoautotrophic Growth Rate Enhancement of Synechocystis sp. PCC6803 by Heterologous Production of 2-Oxoglutarate:Ferredoxin Oxidoreductase from Chlorobaculum tepidum. BIOLOGY 2022; 12:biology12010059. [PMID: 36671751 PMCID: PMC9855186 DOI: 10.3390/biology12010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/27/2022] [Accepted: 12/27/2022] [Indexed: 01/01/2023]
Abstract
2-Oxoglutarate:ferredoxin oxidoreductase from Chlorobaculum tepidum (CtOGOR) is a carbon-fixing enzyme in the reductive TCA cycle that reversibly carboxylates succinyl-CoA to yield 2-oxoglutarate. CtOGOR is a heterotetramer of two large (α = 68 kDa) and two small (β = 38 kDa) subunits. The αβ protomer harbors one thiamine pyrophosphate and two 4Fe-4S clusters. Nonetheless, the enzyme has a considerable oxygen tolerance with a half-life of 143 min at 215 μM dissolved oxygen. Kinetic analyses of the purified recombinant CtOGOR revealed a lower Km for succinyl-CoA than for 2-oxoglutarate. Cellular levels of 2-oxoglutarate and glutamate—a product of glutamine oxoglutarate aminotransferase and glutamate dehydrogenase—increased more than twofold in the exponential phase compared with the control strain, leading to an approximately >30% increase in the photoautotrophic growth rate. Thus, CtOGOR was successfully produced in Synechocystis, thereby boosting carboxylation, resulting in enhanced photoautotrophic growth.
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Affiliation(s)
- June Kim
- Department of Life Science, Sogang University, Seoul 121-742, Republic of Korea
| | - Eun Kyoung Oh
- Department of Life Science, Sogang University, Seoul 121-742, Republic of Korea
| | - Eui-Jin Kim
- Microbial Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea
- Correspondence: (E.-J.K.); (J.K.L.); Tel.: +82-54-530-0860 (E.-J.K.); +82-2-705-8459 (J.K.L.); Fax: +82-54-530-0869 (E.-J.K.); +82-2-704-3601 (J.K.L.)
| | - Jeong K. Lee
- Department of Life Science, Sogang University, Seoul 121-742, Republic of Korea
- Correspondence: (E.-J.K.); (J.K.L.); Tel.: +82-54-530-0860 (E.-J.K.); +82-2-705-8459 (J.K.L.); Fax: +82-54-530-0869 (E.-J.K.); +82-2-704-3601 (J.K.L.)
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17
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Pichaiyotinkul P, Ruankaew N, Incharoensakdi A, Monshupanee T. Enhanced polyglucan contents in divergent cyanobacteria under nutrient-deprived photoautotrophy: transcriptional and metabolic changes in response to increased glycogen accumulation in nitrogen-deprived Synechocystis sp. PCC 6803. World J Microbiol Biotechnol 2022; 39:27. [PMID: 36437374 DOI: 10.1007/s11274-022-03476-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 11/17/2022] [Indexed: 11/29/2022]
Abstract
Cyanobacteria accumulate polyglucan as main carbohydrate storage. Here, the cellular polyglucan content was determined in 27 cyanobacterial strains from 25 genera. The polyglucan contents were significantly enhanced in 20 and 23 strains under nitrogen (-N) and phosphate (-P) deprivation, respectively. High polyglucan accumulation was not associated with particular evolutionary groups but was strain specific. The highest polyglucan accumulations of 46.2% and 52.5% (w/w dry weight; DW) were obtained under -N in Synechocystis sp. PCC 6803 (hereafter Synechocystis) and Chroococcus limneticus, respectively. In Synechocystis, 80-97% (w/w) of the polyglucan was glycogen. Transcriptome and metabolome analyses during glycogen accumulation under -N were determined in Synechocystis. The genes responsible for the supply of the substrates for glycogen synthesis: glycerate-1,3-phosphate and fructose-1,6-phosphate, were significantly up-regulated. The genes encoding the enzymes converting succinate to malate in TCA cycle, were significantly down-regulated. The genes encoding the regulator proteins which inhibits metabolism at lower part of glycolysis pathway, were also significantly up-regulated. The transcript levels of PII protein and the level of 2-oxoglutarate, which form a complex that inhibits lower part of glycolysis pathway, were significantly increased. Thus, the increased Synechocystis glycogen accumulation under -N was likely to be mediated by the increased supply of glycogen synthesis substrates and metabolic inhibitions at lower part of glycolysis pathway and TCA cycle.
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Affiliation(s)
| | - Nathanich Ruankaew
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, 10330, Bangkok, Thailand
| | - Aran Incharoensakdi
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, 10330, Bangkok, Thailand.,Academy of Science, Royal Society of Thailand, 10300, Bangkok, Thailand
| | - Tanakarn Monshupanee
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, 10330, Bangkok, Thailand.
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18
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Sukkasam N, Incharoensakdi A, Monshupanee T. Chemicals Affecting Cyanobacterial Poly(3-hydroxybutyrate) Accumulation: 2-Phenylethanol Treatment Combined with Nitrogen Deprivation Synergistically Enhanced Poly(3-hydroxybutyrate) Storage in Synechocystis sp. PCC6803 and Anabaena sp. TISTR8076. PLANT & CELL PHYSIOLOGY 2022; 63:1253-1272. [PMID: 35818829 DOI: 10.1093/pcp/pcac100] [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: 02/06/2022] [Revised: 07/04/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Various photoautotrophic cyanobacteria increase the accumulation of bioplastic poly(3-hydroxybutyrate) (PHB) under nitrogen deprivation (-N) for energy storage. Several metabolic engineering enhanced cyanobacterial PHB accumulation, but these strategies are not applicable in non-gene-transformable strains. Alternatively, stimulating PHB levels by chemical exposure is desirable because it might be applied to various cyanobacterial strains. However, the study of such chemicals is still limited. Here, 19 compounds previously reported to affect bacterial cellular processes were evaluated for their effect on PHB accumulation in Synechocystis sp. PCC6803, where 3-(3,4-dichlorophenyl)-1,1-dimethylurea, methyl viologen, arsenite, phenoxyethanol and 2-phenylethanol were found to increase PHB accumulation. When cultivated with optimal nitrate supply, Synechocystis contained less than 0.5% [w/w dry weight (DW)] PHB, while cultivation under -N conditions increased the PHB content to 7% (w/w DW). Interestingly, the -N cultivation combined with 2-phenylethanol exposure reduced the Synechocystis protein content by 27% (w/w DW) but significantly increased PHB levels up to 33% (w/w DW), the highest ever reported photoautotrophic cyanobacterial PHB accumulation in a wild-type strain. Results from transcriptomic and metabolomic analysis suggested that under 2-phenylethanol treatment, Synechocystis proteins were degraded to amino acids, which might be subsequently utilized as the source of carbon and energy for PHB biosynthesis. 2-Phenylethanol treatment also increased the levels of metabolites required for Synechocystis PHB synthesis (acetyl-CoA, acetoacetyl-CoA, 3-hydroxybutyryl-CoA and NADPH). Additionally, under -N, the exposure to phenoxyethanol and 2-phenylethanol increased the PHB levels of Anabaena sp. from 0.4% to 4.1% and 6.6% (w/w DW), respectively. The chemicals identified in this study might be applicable for enhancing PHB accumulation in other cyanobacteria.
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Affiliation(s)
- Nannaphat Sukkasam
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Aran Incharoensakdi
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Academy of Science, Royal Society of Thailand, Bangkok 10300, Thailand
| | - Tanakarn Monshupanee
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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19
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Palladino G, Caroselli E, Tavella T, D'Amico F, Prada F, Mancuso A, Franzellitti S, Rampelli S, Candela M, Goffredo S, Biagi E. Metagenomic shifts in mucus, tissue and skeleton of the coral Balanophyllia europaea living along a natural CO 2 gradient. ISME COMMUNICATIONS 2022; 2:65. [PMID: 37938252 PMCID: PMC9723718 DOI: 10.1038/s43705-022-00152-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 07/01/2022] [Accepted: 07/12/2022] [Indexed: 05/13/2023]
Abstract
Using the Mediterranean coral Balanophyllia europaea naturally growing along a pH gradient close to Panarea island (Italy) as a model, we explored the role of host-associated microbiomes in coral acclimatization to ocean acidification (OA). Coral samples were collected at three sites along the gradient, mimicking seawater conditions projected for 2100 under different IPCC (The Intergovernmental Panel on Climate Change) scenarios, and mucus, soft tissue and skeleton associated microbiomes were characterized by shotgun metagenomics. According to our findings, OA induced functional changes in the microbiomes genetic potential that could mitigate the sub-optimal environmental conditions at three levels: i. selection of bacteria genetically equipped with functions related to stress resistance; ii. shifts in microbial carbohydrate metabolism from energy production to maintenance of cell membranes and walls integrity; iii. gain of functions able to respond to variations in nitrogen needs at the holobiont level, such as genes devoted to organic nitrogen mobilization. We hence provided hypotheses about the functional role of the coral associated microbiome in favoring host acclimatation to OA, remarking on the importance of considering the crosstalk among all the components of the holobiont to unveil how and to what extent corals will maintain their functionality under forthcoming ocean conditions.
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Affiliation(s)
- Giorgia Palladino
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126, Bologna, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy
| | - Erik Caroselli
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Teresa Tavella
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126, Bologna, Italy
| | - Federica D'Amico
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126, Bologna, Italy
| | - Fiorella Prada
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Arianna Mancuso
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Silvia Franzellitti
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy
- Animal and Environmental Physiology Laboratory, Department of Biological, Geological and Environmental Sciences, University of Bologna, via Sant'Alberto 163, 48123, Ravenna, Italy
| | - Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126, Bologna, Italy
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126, Bologna, Italy.
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy.
| | - Stefano Goffredo
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy.
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126, Bologna, Italy.
| | - Elena Biagi
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126, Bologna, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy
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20
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Klaus O, Hilgers F, Nakielski A, Hasenklever D, Jaeger KE, Axmann IM, Drepper T. Engineering phototrophic bacteria for the production of terpenoids. Curr Opin Biotechnol 2022; 77:102764. [PMID: 35932511 DOI: 10.1016/j.copbio.2022.102764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/24/2022] [Accepted: 06/30/2022] [Indexed: 12/13/2022]
Abstract
With more than 80 000 compounds, terpenoids represent one of the largest classes of secondary metabolites naturally produced by various plants and other organisms. Owing to the tremendous structural diversity, they offer a wide range of properties relevant for biotechnological and pharmaceutical applications. In this context, heterologous terpenoid production in engineered microbial hosts represents an often cost-effective and eco-friendly way to make these valuable compounds industrially available. This review provides an overview of current strategies to employ and engineer oxygenic and anoxygenic phototrophic bacteria as alternative cell factories for sustainable terpenoid production. Besides terpenoid pathway engineering, the effects of different illumination strategies on terpenoid photoproduction are key elements in the latest studies.
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Affiliation(s)
- Oliver Klaus
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Fabienne Hilgers
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Andreas Nakielski
- Institute for Synthetic Microbiology, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Dennis Hasenklever
- Institute for Synthetic Microbiology, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany; Institute of Bio, and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Ilka M Axmann
- Institute for Synthetic Microbiology, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.
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Yilimulati M, Zhou L, Shevela D, Zhang S. Acetylacetone Interferes with Carbon and Nitrogen Metabolism of Microcystis aeruginosa by Cutting Off the Electron Flow to Ferredoxin. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:9683-9692. [PMID: 35696645 DOI: 10.1021/acs.est.2c00776] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The regulation of photosynthetic machinery with a nonoxidative approach is a powerful but challenging strategy for the selective inhibition of bloom-forming cyanobacteria. Acetylacetone (AA) was recently found to be a target-selective cyanocide for Microcystis aeruginosa, but the cause and effect in the studied system are still unclear. By recording of the chemical fingerprints of the cells at two treatment intervals (12 and 72 h with 0.1 mM AA) with omics assays, the molecular mechanism of AA in inactivating Microcystis aeruginosa was elucidated. The results clearly reveal the effect of AA on ferredoxin and the consequent effects on the physiological and biochemical processes of Microcystis aeruginosa. In addition to its role as an electron acceptor of photosystem I, ferredoxin plays pivotal roles in the assimilation of nitrogen in cyanobacterial cells. The effect of AA on ferredoxin and on nonheme iron of photosystem II first cut off the photosynthetic electron transfer flow and then interrupted the synthesis of adenosine triphosphate (ATP) and reduced nicotinamide adenine dinucleotide phosphate (NADPH), which ultimately might affect carbon fixation and nitrogen assimilation metabolisms. The results here provide missing pieces in the current knowledge on the selective inhibition of cyanobacteria, which should shed light on the better control of harmful blooms.
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Affiliation(s)
- Mihebai Yilimulati
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, People's Republic of China
| | - Lang Zhou
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, People's Republic of China
| | - Dmitry Shevela
- Department of Chemistry, Chemical Biological Centre, Umeå University, 90187 Umeå, Sweden
| | - Shujuan Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, People's Republic of China
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22
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Mills LA, Moreno-Cabezuelo JÁ, Włodarczyk A, Victoria AJ, Mejías R, Nenninger A, Moxon S, Bombelli P, Selão TT, McCormick AJ, Lea-Smith DJ. Development of a Biotechnology Platform for the Fast-Growing Cyanobacterium Synechococcus sp. PCC 11901. Biomolecules 2022; 12:biom12070872. [PMID: 35883428 PMCID: PMC9313322 DOI: 10.3390/biom12070872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 02/07/2023] Open
Abstract
Synechococcus sp. PCC 11901 reportedly demonstrates the highest, most sustained growth of any known cyanobacterium under optimized conditions. Due to its recent discovery, our knowledge of its biology, including the factors underlying sustained, fast growth, is limited. Furthermore, tools specific for genetic manipulation of PCC 11901 are not established. Here, we demonstrate that PCC 11901 shows faster growth than other model cyanobacteria, including the fast-growing species Synechococcuselongatus UTEX 2973, under optimal growth conditions for UTEX 2973. Comparative genomics between PCC 11901 and Synechocystis sp. PCC 6803 reveal conservation of most metabolic pathways but PCC 11901 has a simplified electron transport chain and reduced light harvesting complex. This may underlie its superior light use, reduced photoinhibition, and higher photosynthetic and respiratory rates. To aid biotechnology applications, we developed a vitamin B12 auxotrophic mutant but were unable to generate unmarked knockouts using two negative selectable markers, suggesting that recombinase- or CRISPR-based approaches may be required for repeated genetic manipulation. Overall, this study establishes PCC 11901 as one of the most promising species currently available for cyanobacterial biotechnology and provides a useful set of bioinformatics tools and strains for advancing this field, in addition to insights into the factors underlying its fast growth phenotype.
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Affiliation(s)
- Lauren A. Mills
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
| | - José Ángel Moreno-Cabezuelo
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
| | - Artur Włodarczyk
- Bondi Bio Pty Ltd., c/o Climate Change Cluster, University of Technology Sydney, 745 Harris Street, Ultimo, NSW 2007, Australia;
| | - Angelo J. Victoria
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK; (A.J.V.); (A.N.); (A.J.M.)
| | - Rebeca Mejías
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
| | - Anja Nenninger
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK; (A.J.V.); (A.N.); (A.J.M.)
| | - Simon Moxon
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
| | - Paolo Bombelli
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK;
| | - Tiago T. Selão
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, UK;
| | - Alistair J. McCormick
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK; (A.J.V.); (A.N.); (A.J.M.)
| | - David J. Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
- Correspondence:
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23
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Muth-Pawlak D, Kreula S, Gollan PJ, Huokko T, Allahverdiyeva Y, Aro EM. Patterning of the Autotrophic, Mixotrophic, and Heterotrophic Proteomes of Oxygen-Evolving Cyanobacterium Synechocystis sp. PCC 6803. Front Microbiol 2022; 13:891895. [PMID: 35694301 PMCID: PMC9175036 DOI: 10.3389/fmicb.2022.891895] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Proteomes of an oxygenic photosynthetic cyanobacterium, Synechocystis sp. PCC 6803, were analyzed under photoautotrophic (low and high CO2, assigned as ATLC and ATHC), photomixotrophic (MT), and light-activated heterotrophic (LAH) conditions. Allocation of proteome mass fraction to seven sub-proteomes and differential expression of individual proteins were analyzed, paying particular attention to photosynthesis and carbon metabolism–centered sub-proteomes affected by the quality and quantity of the carbon source and light regime upon growth. A distinct common feature of the ATHC, MT, and LAH cultures was low abundance of inducible carbon-concentrating mechanisms and photorespiration-related enzymes, independent of the inorganic or organic carbon source. On the other hand, these cells accumulated a respiratory NAD(P)H dehydrogenase I (NDH-11) complex in the thylakoid membrane (TM). Additionally, in glucose-supplemented cultures, a distinct NDH-2 protein, NdbA, accumulated in the TM, while the plasma membrane-localized NdbC and terminal oxidase decreased in abundance in comparison to both AT conditions. Photosynthetic complexes were uniquely depleted under the LAH condition but accumulated under the ATHC condition. The MT proteome displayed several heterotrophic features typical of the LAH proteome, particularly including the high abundance of ribosome as well as amino acid and protein biosynthesis machinery-related components. It is also noteworthy that the two equally light-exposed ATHC and MT cultures allocated similar mass fractions of the total proteome to the seven distinct sub-proteomes. Unique trophic condition-specific expression patterns were likewise observed among individual proteins, including the accumulation of phosphate transporters and polyphosphate polymers storing energy surplus in highly energetic bonds under the MT condition and accumulation under the LAH condition of an enzyme catalyzing cyanophycin biosynthesis. It is concluded that the rigor of cell growth in the MT condition results, to a great extent, by combining photosynthetic activity with high intracellular inorganic carbon conditions created upon glucose breakdown and release of CO2, besides the direct utilization of glucose-derived carbon skeletons for growth. This combination provides the MT cultures with excellent conditions for growth that often exceeds that of mere ATHC.
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24
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Meixner K, Daffert C, Dalnodar D, Mrázová K, Hrubanová K, Krzyzanek V, Nebesarova J, Samek O, Šedrlová Z, Slaninova E, Sedláček P, Obruča S, Fritz I. Glycogen, poly(3-hydroxybutyrate) and pigment accumulation in three Synechocystis strains when exposed to a stepwise increasing salt stress. JOURNAL OF APPLIED PHYCOLOGY 2022; 34:1227-1241. [PMID: 35673609 PMCID: PMC9165259 DOI: 10.1007/s10811-022-02693-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/07/2022] [Accepted: 01/07/2022] [Indexed: 06/15/2023]
Abstract
The cyanobacterial genus Synechocystis is of particular interest to science and industry because of its efficient phototrophic metabolism, its accumulation of the polymer poly(3-hydroxybutyrate) (PHB) and its ability to withstand or adapt to adverse growing conditions. One such condition is the increased salinity that can be caused by recycled or brackish water used in cultivation. While overall reduced growth is expected in response to salt stress, other metabolic responses relevant to the efficiency of phototrophic production of biomass or PHB (or both) have been experimentally observed in three Synechocystis strains at stepwise increasing salt concentrations. In response to recent reports on metabolic strategies to increase stress tolerance of heterotrophic and phototrophic bacteria, we focused particularly on the stress-induced response of Synechocystis strains in terms of PHB, glycogen and photoactive pigment dynamics. Of the three strains studied, the strain Synechocystis cf. salina CCALA192 proved to be the most tolerant to salt stress. In addition, this strain showed the highest PHB accumulation. All the three strains accumulated more PHB with increasing salinity, to the point where their photosystems were strongly inhibited and they could no longer produce enough energy to synthesize more PHB.
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Affiliation(s)
- K. Meixner
- Institute of Environmental Biotechnology, Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
- BEST Bioenergy and Sustainable Technologies GmbH, Inffeldgasse 21b, 8010 Graz, Austria
| | - C. Daffert
- Institute of Environmental Biotechnology, Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - D. Dalnodar
- Institute of Environmental Biotechnology, Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - K. Mrázová
- Institute of Scientific Instruments, The Czech Academy of Sciences, Královopolská 147, 61264 Brno, Czech Republic
| | - K. Hrubanová
- Institute of Scientific Instruments, The Czech Academy of Sciences, Královopolská 147, 61264 Brno, Czech Republic
| | - V. Krzyzanek
- Institute of Scientific Instruments, The Czech Academy of Sciences, Královopolská 147, 61264 Brno, Czech Republic
| | - J. Nebesarova
- Institute of Parasitology, Biology Centre, The Czech Academy of Sciences, Branisovska 31, 37005 Ceske Budejovice, Czech Republic
- Faculty of Science, Charles University, Vinicna 7, 128 44 Prague 2, Czech Republic
| | - O. Samek
- Institute of Scientific Instruments, The Czech Academy of Sciences, Královopolská 147, 61264 Brno, Czech Republic
| | - Z. Šedrlová
- Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic
| | - E. Slaninova
- Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic
| | - P. Sedláček
- Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic
| | - S. Obruča
- Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic
| | - I. Fritz
- Institute of Environmental Biotechnology, Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
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25
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Funck D, Sinn M, Fleming JR, Stanoppi M, Dietrich J, López-Igual R, Mayans O, Hartig JS. Discovery of a Ni 2+-dependent guanidine hydrolase in bacteria. Nature 2022; 603:515-521. [PMID: 35264792 DOI: 10.1038/s41586-022-04490-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 01/31/2022] [Indexed: 12/14/2022]
Abstract
Nitrogen availability is a growth-limiting factor in many habitats1, and the global nitrogen cycle involves prokaryotes and eukaryotes competing for this precious resource. Only some bacteria and archaea can fix elementary nitrogen; all other organisms depend on the assimilation of mineral or organic nitrogen. The nitrogen-rich compound guanidine occurs widely in nature2-4, but its utilization is impeded by pronounced resonance stabilization5, and enzymes catalysing hydrolysis of free guanidine have not been identified. Here we describe the arginase family protein GdmH (Sll1077) from Synechocystis sp. PCC 6803 as a Ni2+-dependent guanidine hydrolase. GdmH is highly specific for free guanidine. Its activity depends on two accessory proteins that load Ni2+ instead of the typical Mn2+ ions into the active site. Crystal structures of GdmH show coordination of the dinuclear metal cluster in a geometry typical for arginase family enzymes and allow modelling of the bound substrate. A unique amino-terminal extension and a tryptophan residue narrow the substrate-binding pocket and identify homologous proteins in further cyanobacteria, several other bacterial taxa and heterokont algae as probable guanidine hydrolases. This broad distribution suggests notable ecological relevance of guanidine hydrolysis in aquatic habitats.
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Affiliation(s)
- D Funck
- Department of Chemistry, University of Konstanz, Konstanz, Germany
| | - M Sinn
- Department of Chemistry, University of Konstanz, Konstanz, Germany
| | - J R Fleming
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - M Stanoppi
- Department of Chemistry, University of Konstanz, Konstanz, Germany
| | - J Dietrich
- Department of Chemistry, University of Konstanz, Konstanz, Germany
| | - R López-Igual
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and C.S.I.C, Seville, Spain
| | - O Mayans
- Department of Biology, University of Konstanz, Konstanz, Germany.,Konstanz Graduate School Chemical Biology (KoRS-CB), University of Konstanz, Konstanz, Germany
| | - J S Hartig
- Department of Chemistry, University of Konstanz, Konstanz, Germany. .,Konstanz Graduate School Chemical Biology (KoRS-CB), University of Konstanz, Konstanz, Germany.
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26
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Sukkasam N, Incharoensakdi A, Monshupanee T. Disruption of Hydrogen Gas Synthesis Enhances the Cellular Levels of NAD(P)H, Glycogen, Poly(3-hydroxybutyrate) and Photosynthetic Pigments Under Specific Nutrient Condition(s) in Cyanobacterium Synechocystis sp. PCC 6803. PLANT & CELL PHYSIOLOGY 2022; 63:135-147. [PMID: 34698867 DOI: 10.1093/pcp/pcab156] [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: 08/03/2021] [Revised: 10/15/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
In photoautotrophic Synechocystis sp. PCC 6803, NADPH is generated from photosynthesis and utilized in various metabolism, including the biosynthesis of glyceraldehyde 3-phosphate (the upstream substrate for carbon metabolism), poly(3-hydroxybutyrate) (PHB), photosynthetic pigments, and hydrogen gas (H2). Redirecting NADPH flow from one biosynthesis pathway to another has yet to be studied. Synechocystis's H2 synthesis, one of the pathways consuming NAD(P)H, was disrupted by the inactivation of hoxY and hoxH genes encoding the two catalytic subunits of hydrogenase. Such inactivation with a complete disruption of H2 synthesis led to 1.4-, 1.9-, and 2.1-fold increased cellular NAD(P)H levels when cells were cultured in normal medium (BG11), the medium without nitrate (-N), and the medium without phosphate (-P), respectively. After 49-52 d of cultivation in BG11 (when the nitrogen source in the media was depleted), the cells with disrupted H2 synthesis had 1.3-fold increased glycogen level compared to wild type of 83-85% (w/w dry weight), the highest level reported for cyanobacterial glycogen. The increased glycogen content observed by transmission electron microscopy was correlated with the increased levels of glucose 6-phosphate and glucose 1-phosphate, the two substrates in glycogen synthesis. Disrupted H2 synthesis also enhanced PHB accumulation up to 1.4-fold under -P and 1.6-fold under -N and increased levels of photosynthetic pigments (chlorophyll a, phycocyanin, and allophycocyanin) by 1.3- to 1.5-fold under BG11. Thus, disrupted H2 synthesis increased levels of NAD(P)H, which may be utilized for the biosynthesis of glycogen, PHB, and pigments. This strategy might be applicable for enhancing other biosynthetic pathways that utilize NAD(P)H.
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Affiliation(s)
- Nannaphat Sukkasam
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Aran Incharoensakdi
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Academy of Science, Royal Society of Thailand, Bangkok 10300, Thailand
| | - Tanakarn Monshupanee
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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27
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Nitrogen Availability Affects the Metabolic Profile in Cyanobacteria. Metabolites 2021; 11:metabo11120867. [PMID: 34940625 PMCID: PMC8707274 DOI: 10.3390/metabo11120867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 11/17/2022] Open
Abstract
Nitrogen is essential for the biosynthesis of various molecules in cells, such as amino acids and nucleotides, as well as several types of lipids and sugars. Cyanobacteria can assimilate several forms of nitrogen, including nitrate, ammonium, and urea, and the physiological and genetic responses to these nitrogen sources have been studied previously. However, the metabolic changes in cyanobacteria caused by different nitrogen sources have not yet been characterized. This study aimed to elucidate the influence of nitrate and ammonium on the metabolic profiles of the cyanobacterium Synechocystis sp. strain PCC 6803. When supplemented with NaNO3 or NH4Cl as the nitrogen source, Synechocystis sp. PCC 6803 grew faster in NH4Cl medium than in NaNO3 medium. Metabolome analysis indicated that some metabolites in the CBB cycle, glycolysis, and TCA cycle, and amino acids were more abundant when grown in NH4Cl medium than NaNO3 medium. 15N turnover rate analysis revealed that the nitrogen assimilation rate in NH4Cl medium was higher than in NaNO3 medium. These results indicate that the mechanism of nitrogen assimilation in the GS-GOGAT cycle differs between NaNO3 and NH4Cl. We conclude that the amounts and biosynthetic rate of cyanobacterial metabolites varies depending on the type of nitrogen.
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28
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Lee J, Iwata Y, Suzuki Y, Suzuki I. Rapid phosphate uptake via an ABC transporter induced by sulfate deficiency in Synechocystis sp. PCC 6803. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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29
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A biophotoelectrochemical approach to unravelling the role of cyanobacterial cell structures in exoelectrogenesis. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2021.139214] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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30
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Yu King Hing N, Aryal UK, Morgan JA. Probing Light-Dependent Regulation of the Calvin Cycle Using a Multi-Omics Approach. FRONTIERS IN PLANT SCIENCE 2021; 12:733122. [PMID: 34671374 PMCID: PMC8521058 DOI: 10.3389/fpls.2021.733122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Photoautotrophic microorganisms are increasingly explored for the conversion of atmospheric carbon dioxide into biomass and valuable products. The Calvin-Benson-Bassham (CBB) cycle is the primary metabolic pathway for net CO2 fixation within oxygenic photosynthetic organisms. The cyanobacteria, Synechocystis sp. PCC 6803, is a model organism for the study of photosynthesis and a platform for many metabolic engineering efforts. The CBB cycle is regulated by complex mechanisms including enzymatic abundance, intracellular metabolite concentrations, energetic cofactors and post-translational enzymatic modifications that depend on the external conditions such as the intensity and quality of light. However, the extent to which each of these mechanisms play a role under different light intensities remains unclear. In this work, we conducted non-targeted proteomics in tandem with isotopically non-stationary metabolic flux analysis (INST-MFA) at four different light intensities to determine the extent to which fluxes within the CBB cycle are controlled by enzymatic abundance. The correlation between specific enzyme abundances and their corresponding reaction fluxes is examined, revealing several enzymes with uncorrelated enzyme abundance and their corresponding flux, suggesting flux regulation by mechanisms other than enzyme abundance. Additionally, the kinetics of 13C labeling of CBB cycle intermediates and estimated inactive pool sizes varied significantly as a function of light intensity suggesting the presence of metabolite channeling, an additional method of flux regulation. These results highlight the importance of the diverse methods of regulation of CBB enzyme activity as a function of light intensity, and highlights the importance of considering these effects in future kinetic models.
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Affiliation(s)
- Nathaphon Yu King Hing
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, United States
| | - Uma K. Aryal
- Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN, United States
- Department of Comparative Pathobiology, Purdue University College of Veterinary Medicine, West Lafayette, IN, United States
| | - John A. Morgan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, United States
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
- Center for Plant Biology, Purdue University, West Lafayette, IN, United States
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31
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Mishra A, Gupta J, Kumari T, Pal R, Thakur IS. Unravelling the attributes of novel cyanobacteria Jacksonvillea sp. ISTCYN1 by draft genome sequencing. BIORESOURCE TECHNOLOGY 2021; 337:125473. [PMID: 34320753 DOI: 10.1016/j.biortech.2021.125473] [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: 05/16/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Filamentous cyanobacteria, Jacksonvillea sp. ISTCYN1 was isolated from agriculture field and cultured in BG-11 medium. This study, report the genome sequence of cyanobacteria Jacksonvillea thatto the best of our knowledgeis the firstgenome sequenceof thisgenus. The 5.7 MB draft genome sequence of this cyanobacterium contains 5134 protein-coding genes. The phylogenetic tree was constructed based on genome and Desertifilum sp. IPPAS B-1220 validated the closest relationship with Jacksonvillea sp. ISTCYN1. The growth of strain ISTCYN1 has been reported in the presence of different types of plastic when used as a sole carbon source. SEM analysis revealed biofilm formation by cyanobacterial strain ISTCYN1 on the surface of high and low-density polyethylene and polypropylene. In the presence of these plastics, EPS production has also been reported by this strain. Whole genome sequence analysis reveals the presence of many genes involved in biofilm formation. The presence of key enzymes responsible for plastic degradation laccase, esterase, lipase, thioesterase, and peroxidase have been predicted in the genome analysis. Genome analysis also provides insight into the genes involved in biotin biosynthetic pathways. Furthermore, the presence of many selenoproteins reveals the selenium acquisition by this cyanobacterium.
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Affiliation(s)
- Arti Mishra
- Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Sector-125, Noida 201303, India
| | - Juhi Gupta
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Taruna Kumari
- Department of Statistics, University of Delhi, New Delhi 110007, India
| | - Ruchita Pal
- Advanced Instrumentation Research Facility, Jawaharlal Nehru University, New Delhi 110067, India
| | - I S Thakur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India.
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32
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Lea-Smith DJ, Summerfield TC, Ducat DC, Lu X, McCormick AJ, Purton S. Editorial: Exploring the Growing Role of Cyanobacteria in Industrial Biotechnology and Sustainability. Front Microbiol 2021; 12:725128. [PMID: 34326831 PMCID: PMC8313982 DOI: 10.3389/fmicb.2021.725128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 06/22/2021] [Indexed: 01/17/2023] Open
Affiliation(s)
- David J Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | | | - Daniel C Ducat
- Michigan State University-Department of Energy (MSU-DOE) Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Xuefeng Lu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Alistair J McCormick
- School of Biological Sciences, SynthSys and Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Saul Purton
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
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33
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Nagy C, Thiel K, Mulaku E, Mustila H, Tamagnini P, Aro EM, Pacheco CC, Kallio P. Comparison of alternative integration sites in the chromosome and the native plasmids of the cyanobacterium Synechocystis sp. PCC 6803 in respect to expression efficiency and copy number. Microb Cell Fact 2021; 20:130. [PMID: 34246263 PMCID: PMC8272380 DOI: 10.1186/s12934-021-01622-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 06/29/2021] [Indexed: 11/10/2022] Open
Abstract
Background Synechocystis sp. PCC 6803 provides a well-established reference point to cyanobacterial metabolic engineering as part of basic photosynthesis research, as well as in the development of next-generation biotechnological production systems. This study focused on expanding the current knowledge on genomic integration of expression constructs in Synechocystis, targeting a range of novel sites in the chromosome and in the native plasmids, together with established loci used in literature. The key objective was to obtain quantitative information on site-specific expression in reference to replicon copy numbers, which has been speculated but never compared side by side in this host. Results An optimized sYFP2 expression cassette was successfully integrated in two novel sites in Synechocystis chromosome (slr0944; sll0058) and in all four endogenous megaplasmids (pSYSM/slr5037-slr5038; pSYSX/slr6037; pSYSA/slr7023; pSYSG/slr8030) that have not been previously evaluated for the purpose. Fluorescent analysis of the segregated strains revealed that the expression levels between the megaplasmids and chromosomal constructs were very similar, and reinforced the view that highest expression in Synechocystis can be obtained using RSF1010-derived replicative vectors or the native small plasmid pCA2.4 evaluated in comparison. Parallel replicon copy number analysis by RT-qPCR showed that the expression from the alternative loci is largely determined by the gene dosage in Synechocystis, thereby confirming the dependence formerly proposed based on literature. Conclusions This study brings together nine different integrative loci in the genome of Synechocystis to demonstrate quantitative differences between target sites in the chromosome, the native plasmids, and a RSF1010-based replicative expression vector. To date, this is the most comprehensive comparison of alternative integrative sites in Synechocystis, and provides the first direct reference between expression efficiency and replicon gene dosage in the context. In the light of existing literature, the findings support the view that the small native plasmids can be notably more difficult to target than the chromosome or the megaplasmids, and that the RSF1010-derived vectors may be surprisingly well maintained under non-selective culture conditions in this cyanobacterial host. Altogether, the work broadens our views on genomic integration and the rational use of different integrative loci versus replicative plasmids, when aiming at expressing heterologous genes in Synechocystis. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01622-2.
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Affiliation(s)
- Csaba Nagy
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Kati Thiel
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Edita Mulaku
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Henna Mustila
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Paula Tamagnini
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Edifício FC4, 4169-007, Porto, Portugal
| | - Eva-Mari Aro
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Catarina C Pacheco
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Pauli Kallio
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland.
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Norena-Caro DA, Zuniga C, Pete AJ, Saemundsson SA, Donaldson MR, Adams AJ, Dooley KM, Zengler K, Benton MG. Analysis of the cyanobacterial amino acid metabolism with a precise genome-scale metabolic reconstruction of Anabaena sp. UTEX 2576. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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35
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Figueiredo SAC, Preto M, Moreira G, Martins TP, Abt K, Melo A, Vasconcelos VM, Leão PN. Discovery of Cyanobacterial Natural Products Containing Fatty Acid Residues**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sandra A. C. Figueiredo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR) University of Porto Avenida General Norton de Matos, s/n 4450-208 Matosinhos Portugal
| | - Marco Preto
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR) University of Porto Avenida General Norton de Matos, s/n 4450-208 Matosinhos Portugal
| | - Gabriela Moreira
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR) University of Porto Avenida General Norton de Matos, s/n 4450-208 Matosinhos Portugal
| | - Teresa P. Martins
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR) University of Porto Avenida General Norton de Matos, s/n 4450-208 Matosinhos Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS) University of Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
| | - Kathleen Abt
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR) University of Porto Avenida General Norton de Matos, s/n 4450-208 Matosinhos Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS) University of Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
| | - André Melo
- LAQV@REQUIMTE/Department of Chemistry and Biochemistry Faculty of Sciences University of Porto Rua do Campo Alegre 4169-007 Porto Portugal
| | - Vitor M. Vasconcelos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR) University of Porto Avenida General Norton de Matos, s/n 4450-208 Matosinhos Portugal
- Department of Biology Faculty of Sciences University of Porto Rua do Campo Alegre 4169-007 Porto Portugal
| | - Pedro N. Leão
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR) University of Porto Avenida General Norton de Matos, s/n 4450-208 Matosinhos Portugal
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36
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Figueiredo SAC, Preto M, Moreira G, Martins TP, Abt K, Melo A, Vasconcelos VM, Leão PN. Discovery of Cyanobacterial Natural Products Containing Fatty Acid Residues*. Angew Chem Int Ed Engl 2021; 60:10064-10072. [PMID: 33599093 PMCID: PMC8252387 DOI: 10.1002/anie.202015105] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Indexed: 12/16/2022]
Abstract
In recent years, extensive sequencing and annotation of bacterial genomes has revealed an unexpectedly large number of secondary metabolite biosynthetic gene clusters whose products are yet to be discovered. For example, cyanobacterial genomes contain a variety of gene clusters that likely incorporate fatty acid derived moieties, but for most cases we lack the knowledge and tools to effectively predict or detect the encoded natural products. Here, we exploit the apparent absence of a functional β-oxidation pathway in cyanobacteria to achieve efficient stable-isotope-labeling of their fatty acid derived lipidome. We show that supplementation of cyanobacterial cultures with deuterated fatty acids can be used to easily detect natural product signatures in individual strains. The utility of this strategy is demonstrated in two cultured cyanobacteria by uncovering analogues of the multidrug-resistance reverting hapalosin, and novel, cytotoxic, lactylate-nocuolin A hybrids-the nocuolactylates.
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Affiliation(s)
- Sandra A. C. Figueiredo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR)University of PortoAvenida General Norton de Matos, s/n4450-208MatosinhosPortugal
| | - Marco Preto
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR)University of PortoAvenida General Norton de Matos, s/n4450-208MatosinhosPortugal
| | - Gabriela Moreira
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR)University of PortoAvenida General Norton de Matos, s/n4450-208MatosinhosPortugal
| | - Teresa P. Martins
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR)University of PortoAvenida General Norton de Matos, s/n4450-208MatosinhosPortugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS)University of PortoRua de Jorge Viterbo Ferreira, 2284050-313PortoPortugal
| | - Kathleen Abt
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR)University of PortoAvenida General Norton de Matos, s/n4450-208MatosinhosPortugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS)University of PortoRua de Jorge Viterbo Ferreira, 2284050-313PortoPortugal
| | - André Melo
- LAQV@REQUIMTE/Department of Chemistry and BiochemistryFaculty of SciencesUniversity of PortoRua do Campo Alegre4169-007PortoPortugal
| | - Vitor M. Vasconcelos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR)University of PortoAvenida General Norton de Matos, s/n4450-208MatosinhosPortugal
- Department of BiologyFaculty of SciencesUniversity of PortoRua do Campo Alegre4169-007PortoPortugal
| | - Pedro N. Leão
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR)University of PortoAvenida General Norton de Matos, s/n4450-208MatosinhosPortugal
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Genetic, Genomics, and Responses to Stresses in Cyanobacteria: Biotechnological Implications. Genes (Basel) 2021; 12:genes12040500. [PMID: 33805386 PMCID: PMC8066212 DOI: 10.3390/genes12040500] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/25/2021] [Accepted: 03/25/2021] [Indexed: 02/07/2023] Open
Abstract
Cyanobacteria are widely-diverse, environmentally crucial photosynthetic prokaryotes of great interests for basic and applied science. Work to date has focused mostly on the three non-nitrogen fixing unicellular species Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002, which have been selected for their genetic and physiological interests summarized in this review. Extensive "omics" data sets have been generated, and genome-scale models (GSM) have been developed for the rational engineering of these cyanobacteria for biotechnological purposes. We presently discuss what should be done to improve our understanding of the genotype-phenotype relationships of these models and generate robust and predictive models of their metabolism. Furthermore, we also emphasize that because Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002 represent only a limited part of the wide biodiversity of cyanobacteria, other species distantly related to these three models, should be studied. Finally, we highlight the need to strengthen the communication between academic researchers, who know well cyanobacteria and can engineer them for biotechnological purposes, but have a limited access to large photobioreactors, and industrial partners who attempt to use natural or engineered cyanobacteria to produce interesting chemicals at reasonable costs, but may lack knowledge on cyanobacterial physiology and metabolism.
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38
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Lumian JE, Jungblut AD, Dillion ML, Hawes I, Doran PT, Mackey TJ, Dick GJ, Grettenberger CL, Sumner DY. Metabolic Capacity of the Antarctic Cyanobacterium Phormidium pseudopriestleyi That Sustains Oxygenic Photosynthesis in the Presence of Hydrogen Sulfide. Genes (Basel) 2021; 12:genes12030426. [PMID: 33809699 PMCID: PMC8002359 DOI: 10.3390/genes12030426] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/05/2021] [Accepted: 03/12/2021] [Indexed: 01/11/2023] Open
Abstract
Sulfide inhibits oxygenic photosynthesis by blocking electron transfer between H2O and the oxygen-evolving complex in the D1 protein of Photosystem II. The ability of cyanobacteria to counter this effect has implications for understanding the productivity of benthic microbial mats in sulfidic environments throughout Earth history. In Lake Fryxell, Antarctica, the benthic, filamentous cyanobacterium Phormidium pseudopriestleyi creates a 1–2 mm thick layer of 50 µmol L−1 O2 in otherwise sulfidic water, demonstrating that it sustains oxygenic photosynthesis in the presence of sulfide. A metagenome-assembled genome of P. pseudopriestleyi indicates a genetic capacity for oxygenic photosynthesis, including multiple copies of psbA (encoding the D1 protein of Photosystem II), and anoxygenic photosynthesis with a copy of sqr (encoding the sulfide quinone reductase protein that oxidizes sulfide). The genomic content of P. pseudopriestleyi is consistent with sulfide tolerance mechanisms including increasing psbA expression or directly oxidizing sulfide with sulfide quinone reductase. However, the ability of the organism to reduce Photosystem I via sulfide quinone reductase while Photosystem II is sulfide-inhibited, thereby performing anoxygenic photosynthesis in the presence of sulfide, has yet to be demonstrated.
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Affiliation(s)
- Jessica E. Lumian
- Microbiology Graduate Group, University of California, Davis, CA 95616, USA;
| | - Anne D. Jungblut
- Life Sciences Department, The Natural History Museum, London SW7 5BD, UK;
| | - Megan L. Dillion
- Genomics and Bioinformatics, Novozymes, Inc., Davis, CA 95616, USA;
| | - Ian Hawes
- Coastal Marine Field Station, University of Waikato, Tauranga 3110, New Zealand;
| | - Peter T. Doran
- Geology and Geophysics, Louisiana State University, Baton Rouge, LA 70803, USA;
| | - Tyler J. Mackey
- Department of Earth and Planetary Sciences, University of New Mexico, Albuquerque, NM 87131, USA;
| | - Gregory J. Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, USA;
| | | | - Dawn Y. Sumner
- Department of Earth and Planetary Sciences, University of California, Davis, CA 95616, USA;
- Correspondence: ; Tel.: +1-530-752-5353
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Jodlbauer J, Rohr T, Spadiut O, Mihovilovic MD, Rudroff F. Biocatalysis in Green and Blue: Cyanobacteria. Trends Biotechnol 2021; 39:875-889. [PMID: 33468423 DOI: 10.1016/j.tibtech.2020.12.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 12/17/2022]
Abstract
Recently, several studies have proven the potential of cyanobacteria as whole-cell biocatalysts for biotransformation. Compared to heterotrophic hosts, cyanobacteria show unique advantages thanks to their photoautotrophic metabolism. Their ability to use light as energy and CO2 as carbon source promises a truly sustainable production platform. Their photoautotrophic metabolism offers an encouraging source of reducing power, which makes them attractive for redox-based biotechnological purposes. To exploit the full potential of these whole-cell biocatalysts, cyanobacterial cells must be considered in their entirety. With this emphasis, this review summarizes the latest developments in cyanobacteria research with a strong focus on the benefits associated with their unique metabolism. Remaining bottlenecks and recent strategies to overcome them are evaluated for their potential in future applications.
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Affiliation(s)
- Julia Jodlbauer
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9/OC-163, 1060 Vienna, Austria
| | - Thomas Rohr
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9/OC-163, 1060 Vienna, Austria
| | - Oliver Spadiut
- Institute of Chemical Engineering, research area Biochemical Engineering, TU Wien, Gumpendorfer Strasse 1a, 1060 Vienna, Austria
| | - Marko D Mihovilovic
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9/OC-163, 1060 Vienna, Austria
| | - Florian Rudroff
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9/OC-163, 1060 Vienna, Austria.
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40
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Characterization of Light-Enhanced Respiration in Cyanobacteria. Int J Mol Sci 2020; 22:ijms22010342. [PMID: 33396191 PMCID: PMC7796093 DOI: 10.3390/ijms22010342] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/27/2020] [Accepted: 12/28/2020] [Indexed: 01/12/2023] Open
Abstract
In eukaryotic algae, respiratory O2 uptake is enhanced after illumination, which is called light-enhanced respiration (LER). It is likely stimulated by an increase in respiratory substrates produced during photosynthetic CO2 assimilation and function in keeping the metabolic and redox homeostasis in the light in eukaryotic cells, based on the interactions among the cytosol, chloroplasts, and mitochondria. Here, we first characterize LER in photosynthetic prokaryote cyanobacteria, in which respiration and photosynthesis share their metabolisms and electron transport chains in one cell. From the physiological analysis, the cyanobacterium Synechocystis sp. PCC 6803 performs LER, similar to eukaryotic algae, which shows a capacity comparable to the net photosynthetic O2 evolution rate. Although the respiratory and photosynthetic electron transports share the interchain, LER was uncoupled from photosynthetic electron transport. Mutant analyses demonstrated that LER is motivated by the substrates directly provided by photosynthetic CO2 assimilation, but not by glycogen. Further, the light-dependent activation of LER was observed even with exogenously added glucose, implying a regulatory mechanism for LER in addition to the substrate amounts. Finally, we discuss the physiological significance of the large capacity of LER in cyanobacteria and eukaryotic algae compared to those in plants that normally show less LER.
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41
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Revisiting nitrogen utilization in algae: A review on the process of regulation and assimilation. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.biteb.2020.100584] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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42
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Srivastava A, Varshney RK, Shukla P. Sigma Factor Modulation for Cyanobacterial Metabolic Engineering. Trends Microbiol 2020; 29:266-277. [PMID: 33229204 DOI: 10.1016/j.tim.2020.10.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 10/25/2020] [Accepted: 10/26/2020] [Indexed: 11/18/2022]
Abstract
Sigma (σ) factors are key regulatory proteins that control the transcription initiation in prokaryotes. In response to environmental or developmental cues, σ factors initiate the transcription of necessary genes responsible for maintaining a life-sustaining metabolic balance. Due to the significant role of σ factors in bacterial metabolism, their rational engineering for commercial metabolite production in photoautotrophic, cyanobacterial cells is a desirable venture. As cyanobacterial genomes typically encode multiple σ factors, effective execution of metabolic engineering efforts largely relies on uncovering the complicated gene regulatory network and further characterization of the members of σ factor regulatory circuits. This review outlines the prospects of σ factor in metabolic engineering of cyanobacteria, summarizes the challenges in the path towards an efficient strain construction and highlights the genomic context of putative regulators of cyanobacterial σ factors.
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Affiliation(s)
- Amit Srivastava
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak-124001, Haryana, India.
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Vijayakumar S, Rahman PKSM, Angione C. A Hybrid Flux Balance Analysis and Machine Learning Pipeline Elucidates Metabolic Adaptation in Cyanobacteria. iScience 2020; 23:101818. [PMID: 33354660 PMCID: PMC7744713 DOI: 10.1016/j.isci.2020.101818] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/23/2020] [Accepted: 11/13/2020] [Indexed: 01/20/2023] Open
Abstract
Machine learning has recently emerged as a promising tool for inferring multi-omic relationships in biological systems. At the same time, genome-scale metabolic models (GSMMs) can be integrated with such multi-omic data to refine phenotypic predictions. In this work, we use a multi-omic machine learning pipeline to analyze a GSMM of Synechococcus sp. PCC 7002, a cyanobacterium with large potential to produce renewable biofuels. We use regularized flux balance analysis to observe flux response between conditions across photosynthesis and energy metabolism. We then incorporate principal-component analysis, k-means clustering, and LASSO regularization to reduce dimensionality and extract key cross-omic features. Our results suggest that combining metabolic modeling with machine learning elucidates mechanisms used by cyanobacteria to cope with fluctuations in light intensity and salinity that cannot be detected using transcriptomics alone. Furthermore, GSMMs introduce critical mechanistic details that improve the performance of omic-based machine learning methods. A pipeline for metabolic modeling in Synechococcus sp. PCC 7002 is presented Metabolic fluxes display clear differences in pathway activity across conditions Omic-informed GSMMs provide critical mechanistic details within machine learning Combining GSMM and machine learning improves methods based on transcriptomics alone
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Affiliation(s)
- Supreeta Vijayakumar
- Department of Computer Science and Information Systems, Teesside University, Middlesbrough, North Yorkshire TS1 3BX, UK
| | - Pattanathu K S M Rahman
- Centre for Enzyme Innovation, Institute of Biological and Biomedical Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth, Hampshire PO1 2UP, UK.,Tara Biologics, Woking, Surrey GU21 6BP, UK
| | - Claudio Angione
- Department of Computer Science and Information Systems, Teesside University, Middlesbrough, North Yorkshire TS1 3BX, UK.,Centre for Digital Innovation, Teesside University, Middlesbrough TS1 3BX, UK.,Healthcare Innovation Centre, Teesside University, Middlesbrough TS1 3BX, UK
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Modifying the Cyanobacterial Metabolism as a Key to Efficient Biopolymer Production in Photosynthetic Microorganisms. Int J Mol Sci 2020; 21:ijms21197204. [PMID: 33003478 PMCID: PMC7582838 DOI: 10.3390/ijms21197204] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 09/26/2020] [Accepted: 09/28/2020] [Indexed: 12/22/2022] Open
Abstract
Cyanobacteria are photoautotrophic bacteria commonly found in the natural environment. Due to the ecological benefits associated with the assimilation of carbon dioxide from the atmosphere and utilization of light energy, they are attractive hosts in a growing number of biotechnological processes. Biopolymer production is arguably one of the most critical areas where the transition from fossil-derived chemistry to renewable chemistry is needed. Cyanobacteria can produce several polymeric compounds with high applicability such as glycogen, polyhydroxyalkanoates, or extracellular polymeric substances. These important biopolymers are synthesized using precursors derived from central carbon metabolism, including the tricarboxylic acid cycle. Due to their unique metabolic properties, i.e., light harvesting and carbon fixation, the molecular and genetic aspects of polymer biosynthesis and their relationship with central carbon metabolism are somehow different from those found in heterotrophic microorganisms. A greater understanding of the processes involved in cyanobacterial metabolism is still required to produce these molecules more efficiently. This review presents the current state of the art in the engineering of cyanobacterial metabolism for the efficient production of these biopolymers.
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