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Lucius S, Hagemann M. The primary carbon metabolism in cyanobacteria and its regulation. FRONTIERS IN PLANT SCIENCE 2024; 15:1417680. [PMID: 39036361 PMCID: PMC11257934 DOI: 10.3389/fpls.2024.1417680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 06/24/2024] [Indexed: 07/23/2024]
Abstract
Cyanobacteria are the only prokaryotes capable of performing oxygenic photosynthesis. Many cyanobacterial strains can live in different trophic modes, ranging from photoautotrophic and heterotrophic to mixotrophic growth. However, the regulatory mechanisms allowing a flexible switch between these lifestyles are poorly understood. As anabolic fixation of CO2 in the Calvin-Benson-Bassham (CBB) cycle and catabolic sugar-degradation pathways share intermediates and enzymatic capacity, a tight regulatory network is required to enable simultaneous opposed metabolic fluxes. The Entner-Doudoroff (ED) pathway was recently predicted as one glycolytic route, which cooperates with other pathways in glycogen breakdown. Despite low carbon flux through the ED pathway, metabolite analyses of mutants deficient in the ED pathway revealed a distinct phenotype pointing at a strong regulatory impact of this route. The small Cp12 protein downregulates the CBB cycle in darkness by inhibiting phosphoribulokinase and glyceraldehyde 3-phosphate dehydrogenase. New results of metabolomic and redox level analyses on strains with Cp12 variants extend the known role of Cp12 regulation towards the acclimation to external glucose supply under diurnal conditions as well as to fluctuations in CO2 levels in the light. Moreover, carbon and nitrogen metabolism are closely linked to maintain an essential C/N homeostasis. The small protein PirC was shown to be an important regulator of phosphoglycerate mutase, which identified this enzyme as central branching point for carbon allocation from CBB cycle towards lower glycolysis. Altered metabolite levels in the mutant ΔpirC during nitrogen starvation experiments confirm this regulatory mechanism. The elucidation of novel mechanisms regulating carbon allocation at crucial metabolic branching points could identify ways for targeted redirection of carbon flow towards desired compounds, and thus help to further establish cyanobacteria as green cell factories for biotechnological applications with concurrent utilization of sunlight and CO2.
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Affiliation(s)
| | - Martin Hagemann
- Department Plant Physiology, University of Rostock, Rostock, Germany
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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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Kukil K, Lindberg P. Metabolic engineering of Synechocystis sp. PCC 6803 for the improved production of phenylpropanoids. Microb Cell Fact 2024; 23:57. [PMID: 38369470 PMCID: PMC10875765 DOI: 10.1186/s12934-024-02330-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/09/2024] [Indexed: 02/20/2024] Open
Abstract
BACKGROUND Phenylpropanoids are a large group of plant secondary metabolites with various biological functions, derived from aromatic amino acids. Cyanobacteria are promising host organisms for sustainable production of plant phenylpropanoids. We have previously engineered Synechocystis sp. PCC 6803 to produce trans-cinnamic acid (tCA) and p-coumaric acid (pCou), the first intermediates of phenylpropanoid pathway, by overexpression of phenylalanine- and tyrosine ammonia lyases. In this study, we aimed to enhance the production of the target compounds tCA and pCou in Synechocystis. RESULTS We eliminated the 4-hydroxyphenylpyruvate dioxygenase (HPPD) activity, which is a competing pathway consuming tyrosine and, possibly, phenylalanine for tocopherol synthesis. Moreover, several genes of the terminal steps of the shikimate pathway were overexpressed alone or in operons, such as aromatic transaminases, feedback insensitive cyclohexadienyl dehydrogenase (TyrC) from Zymomonas mobilis and the chorismate mutase (CM) domain of the fused chorismate mutase/prephenate dehydratase enzyme from Escherichia coli. The obtained engineered strains demonstrated nearly 1.5 times enhanced tCA and pCou production when HPPD was knocked out compared to the parental production strains, accumulating 138 ± 3.5 mg L-1 of tCA and 72.3 ± 10.3 mg L-1 of pCou after seven days of photoautotrophic growth. However, there was no further improvement when any of the pathway genes were overexpressed. Finally, we used previously obtained AtPRM8 and TsPRM8 Synechocystis strains with deregulated shikimate pathway as a background for the overexpression of synthetic constructs with ppd knockout. CONCLUSIONS HPPD elimination enhances the tCA and pCou productivity to a similar extent. The use of PRM8 based strains as a background for overexpression of synthetic constructs, however, did not promote tCA and pCou titers, which indicates a tight regulation of the terminal steps of phenylalanine and tyrosine synthesis. This work contributes to establishing cyanobacteria as hosts for phenylpropanoid production.
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Affiliation(s)
- Kateryna Kukil
- Microbial Chemistry, Department of Chemistry - Ångström, Uppsala University, Box 523, SE 751 20, Uppsala, Sweden
| | - Pia Lindberg
- Microbial Chemistry, Department of Chemistry - Ångström, Uppsala University, Box 523, SE 751 20, Uppsala, Sweden.
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Cui J, Chen R, Sun H, Xue Y, Diao Z, Song J, Wang X, Zhang J, Wang C, Ma B, Xu J, Luan G, Lu X. Culture-free identification of fast-growing cyanobacteria cells by Raman-activated gravity-driven encapsulation and sequencing. Synth Syst Biotechnol 2023; 8:708-715. [PMID: 38053584 PMCID: PMC10693988 DOI: 10.1016/j.synbio.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/03/2023] [Accepted: 11/05/2023] [Indexed: 12/07/2023] Open
Abstract
By directly converting solar energy and carbon dioxide into biobased products, cyanobacteria are promising chassis for photosynthetic biosynthesis. To make cyanobacterial photosynthetic biosynthesis technology economically feasible on industrial scales, exploring and engineering cyanobacterial chassis and cell factories with fast growth rates and carbon fixation activities facing environmental stresses are of great significance. To simplify and accelerate the screening for fast-growing cyanobacteria strains, a method called Individual Cyanobacteria Vitality Tests and Screening (iCyanVS) was established. We show that the 13C incorporation ratio of carotenoids can be used to measure differences in cell growth and carbon fixation rates in individual cyanobacterial cells of distinct genotypes that differ in growth rates in bulk cultivations, thus greatly accelerating the process screening for fastest-growing cells. The feasibility of this approach is further demonstrated by phenotypically and then genotypically identifying individual cyanobacterial cells with higher salt tolerance from an artificial mutant library via Raman-activated gravity-driven encapsulation and sequencing. Therefore, this method should find broad applications in growth rate or carbon intake rate based screening of cyanobacteria and other photosynthetic cell factories.
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Affiliation(s)
- Jinyu Cui
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Rongze Chen
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Huili Sun
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yingyi Xue
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Zhidian Diao
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Jingyun Song
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Xiaohang Wang
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Jia Zhang
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Chen Wang
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Bo Ma
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Jian Xu
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Guodong Luan
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Dalian National Laboratory for Clean Energy, Dalian, 116023, China
| | - Xuefeng Lu
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Dalian National Laboratory for Clean Energy, Dalian, 116023, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Xu Z. A Specific Protective Mechanism Against Chloroplast Photo-Reactive Oxygen Species in Phosphate-Starved Rice Plants. Adv Biol (Weinh) 2023; 7:e2300106. [PMID: 37409401 DOI: 10.1002/adbi.202300106] [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: 03/10/2023] [Revised: 05/22/2023] [Indexed: 07/07/2023]
Abstract
Phosphorus (Pi) starvation prevents a good match between light energy absorption and photosynthetic carbon metabolism, generating photo-reactive oxygen species (photo-ROS) in chloroplasts. Plants have evolved to withstand photo-oxidative stress, but the key regulatory mechanism underlying it remains unclear. In rice (Oryza sativa), DEEP GREEN PANICLE1 (DGP1) is robustly up-regulated in response to Pi deficiency. DGP1 decreases the DNA-binding capacities of the transcriptional activators GLK1/2 on the photosynthetic genes involved in chlorophyll biosynthesis, light harvesting, and electron transport. This Pi-starvation-induced mechanism dampens both electron transport rates through photosystem I and II (ETRI and ETRII) and thus mitigates the electron-excessive stress in mesophyll cells. Meanwhile, DGP1 hijacks glycolytic enzymes GAPC1/2/3, redirecting glucose metabolism toward the pentose phosphate pathway with superfluous NADPH production. Phenotypically, light irradiation induces O2 - production in Pi-starved WT leaves but is observably accelerated in dgp1 mutant and impaired in GAPCsRNAi and glk1glk2 lines. Interestingly, overexpressed DGP1 in rice caused hyposensitivity to ROS-inducers (catechin and methyl viologen), but the dgp1 mutant shows a similar inhibitory phenotype with the WT seedlings. Overall, the DGP1 gene serves as a specific antagonizer against photo-ROS in Pi-starved rice plants, which coordinates light-absorbing and anti-oxidative systems by orchestrating transcriptional and metabolic regulations, respectively.
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Affiliation(s)
- Zhan Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangzhou City Academy of Agricultural Sciences, Key Laboratory of Biology, Genetics and Breeding, Guangzhou, 510000, China
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Wang B, Zuniga C, Guarnieri MT, Zengler K, Betenbaugh M, Young JD. Metabolic engineering of Synechococcus elongatus 7942 for enhanced sucrose biosynthesis. Metab Eng 2023; 80:12-24. [PMID: 37678664 DOI: 10.1016/j.ymben.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/28/2023] [Accepted: 09/03/2023] [Indexed: 09/09/2023]
Abstract
The capability of cyanobacteria to produce sucrose from CO2 and light has a remarkable societal and biotechnological impact since sucrose can serve as a carbon and energy source for a variety of heterotrophic organisms and can be converted into value-added products. However, most metabolic engineering efforts have focused on understanding local pathway alterations that drive sucrose biosynthesis and secretion in cyanobacteria rather than analyzing the global flux re-routing that occurs following induction of sucrose production by salt stress. Here, we investigated global metabolic flux alterations in a sucrose-secreting (cscB-overexpressing) strain relative to its wild-type Synechococcus elongatus 7942 parental strain. We used targeted metabolomics, 13C metabolic flux analysis (MFA), and genome-scale modeling (GSM) as complementary approaches to elucidate differences in cellular resource allocation by quantifying metabolic profiles of three cyanobacterial cultures - wild-type S. elongatus 7942 without salt stress (WT), wild-type with salt stress (WT/NaCl), and the cscB-overexpressing strain with salt stress (cscB/NaCl) - all under photoautotrophic conditions. We quantified the substantial rewiring of metabolic fluxes in WT/NaCl and cscB/NaCl cultures relative to WT and identified a metabolic bottleneck limiting carbon fixation and sucrose biosynthesis. This bottleneck was subsequently mitigated through heterologous overexpression of glyceraldehyde-3-phosphate dehydrogenase in an engineered sucrose-secreting strain. Our study also demonstrates that combining 13C-MFA and GSM is a useful strategy to both extend the coverage of MFA beyond central metabolism and to improve the accuracy of flux predictions provided by GSM.
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Affiliation(s)
- Bo Wang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - Cristal Zuniga
- Department of Pediatrics, University of California, San Diego, CA, 92093, USA; Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Michael T Guarnieri
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, CA, 92093, USA; Department of Bioengineering, University of California, San Diego, CA, 92093, USA; Center for Microbiome Innovation, University of California, San Diego, CA, 92093, USA
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37235, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37235, USA.
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7
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Liang J, Chen Z, Yin P, Hu H, Cheng W, Shang J, Yang Y, Yuan Z, Pan J, Yin Y, Li W, Chen X, Gao X, Qiu B, Wang B. Efficient Semi-Artificial Photosynthesis of Ethylene by a Self-Assembled InP-Cyanobacterial Biohybrid System. CHEMSUSCHEM 2023; 16:e202300773. [PMID: 37381086 DOI: 10.1002/cssc.202300773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 06/19/2023] [Accepted: 06/27/2023] [Indexed: 06/30/2023]
Abstract
Biomanufacturing of ethylene is particularly important for modern society. Cyanobacterial cells are able to photosynthesize various valuable chemicals. A promising platform for next-generation biomanufacturing, the semiconductor-cyanobacterial hybrid systems are capable of enhancing the solar-to-chemical conversion efficiency. Herein, the native ethylene-producing capability of a filamentous cyanobacterium Nostoc sphaeroides is confirmed experimentally. The self-assembly characteristic of N. sphaeroides is exploited to facilitate its interaction with InP nanomaterial, and the resulting biohybrid system gave rise to further elevated photosynthetic ethylene production. Based on chlorophyll fluorescence measurement and metabolic analysis, the InP nanomaterial-augmented photosystem I activity and enhanced ethylene production metabolism of biohybrid cells are confirmed, the mechanism underlying the material-cell energy transduction as well as nanomaterial-modulated photosynthetic light and dark reactions are established. This work not only demonstrates the potential application of semiconductor-N. sphaeroides biohybrid system as a good platform for sustainable ethylene production but also provides an important reference for future studies to construct and optimize nano-cell biohybrid systems for efficient solar-driven valuable chemical production.
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Affiliation(s)
- Jun Liang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
| | - Zhen Chen
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, Hubei, 435002, P. R. China
| | - Panqing Yin
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
| | - Haitao Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
| | - Wenbo Cheng
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, P. R. China
| | - Jinlong Shang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, P. R. China
| | - Yiwen Yang
- College of Pharmacy and Life Sciences, Jiujiang University, Jiujiang, Jiangxi, 332000, P.R. China
| | - Zuwen Yuan
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, Hubei, 435002, P. R. China
| | - Jinlong Pan
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, Hubei, 435002, P. R. China
| | - Yongqi Yin
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, Hubei, 435002, P. R. China
| | - Weizhi Li
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, Hubei, 435002, P. R. China
| | - Xiongwen Chen
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, Hubei, 435002, P. R. China
| | - Xiang Gao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
| | - Baosheng Qiu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, P. R. China
| | - Bo Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
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8
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Wu C, Guarnieri M, Xiong W. FreeFlux: A Python Package for Time-Efficient Isotopically Nonstationary Metabolic Flux Analysis. ACS Synth Biol 2023; 12:2707-2714. [PMID: 37561998 PMCID: PMC10510750 DOI: 10.1021/acssynbio.3c00265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Indexed: 08/12/2023]
Abstract
13C metabolic flux analysis is a powerful tool for metabolism characterization in metabolic engineering and synthetic biology. However, the widespread adoption of this tool is hindered by limited software availability and computational efficiency. Currently, the most widely accepted 13C-flux tools, such as INCA and 13CFLUX2, are developed in a closed-source environment. While several open-source packages or software are available, they are either computationally inefficient or only suitable for flux estimation at isotopic steady state. To address the need for a time-efficient computational tool for the more complicated flux analysis at an isotopically nonstationary state, especially for understanding the single-carbon substrate metabolism, we present FreeFlux. FreeFlux is an open-source Python package that performs labeling pattern simulation and flux analysis at both isotopic steady state and transient state, enabling a more comprehensive analysis of cellular metabolism. FreeFlux provides a set of interfaces to manipulate the objects abstracted from a labeling experiment and computational process, making it easy to integrate into other programs or pipelines. The flux estimation by FreeFlux is fast and reliable, and its validity has been confirmed by comparison with results from other computational tools using both synthetic and experimental data. FreeFlux is freely available at https://github.com/Chaowu88/freeflux with a detailed online tutorial and documentation provided at https://freeflux.readthedocs.io/en/latest/index.html.
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Affiliation(s)
- Chao Wu
- Biosciences Center, National
Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Michael Guarnieri
- Biosciences Center, National
Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Wei Xiong
- Biosciences Center, National
Renewable Energy Laboratory, Golden, Colorado 80401, United States
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Huang Y, Wan X, Zhao Z, Liu H, Wen Y, Wu W, Ge X, Zhao C. Metabolomic analysis and pathway profiling of paramylon production in Euglena gracilis grown on different carbon sources. Int J Biol Macromol 2023; 246:125661. [PMID: 37399871 DOI: 10.1016/j.ijbiomac.2023.125661] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 05/18/2023] [Accepted: 06/30/2023] [Indexed: 07/05/2023]
Abstract
Paramylon (β-1,3-glucan) produced by Euglena gracilis displays antioxidant, antitumor, and hypolipidaemic functions. The biological properties of paramylon production by E. gracilis can be understood by elucidating the metabolic changes within the algae. In this study, the carbon sources in AF-6 medium were replaced with glucose, sodium acetate, glycerol, or ethanol, and the paramylon yield was measured. Adding 0.1260 g/L glucose to the culture medium resulted in the highest paramylon yield of 70.48 %. The changes in metabolic pathways in E. gracilis grown on glucose were assessed via non-targeted metabolomics analysis using ultra-high-performance liquid chromatography coupled to high-resolution quadrupole-Orbitrap mass spectrometry. We found that glucose, as a carbon source, regulated some differentially expressed metabolites, including l-glutamic acid, γ-aminobutyric acid (GABA), and l-aspartic acid. Pathway analysis using the Kyoto Encyclopedia of Genes and Genomes further showed that glucose regulated the carbon and nitrogen balance through the GABA shunt, which enhanced photosynthesis, regulated the flux of carbon and nitrogen into the tricarboxylic acid cycle, promoted glucose uptake, and increased the accumulation of paramylon. This study provides new insights into E. gracilis metabolism during paramylon synthesis.
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Affiliation(s)
- Yajun Huang
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuzhi Wan
- Department of Food Science and Nutrition, Zhejiang Key Laboratory for Agro-Food Processing, Fuli Institute of Food Science, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Zexu Zhao
- College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hanqi Liu
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuxi Wen
- College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Universidade de Vigo, Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Sciences, 32004 Ourense, Spain
| | - Weihao Wu
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaodong Ge
- College of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng 224051, China
| | - Chao Zhao
- College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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10
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Bai F, Gao G, Li T, Liu J, Li L, Jia Y, Song L. Integrated physiological and metabolomic analysis reveals new insights into toxicity pathways of paraquat to Microcystis aeruginosa. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 259:106521. [PMID: 37061422 DOI: 10.1016/j.aquatox.2023.106521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/04/2023] [Accepted: 04/02/2023] [Indexed: 05/15/2023]
Abstract
Chemical pollutants, such as herbicides, released into the aquatic environment adversely affect the phytoplankton community structure. While majority of herbicides are specifically designed to target photosynthetic processes, they also can be toxic to phytoplankton; however, despite the photosynthetic toxicity, some herbicides can target multiple physiological processes. Therefore, a full picture of toxicity pathway of herbicide to phytoplankton is necessary. In the present study, the cyanobacterium Microcystis aeruginosa was exposed to two levels (17 μg L-1 (EC10) and 65 μg L-1 (EC50)) of paraquat for 72 h. The physiological and metabolic responses were analyzed to elucidate the toxicity pathway and establish the adverse outcome pathway of paraquat to M. aeruginosa. The results revealed that enhanced glycolysis (upregulation of pyruvic acid level) and tricarboxylic acid cycle (upregulation of the levels of malic acid, isocitric acid and citric acid) exposed to EC10 level of paraquat, which probably acted as a temporary strategy to maintain a healthy energy status in M. aeruginosa cells. Meanwhile, the expressions of glutathione and benzoic acid were enhanced to scavenge the excessive reactive oxygen species (ROS). Additionally, the accumulation of pigments (chlorophyll a and carotenoid) might play a supplementary role in the acclimation to EC10 level paraquat treatment. In cells exposed to paraquat by EC50 level, the levels of SOD, CAT, glutathione and benzoic acid increased significantly; however, the ROS exceeded the tolerance level of antioxidant system in M. aeruginosa. The adverse effects were revealed by inhibition of chlorophyll a fluorescence, the decreases in several carbohydrates (e.g., glucose 1-phosphate, fructose and galactose) and total protein content. Consequently, paraquat-induced oxidative stress caused the growth inhibition of M. aeruginosa. These findings provide new insights into the mode of action of paraquat in M. aeruginosa.
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Affiliation(s)
- Fang Bai
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Guangbin Gao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Tianli Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jin Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Lin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yunlu Jia
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Lirong Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
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11
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Xu Z, Zhang J, Wang X, Essemine J, Jin J, Qu M, Xiang Y, Chen W. Cold-induced inhibition of photosynthesis-related genes integrated by a TOP6 complex in rice mesophyll cells. Nucleic Acids Res 2023; 51:1823-1842. [PMID: 36660855 PMCID: PMC9976896 DOI: 10.1093/nar/gkac1275] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 12/18/2022] [Accepted: 12/25/2022] [Indexed: 01/21/2023] Open
Abstract
Photosynthesis is the most temperature-sensitive process in the plant kingdom, but how the photosynthetic pathway responds during low-temperature exposure remains unclear. Herein, cold stress (4°C) induced widespread damage in the form DNA double-stranded breaks (DSBs) in the mesophyll cells of rice (Oryza sativa), subsequently causing a global inhibition of photosynthetic carbon metabolism (PCM) gene expression. Topoisomerase genes TOP6A3 and TOP6B were induced at 4°C and their encoded proteins formed a complex in the nucleus. TOP6A3 directly interacted with KU70 to inhibit its binding to cold-induced DSBs, which was facilitated by TOP6B, finally blocking the loading of LIG4, a component of the classic non-homologous end joining (c-NHEJ) pathway. The repression of c-NHEJ repair imposed by cold extended DSB damage signaling, thus prolonging the inhibition of photosynthesis in leaves. Furthermore, the TOP6 complex negatively regulated 13 crucial PCM genes by directly binding to their proximal promoter regions. Phenotypically, TOP6A3 overexpression exacerbated the γ-irradiation-triggered suppression of PCM genes and led to the hypersensitivity of photosynthesis parameters to cold stress, dependent on the DSB signal transducer ATM. Globally, the TOP6 complex acts as a signal integrator to control PCM gene expression and synchronize cold-induced photosynthesis inhibition, which modulates carbon assimilation rates immediately in response to changes in ambient temperature.
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Affiliation(s)
- Zhan Xu
- Guangzhou City Academy of Agricultural Sciences, Key Laboratory of Biology, Genetics and Breeding, Pazhou Dadao Rd 17-19, Haizhu District, Guangzhou 510000, China
| | - Jianxiang Zhang
- Key Laboratory of Plant Functional Genomics of Ministry of Education/Jiangsu Key Laboratory of Crop Genetics, Yangzhou University, Yangzhou 225009, China
| | - Xu Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Jemaa Essemine
- Laboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jing Jin
- Laboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Mingnan Qu
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Yong Xiang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Weixiong Chen
- Guangzhou City Academy of Agricultural Sciences, Key Laboratory of Biology, Genetics and Breeding, Pazhou Dadao Rd 17-19, Haizhu District, Guangzhou 510000, China
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12
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Li P, Hu Z, Yin Q, Song C. Improving the growth of Spirulina in CO 2 absorption and microalgae conversion (CAMC) system through mixotrophic cultivation: Reveal of metabolomics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159920. [PMID: 36356767 DOI: 10.1016/j.scitotenv.2022.159920] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 10/07/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
Mixotrophic cultivation was proposed to enhance the biomass and carbon sequestration efficiency of Spirulina in CO2 absorption and microalgae conversion (CAMC) system, and the underlying metabolic mechanism was also explored. The result showed that mixotrophic enhanced the performance of CAMC system, the maximum biomass, total carbon conversion capacity and efficiency was obtained at 0.5 g/L acetate group, which was 60.47 %, 63.06 % and 59.77 % higher than control. Adding 0.5 g/L acetate enhanced the activities of Rubisco and Acetyl-CoA, arrived at 89.59 U/g and 5.16 nmol/g, respectively. Metabolomics analyses suggested that mixotrophic changed metabolic flux and affected intracellular composition. Mixotrophic up-regulated Calvin cycle, glycolysis, and tricarboxylic acid (TCA) cycle, induced more carbon fluxes into central carbon metabolism for the growth of Spirulina. These results suggested that mixotrophic could supply effective energy and carbon skeleton for rapid growth of Spirulina, and provided a theoretical basis for large-scale application of CAMC system.
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Affiliation(s)
- Pengcheng Li
- Tianjin Key Laboratory of Indoor Air Environmental Quality Control, School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, PR China
| | - Zhan Hu
- Tianjin Key Laboratory of Indoor Air Environmental Quality Control, School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, PR China
| | - Qingrong Yin
- Tianjin Key Laboratory of Indoor Air Environmental Quality Control, School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, PR China
| | - Chunfeng Song
- Tianjin Key Laboratory of Indoor Air Environmental Quality Control, School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, PR China.
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13
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Patel A, Tiwari S, Prasad SM. Modulation of salt stress in paddy field cyanobacteria with exogenous application of gibberellic acid: growth behavior and antioxidative status. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:51-68. [PMID: 36733835 PMCID: PMC9886751 DOI: 10.1007/s12298-022-01266-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 11/18/2022] [Accepted: 12/09/2022] [Indexed: 06/18/2023]
Abstract
The present study explores the possible function of gibberellic acid (GA: 20 µM) in reducing salt (NaCl) induced toxicity in two diazo-trophic cyanobacteria i.e. Nostoc muscorum and Phormidium foveolarum. The physiological and biochemical parameters viz. growth, photosynthetic pigments (chlorophyll a, carotenoids, and phycocyanin), photosynthetic and respiratory rates, oxidative stress biomarkers (superoxide radicle, hydrogen peroxide, and malondialdehyde contents) antioxidant activities (superoxide dismutase, peroxidase, catalase, and glutathione-S-transferase) and non-enzymatic antioxidants were studied under both the doses i.e. 40 mM (LC 10) and mM (LC 30) of NaCl. The growth, photosynthetic pigments and photosynthetic rate were found to be declined under concentration-dependent manner of NaCl. Contrastingly, the respiratory rate, oxidative stress biomarkers, and the activity of antioxidant enzymes i.e. superoxide dismutase (SOD), peroxidases (POD), catalase (CAT), and glutathione-S-transferase (GST) together with contents of non-enzymatic antioxidants (proline and cysteine) were found to increase in the test cyanobacteria. PSII photochemistry in both the cyanobacteria was negatively affected showing an inhibitory effect of NaCl on JIP parameters, while an enhancement effect was noticed in the values related to energy flux parameters. Further, the addition of GA to the growth medium caused an alleviating effect as it completely mitigated NaCl toxicity induced by a lower dose i.e. 40 mM of NaCl, while it partially alleviated the growth and photosynthetic parameters of 80 mM NaCl stressed cyanobacteria. Supplementation of GA significantly reduced the contents of oxidative stress tested cyanobacteria due to an improved antioxidant system (increased activities of enzymatic and non-enzymatic antioxidants) as evident from the biochemical analysis. In brief, our findings reflect the possible role of GA as a potential modulator of salt toxicity. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-022-01266-5.
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Affiliation(s)
- Anuradha Patel
- Ranjan Plant Physiology and Biochemistry Laboratory, Department of Botany, University of Allahabad, Prayagraj, 211002 India
- Department of Botany Dayalbagh Educational institute (Deemed University), Agra, 282005 India
| | - Sanjesh Tiwari
- Ranjan Plant Physiology and Biochemistry Laboratory, Department of Botany, University of Allahabad, Prayagraj, 211002 India
- Department of Botany, Ghatsila College, Jamshedpur, East Singhbhum, Jharkhand India
| | - Sheo Mohan Prasad
- Ranjan Plant Physiology and Biochemistry Laboratory, Department of Botany, University of Allahabad, Prayagraj, 211002 India
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Witthohn M, Strieth D, Kollmen J, Schwarz A, Ulber R, Muffler K. Process Technologies of Cyanobacteria. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2022. [PMID: 36571615 DOI: 10.1007/10_2022_214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Although the handling and exploitation of cyanobacteria is associated with some challenges, these phototrophic bacteria offer great opportunities for innovative biotechnological processes. This chapter covers versatile aspects of working with cyanobacteria, starting with up-to-date in silico and in vitro screening methods for bioactive substances. Subsequently, common conservation techniques and vitality/viability estimation methods are compared and supplemented by own data regarding the non-invasive vitality evaluation via pulse amplitude modulated fluorometry. Moreover, novel findings about the influence the state of the pre-cultures have on main cultures are presented. The following sub-chapters deal with different photobioreactor-designs, with special regard to biofilm photobioreactors, as well as with heterotrophic and mixotrophic cultivation modes. The latter topic provides information from literature on successfully enhanced cyanobacterial production processes, augmented by own data.
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Affiliation(s)
- Marco Witthohn
- Department of Life Sciences and Engineering, University of Applied Sciences Bingen, Bingen, Germany
| | - Dorina Strieth
- Chair of Bioprocess Engineering, Technical University of Kaiserslautern, Kaiserslautern, Germany
| | - Jonas Kollmen
- Chair of Bioprocess Engineering, Technical University of Kaiserslautern, Kaiserslautern, Germany
| | - Anna Schwarz
- Department of Life Sciences and Engineering, University of Applied Sciences Bingen, Bingen, Germany
| | - Roland Ulber
- Chair of Bioprocess Engineering, Technical University of Kaiserslautern, Kaiserslautern, Germany.
| | - Kai Muffler
- Department of Life Sciences and Engineering, University of Applied Sciences Bingen, Bingen, Germany
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15
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Kumar N, Kar S, Shukla P. Role of regulatory pathways and multi-omics approaches for carbon capture and mitigation in cyanobacteria. BIORESOURCE TECHNOLOGY 2022; 366:128104. [PMID: 36257524 DOI: 10.1016/j.biortech.2022.128104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Cyanobacteria are known for their metabolic potential and carbon capture and sequestration capabilities. These cyanobacteria are not only an effective source for carbon minimization and resource mobilization into value-added products for biotechnological gains. The present review focuses on the detailed description of carbon capture mechanisms exerted by the various cyanobacterial strains, the role of important regulatory pathways, and their subsequent genes responsible for such mechanisms. Moreover, this review will also describe effectual mechanisms of central carbon metabolism like isoprene synthesis, ethylene production, MEP pathway, and the role of Glyoxylate shunt in the carbon sequestration mechanisms. This review also describes some interesting facets of using carbon assimilation mechanisms for valuable bio-products. The role of regulatory pathways and multi-omics approaches in cyanobacteria will not only be crucial towards improving carbon utilization but also will give new insights into utilizing cyanobacterial bioresource for carbon neutrality.
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Affiliation(s)
- Niwas Kumar
- Society for Research and Initiatives for Sustainable Technologies and Institutions, Navrangapura, Ahmedabad 380009, India
| | - Srabani Kar
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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16
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Bachhar A, Jablonsky J. Entner-Doudoroff pathway in Synechocystis PCC 6803: Proposed regulatory roles and enzyme multifunctionalities. Front Microbiol 2022; 13:967545. [PMID: 36051759 PMCID: PMC9424857 DOI: 10.3389/fmicb.2022.967545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
The Entner-Doudoroff pathway (ED-P) was established in 2016 as the fourth glycolytic pathway in Synechocystis sp. PCC 6803. ED-P consists of two reactions, the first catalyzed by 6-phosphogluconate dehydratase (EDD), the second by keto3-deoxygluconate-6-phosphate aldolase/4-hydroxy-2-oxoglutarate aldolase (EDA). ED-P was previously concluded to be a widespread (∼92%) pathway among cyanobacteria, but current bioinformatic analysis estimated the occurrence of ED-P to be either scarce (∼1%) or uncommon (∼47%), depending if dihydroxy-acid dehydratase (ilvD) also functions as EDD (currently assumed). Thus, the biochemical characterization of ilvD is a task pending to resolve this uncertainty. Next, we have provided new insights into several single and double glycolytic mutants based on kinetic model of central carbon metabolism of Synechocystis. The model predicted that silencing 6-phosphogluconate dehydrogenase (gnd) could be coupled with ∼90% down-regulation of G6P-dehydrogenase, also limiting the metabolic flux via ED-P. Furthermore, our metabolic flux estimation implied that growth impairment linked to silenced EDA under mixotrophic conditions is not caused by diminished carbon flux via ED-P but rather by a missing mechanism related to the role of EDA in metabolism. We proposed two possible, mutually non-exclusive explanations: (i) Δeda leads to disrupted carbon catabolite repression, regulated by 2-keto3-deoxygluconate-6-phosphate (ED-P intermediate), and (ii) EDA catalyzes the interconversion between glyoxylate and 4-hydroxy-2-oxoglutarate + pyruvate in the proximity of TCA cycle, possibly effecting the levels of 2-oxoglutarate under Δeda. We have also proposed a new pathway from EDA toward proline, which could explain the proline accumulation under Δeda. In addition, the presented in silico method provides an alternative to 13C metabolic flux analysis for marginal metabolic pathways around/below the threshold of ultrasensitive LC-MS. Finally, our in silico analysis provided alternative explanations for the role of ED-P in Synechocystis while identifying some severe uncertainties.
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17
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Tan LR, Cao YQ, Li JW, Xia PF, Wang SG. Transcriptomics and metabolomics of engineered Synechococcus elongatus during photomixotrophic growth. Microb Cell Fact 2022; 21:31. [PMID: 35248031 PMCID: PMC8897908 DOI: 10.1186/s12934-022-01760-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/22/2022] [Indexed: 12/18/2022] Open
Abstract
Background Converting carbon dioxide (CO2) into value-added chemicals using engineered cyanobacteria is a promising strategy to tackle the global warming and energy shortage issues. However, most cyanobacteria are autotrophic and use CO2 as a sole carbon source, which makes it hard to compete with heterotrophic hosts in either growth or productivity. One strategy to overcome this bottleneck is to introduce sugar utilization pathways to enable photomixotrophic growth with CO2 and sugar (e.g., glucose and xylose). Advances in engineering mixotrophic cyanobacteria have been obtained, while a systematic interrogation of these engineered strains is missing. This work aimed to fill the gap at omics level. Results We first constructed two engineered Synechococcus elongatus YQ2-gal and YQ3-xyl capable of utilizing glucose and xylose, respectively. To investigate the metabolic mechanism, transcriptomic and metabolomic analysis were then performed in the engineered photomixotrophic strains YQ2-gal and YQ3-xyl. Transcriptome and metabolome of wild-type S. elongatus were set as baselines. Increased abundance of metabolites in glycolysis or pentose phosphate pathway indicated that efficient sugar utilization significantly enhanced carbon flux in S. elongatus as expected. However, carbon flux was redirected in strain YQ2-gal as more flowed into fatty acids biosynthesis but less into amino acids. In strain YQ3-xyl, more carbon flux was directed into synthesis of sucrose, glucosamine and acetaldehyde, while less into fatty acids and amino acids. Moreover, photosynthesis and bicarbonate transport could be affected by upregulated genes, while nitrogen transport and assimilation were regulated by less transcript abundance of related genes in strain YQ3-xyl with utilization of xylose. Conclusions Our work identified metabolic mechanism in engineered S. elongatus during photomixotrophic growth, where regulations of fatty acids metabolism, photosynthesis, bicarbonate transport, nitrogen assimilation and transport are dependent on different sugar utilization. Since photomixotrophic cyanobacteria is regarded as a promising cell factory for bioproduction, this comprehensive understanding of metabolic mechanism of engineered S. elongatus during photomixotrophic growth would shed light on the engineering of more efficient and controllable bioproduction systems based on this potential chassis. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01760-1.
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18
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de Carvalho Silvello MA, Severo Gonçalves I, Patrícia Held Azambuja S, Silva Costa S, Garcia Pereira Silva P, Oliveira Santos L, Goldbeck R. Microalgae-based carbohydrates: A green innovative source of bioenergy. BIORESOURCE TECHNOLOGY 2022; 344:126304. [PMID: 34752879 DOI: 10.1016/j.biortech.2021.126304] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/01/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
Microalgae contribute significantly to the global carbon cycle through photosynthesis. Given their ability to efficiently convert solar energy and atmospheric carbon dioxide into chemical compounds, such as carbohydrates, and generate oxygen during the process, microalgae represent an excellent and feasible carbohydrate bioresource. Microalgae-based biofuels are technically viable and, delineate a green and innovative field of opportunity for bioenergy exploitation. Microalgal polysaccharides are one of the most versatile groups for biotechnological applications and its content can be increased by manipulating cultivation conditions. Microalgal carbohydrates can be used to produce a variety of biofuels, including bioethanol, biobutanol, biomethane, and biohydrogen. This review provides an overview of microalgal carbohydrates, focusing on their use as feedstock for biofuel production, highlighting the carbohydrate metabolism and approaches for their enhancement. Moreover, biofuels produced from microalgal carbohydrate are showed, in addition to a new bibliometric study of current literature on microalgal carbohydrates and their use.
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Affiliation(s)
- Maria Augusta de Carvalho Silvello
- Bioprocess and Metabolic Engineering Laboratory, School of Food Engineering, University of Campinas (UNICAMP), Campinas, São Paulo 13083-862, Brazil
| | - Igor Severo Gonçalves
- Bioprocess and Metabolic Engineering Laboratory, School of Food Engineering, University of Campinas (UNICAMP), Campinas, São Paulo 13083-862, Brazil
| | - Suéllen Patrícia Held Azambuja
- Bioprocess and Metabolic Engineering Laboratory, School of Food Engineering, University of Campinas (UNICAMP), Campinas, São Paulo 13083-862, Brazil
| | - Sharlene Silva Costa
- Laboratory of Biotechnology, School of Chemistry and Food, Federal University of Rio Grande, Rio Grande, RS 96203-900, Brazil
| | - Pedro Garcia Pereira Silva
- Laboratory of Biotechnology, School of Chemistry and Food, Federal University of Rio Grande, Rio Grande, RS 96203-900, Brazil
| | - Lucielen Oliveira Santos
- Laboratory of Biotechnology, School of Chemistry and Food, Federal University of Rio Grande, Rio Grande, RS 96203-900, Brazil
| | - Rosana Goldbeck
- Bioprocess and Metabolic Engineering Laboratory, School of Food Engineering, University of Campinas (UNICAMP), Campinas, São Paulo 13083-862, Brazil.
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Dhakal D, Chen M, Luesch H, Ding Y. Heterologous production of cyanobacterial compounds. J Ind Microbiol Biotechnol 2021; 48:6119914. [PMID: 33928376 PMCID: PMC8210676 DOI: 10.1093/jimb/kuab003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/17/2020] [Indexed: 12/29/2022]
Abstract
Cyanobacteria produce a plethora of compounds with unique chemical structures and diverse biological activities. Importantly, the increasing availability of cyanobacterial genome sequences and the rapid development of bioinformatics tools have unraveled the tremendous potential of cyanobacteria in producing new natural products. However, the discovery of these compounds based on cyanobacterial genomes has progressed slowly as the majority of their corresponding biosynthetic gene clusters (BGCs) are silent. In addition, cyanobacterial strains are often slow-growing, difficult for genetic engineering, or cannot be cultivated yet, limiting the use of host genetic engineering approaches for discovery. On the other hand, genetically tractable hosts such as Escherichia coli, Actinobacteria, and yeast have been developed for the heterologous expression of cyanobacterial BGCs. More recently, there have been increased interests in developing model cyanobacterial strains as heterologous production platforms. Herein, we present recent advances in the heterologous production of cyanobacterial compounds in both cyanobacterial and noncyanobacterial hosts. Emerging strategies for BGC assembly, host engineering, and optimization of BGC expression are included for fostering the broader applications of synthetic biology tools in the discovery of new cyanobacterial natural products.
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Affiliation(s)
- Dipesh Dhakal
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 31610, USA
| | - Manyun Chen
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 31610, USA
| | - Hendrik Luesch
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 31610, USA
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 31610, USA
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20
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Meng H, Zhang W, Zhu H, Yang F, Zhang Y, Zhou J, Li Y. Over-expression of an electron transport protein OmcS provides sufficient NADH for D-lactate production in cyanobacterium. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:109. [PMID: 33926521 PMCID: PMC8082822 DOI: 10.1186/s13068-021-01956-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/12/2021] [Indexed: 06/10/2023]
Abstract
BACKGROUND An efficient supply of reducing equivalent is essential for chemicals production by engineered microbes. In phototrophic microbes, the NADPH generated from photosynthesis is the dominant form of reducing equivalent. However, most dehydrogenases prefer to utilize NADH as a cofactor. Thus, sufficient NADH supply is crucial to produce dehydrogenase-derived chemicals in cyanobacteria. Photosynthetic electron is the sole energy source and excess electrons are wasted in the light reactions of photosynthesis. RESULTS Here we propose a novel strategy to direct the electrons to generate more ATP from light reactions to provide sufficient NADH for lactate production. To this end, we introduced an electron transport protein-encoding gene omcS into cyanobacterium Synechococcus elongatus UTEX 2973 and demonstrated that the introduced OmcS directs excess electrons from plastoquinone (PQ) to photosystem I (PSI) to stimulate cyclic electron transfer (CET). As a result, an approximately 30% increased intracellular ATP, 60% increased intracellular NADH concentrations and up to 60% increased biomass production with fourfold increased D-lactate production were achieved. Comparative transcriptome analysis showed upregulation of proteins involved in linear electron transfer (LET), CET, and downregulation of proteins involved in respiratory electron transfer (RET), giving hints to understand the increased levels of ATP and NADH. CONCLUSIONS This strategy provides a novel orthologous way to improve photosynthesis via enhancing CET and supply sufficient NADH for the photosynthetic production of chemicals.
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Affiliation(s)
- Hengkai Meng
- Department of Cellular Biology, University of Science and Technology of China, Hefei, China
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
- State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Zhang
- Department of Cellular Biology, University of Science and Technology of China, Hefei, China
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Huawei Zhu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fan Yang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanping Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Jie Zhou
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.
| | - Yin Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.
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21
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Song X, Diao J, Yao J, Cui J, Sun T, Chen L, Zhang W. Engineering a Central Carbon Metabolism Pathway to Increase the Intracellular Acetyl-CoA Pool in Synechocystis sp. PCC 6803 Grown under Photomixotrophic Conditions. ACS Synth Biol 2021; 10:836-846. [PMID: 33779148 DOI: 10.1021/acssynbio.0c00629] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In cyanobacteria, photomixotrophic growth is considered as a promising strategy to achieve both high cell density and product accumulation. However, the conversion of glucose to acetyl coenzyme A (acetyl-CoA) in the native glycolytic pathway is insufficient, which decreases the carbon utilization and productivity of engineered cyanobacteria under photomixotrophic conditions. To increase the carbon flux from glucose to key intracellular precursor acetyl-CoA in Synechocystis sp. PCC 6803 (hereafter, Synechocystis 6803) under photomixotrophic conditions, a synthetic nonoxidative cyclic glycolysis (NOG) pathway was introduced into the wild type strain, which successfully increased the intracellular pool of acetyl-CoA by approximately 1-fold. To minimize the competition for glucose, the native Embden-Meyerhof-Parnas (EMP) and Entner-Doudoroff (ED) pathways were knocked out, respectively. Notably, eliminating the native ED pathway in the engineered strain carrying the NOG pathway further increased the intracellular pool of acetyl-CoA up to 2.8-fold. Another carbon consuming pathway in Synechocystis 6803, the glycogen biosynthesis pathway, was additionally knocked out in the above-mentioned engineered strain, which enabled an increase of the intracellular acetyl-CoA pool by up to 3.5-fold when compared with the wild type strain. Finally, the content of intracellular lipids was analyzed as an index of the productive capacity of the engineered Synechocystis 6803 cell factory under photomixotrophic conditions. The results showed the total lipids yield increased about 26% compared to the wild type (from 15.71% to 34.12%, g/g glucose), demonstrating that this integrated approach could represent a general strategy not only for the improvement of the intracellular concentration of acetyl-CoA, but also for the production of value-added chemicals that require acetyl-CoA as a key precursor in cyanobacteria.
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Affiliation(s)
- Xinyu Song
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, People’s Republic of China
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Law School of Tianjin University, Tianjin 300072, P.R. China
| | - Jinjin Diao
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, People’s Republic of China
| | - Jiaqi Yao
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, People’s Republic of China
| | - Jinyu Cui
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, People’s Republic of China
| | - Tao Sun
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, People’s Republic of China
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Law School of Tianjin University, Tianjin 300072, P.R. China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, People’s Republic of China
| | - Weiwen Zhang
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, People’s Republic of China
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Law School of Tianjin University, Tianjin 300072, P.R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, People’s Republic of China
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22
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Vasile NS, Cordara A, Usai G, Re A. Computational Analysis of Dynamic Light Exposure of Unicellular Algal Cells in a Flat-Panel Photobioreactor to Support Light-Induced CO 2 Bioprocess Development. Front Microbiol 2021; 12:639482. [PMID: 33868196 PMCID: PMC8049116 DOI: 10.3389/fmicb.2021.639482] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/25/2021] [Indexed: 02/05/2023] Open
Abstract
Cyanobacterial cell factories trace a vibrant pathway to climate change neutrality and sustainable development owing to their ability to turn carbon dioxide-rich waste into a broad portfolio of renewable compounds, which are deemed valuable in green chemistry cross-sectorial applications. Cell factory design requires to define the optimal operational and cultivation conditions. The paramount parameter in biomass cultivation in photobioreactors is the light intensity since it impacts cellular physiology and productivity. Our modeling framework provides a basis for the predictive control of light-limited, light-saturated, and light-inhibited growth of the Synechocystis sp. PCC 6803 model organism in a flat-panel photobioreactor. The model here presented couples computational fluid dynamics, light transmission, kinetic modeling, and the reconstruction of single cell trajectories in differently irradiated areas of the photobioreactor to relate key physiological parameters to the multi-faceted processes occurring in the cultivation environment. Furthermore, our analysis highlights the need for properly constraining the model with decisive qualitative and quantitative data related to light calibration and light measurements both at the inlet and outlet of the photobioreactor in order to boost the accuracy and extrapolation capabilities of the model.
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Affiliation(s)
- Nicolò S Vasile
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Genova, Italy
| | - Alessandro Cordara
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Genova, Italy
| | - Giulia Usai
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Genova, Italy.,Department of Applied Science and Technology, Politecnico di Torino, Torino, Italy
| | - Angela Re
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Genova, Italy
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23
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Ofaim S, Sulheim S, Almaas E, Sher D, Segrè D. Dynamic Allocation of Carbon Storage and Nutrient-Dependent Exudation in a Revised Genome-Scale Model of Prochlorococcus. Front Genet 2021; 12:586293. [PMID: 33633777 PMCID: PMC7900632 DOI: 10.3389/fgene.2021.586293] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 01/14/2021] [Indexed: 12/02/2022] Open
Abstract
Microbial life in the oceans impacts the entire marine ecosystem, global biogeochemistry and climate. The marine cyanobacterium Prochlorococcus, an abundant component of this ecosystem, releases a significant fraction of the carbon fixed through photosynthesis, but the amount, timing and molecular composition of released carbon are still poorly understood. These depend on several factors, including nutrient availability, light intensity and glycogen storage. Here we combine multiple computational approaches to provide insight into carbon storage and exudation in Prochlorococcus. First, with the aid of a new algorithm for recursive filling of metabolic gaps (ReFill), and through substantial manual curation, we extended an existing genome-scale metabolic model of Prochlorococcus MED4. In this revised model (iSO595), we decoupled glycogen biosynthesis/degradation from growth, thus enabling dynamic allocation of carbon storage. In contrast to standard implementations of flux balance modeling, we made use of forced influx of carbon and light into the cell, to recapitulate overflow metabolism due to the decoupling of photosynthesis and carbon fixation from growth during nutrient limitation. By using random sampling in the ensuing flux space, we found that storage of glycogen or exudation of organic acids are favored when the growth is nitrogen limited, while exudation of amino acids becomes more likely when phosphate is the limiting resource. We next used COMETS to simulate day-night cycles and found that the model displays dynamic glycogen allocation and exudation of organic acids. The switch from photosynthesis and glycogen storage to glycogen depletion is associated with a redistribution of fluxes from the Entner–Doudoroff to the Pentose Phosphate pathway. Finally, we show that specific gene knockouts in iSO595 exhibit dynamic anomalies compatible with experimental observations, further demonstrating the value of this model as a tool to probe the metabolic dynamic of Prochlorococcus.
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Affiliation(s)
- Shany Ofaim
- Bioinformatics Program and Biological Design Center, Boston University, Boston, MA, United States.,Department of Marine Biology, University of Haifa, Haifa, Israel
| | - Snorre Sulheim
- Bioinformatics Program and Biological Design Center, Boston University, Boston, MA, United States.,Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway.,Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Eivind Almaas
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway.,K.G. Jebsen Center for Genetic Epidemiology, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Daniel Sher
- Department of Marine Biology, University of Haifa, Haifa, Israel
| | - Daniel Segrè
- Bioinformatics Program and Biological Design Center, Boston University, Boston, MA, United States.,Department of Biomedical Engineering, Boston University, Boston, MA, United States.,Department of Physics, Boston University, Boston, MA, United States.,Department of Biology, Boston University, Boston, MA, United States
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24
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Madsen MA, Hamilton G, Herzyk P, Amtmann A. Environmental Regulation of PndbA600, an Auto-Inducible Promoter for Two-Stage Industrial Biotechnology in Cyanobacteria. Front Bioeng Biotechnol 2021; 8:619055. [PMID: 33542914 PMCID: PMC7853294 DOI: 10.3389/fbioe.2020.619055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/09/2020] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria are photosynthetic prokaryotes being developed as sustainable platforms that use renewable resources (light, water, and air) for diverse applications in energy, food, environment, and medicine. Despite the attractive promise that cyanobacteria offer to industrial biotechnology, slow growth rates pose a major challenge in processes which typically require large amounts of biomass and are often toxic to the cells. Two-stage cultivation strategies are an attractive solution to prevent any undesired growth inhibition by de-coupling biomass accumulation (stage I) and the industrial process (stage II). In cyanobacteria, two-stage strategies involve costly transfer methods between stages I and II, and little work has been focussed on using the distinct growth and stationary phases of batch cultures to autoregulate stage transition. In the present study, we identified and characterised a growth phase-specific promoter, which can serve as an auto-inducible switch to regulate two-stage bioprocesses in cyanobacteria. First, growth phase-specific genes were identified from a new RNAseq dataset comparing two growth phases and six nutrient conditions in Synechocystis sp. PCC 6803, including two new transcriptomes for low Mg and low K. A type II NADH dehydrogenase (ndbA) showed robust induction when the cultures transitioned from exponential to stationary phase growth. Behaviour of a 600-bp promoter sequence (PndbA600) was then characterised in detail following the expression of PndbA600:GFP in Synechococcus sp. PCC 7002. Culture density and growth media analyses showed that PndbA600 activation was not dependent on increases in culture density per se but on N availability and on another activating factor present in the spent media of stationary phase cultures (Factor X). PndbA600 deactivation was dependent on the changes in culture density and in either N availability or Factor X. Electron transport inhibition studies revealed a photosynthesis-specific enhancement of active PndbA600 levels. Our findings are summarised in a model describing the environmental regulation of PndbA600, which can now inform the rational design of two-stage industrial processes in cyanobacteria.
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Affiliation(s)
- Mary Ann Madsen
- College of Medical, Veterinary and Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom
| | - Graham Hamilton
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Pawel Herzyk
- College of Medical, Veterinary and Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom.,Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Anna Amtmann
- College of Medical, Veterinary and Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom
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25
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A new insight into role of phosphoketolase pathway in Synechocystis sp. PCC 6803. Sci Rep 2020; 10:22018. [PMID: 33328526 PMCID: PMC7744508 DOI: 10.1038/s41598-020-78475-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/25/2020] [Indexed: 11/29/2022] Open
Abstract
Phosphoketolase (PKET) pathway is predominant in cyanobacteria (around 98%) but current opinion is that it is virtually inactive under autotrophic ambient CO2 condition (AC-auto). This creates an evolutionary paradox due to the existence of PKET pathway in obligatory photoautotrophs. We aim to answer the paradox with the aid of bioinformatic analysis along with metabolic, transcriptomic, fluxomic and mutant data integrated into a multi-level kinetic model. We discussed the problems linked to neglected isozyme, pket2 (sll0529) and inconsistencies towards the explanation of residual flux via PKET pathway in the case of silenced pket1 (slr0453) in Synechocystis sp. PCC 6803. Our in silico analysis showed: (1) 17% flux reduction via RuBisCO for Δpket1 under AC-auto, (2) 11.2–14.3% growth decrease for Δpket2 in turbulent AC-auto, and (3) flux via PKET pathway reaching up to 252% of the flux via phosphoglycerate mutase under AC-auto. All results imply that PKET pathway plays a crucial role under AC-auto by mitigating the decarboxylation occurring in OPP pathway and conversion of pyruvate to acetyl CoA linked to EMP glycolysis under the carbon scarce environment. Finally, our model predicted that PKETs have low affinity to S7P as a substrate.
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26
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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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27
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Engineering salt tolerance of photosynthetic cyanobacteria for seawater utilization. Biotechnol Adv 2020; 43:107578. [PMID: 32553809 DOI: 10.1016/j.biotechadv.2020.107578] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/17/2020] [Accepted: 06/05/2020] [Indexed: 02/04/2023]
Abstract
Photosynthetic cyanobacteria are capable of utilizing sunlight and CO2 as sole energy and carbon sources, respectively. With genetically modified cyanobacteria being used as a promising chassis to produce various biofuels and chemicals in recent years, future large-scale cultivation of cyanobacteria would have to be performed in seawater, since freshwater supplies of the earth are very limiting. However, high concentration of salt is known to inhibit the growth of cyanobacteria. This review aims at comparing the mechanisms that different cyanobacteria respond to salt stress, and then summarizing various strategies of developing salt-tolerant cyanobacteria for seawater cultivation, including the utilization of halotolerant cyanobacteria and the engineering of salt-tolerant freshwater cyanobacteria. In addition, the challenges and potential strategies related to further improving salt tolerance in cyanobacteria are also discussed.
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28
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Veaudor T, Blanc-Garin V, Chenebault C, Diaz-Santos E, Sassi JF, Cassier-Chauvat C, Chauvat F. Recent Advances in the Photoautotrophic Metabolism of Cyanobacteria: Biotechnological Implications. Life (Basel) 2020; 10:E71. [PMID: 32438704 PMCID: PMC7281370 DOI: 10.3390/life10050071] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/16/2020] [Accepted: 05/18/2020] [Indexed: 12/13/2022] Open
Abstract
Cyanobacteria constitute the only phylum of oxygen-evolving photosynthetic prokaryotes that shaped the oxygenic atmosphere of our planet. Over time, cyanobacteria have evolved as a widely diverse group of organisms that have colonized most aquatic and soil ecosystems of our planet and constitute a large proportion of the biomass that sustains the biosphere. Cyanobacteria synthesize a vast array of biologically active metabolites that are of great interest for human health and industry, and several model cyanobacteria can be genetically manipulated. Hence, cyanobacteria are regarded as promising microbial factories for the production of chemicals from highly abundant natural resources, e.g., solar energy, CO2, minerals, and waters, eventually coupled to wastewater treatment to save costs. In this review, we summarize new important discoveries on the plasticity of the photoautotrophic metabolism of cyanobacteria, emphasizing the coordinated partitioning of carbon and nitrogen towards growth or compound storage, and the importance of these processes for biotechnological perspectives. We also emphasize the importance of redox regulation (including glutathionylation) on these processes, a subject which has often been overlooked.
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Affiliation(s)
- Théo Veaudor
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (T.V.); (V.B.-G.); (C.C.); (E.D.-S.); (C.C.-C.)
| | - Victoire Blanc-Garin
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (T.V.); (V.B.-G.); (C.C.); (E.D.-S.); (C.C.-C.)
| | - Célia Chenebault
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (T.V.); (V.B.-G.); (C.C.); (E.D.-S.); (C.C.-C.)
| | - Encarnación Diaz-Santos
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (T.V.); (V.B.-G.); (C.C.); (E.D.-S.); (C.C.-C.)
| | - Jean-François Sassi
- Commissariat à l’énergie atomique et aux énergies alternatives (CEA), Centre de Cadarache St Paul Lez, 13108 Durance, France;
| | - Corinne Cassier-Chauvat
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (T.V.); (V.B.-G.); (C.C.); (E.D.-S.); (C.C.-C.)
| | - Franck Chauvat
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (T.V.); (V.B.-G.); (C.C.); (E.D.-S.); (C.C.-C.)
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29
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Wang L, Chen L, Yang S, Tan X. Photosynthetic Conversion of Carbon Dioxide to Oleochemicals by Cyanobacteria: Recent Advances and Future Perspectives. Front Microbiol 2020; 11:634. [PMID: 32362881 PMCID: PMC7181335 DOI: 10.3389/fmicb.2020.00634] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 03/20/2020] [Indexed: 11/21/2022] Open
Abstract
Sustainable production of biofuels and biochemicals has been broadly accepted as a solution to lower carbon dioxide emissions. Besides being used as lubricants or detergents, oleochemicals are also attractive biofuels as they are compatible with existing transport infrastructures. Cyanobacteria are autotrophic prokaryotes possessing photosynthetic abilities with mature genetic manipulation systems. Through the introduction of exogenous or the modification of intrinsic metabolic pathways, cyanobacteria have been engineered to produce various bio-chemicals and biofuels over the past decade. In this review, we specifically summarize recent progress on photosynthetic production of fatty acids, fatty alcohols, fatty alk(a/e)nes, and fatty acid esters by genetically engineered cyanobacteria. We also summarize recent reports on fatty acid and lipid metabolisms of cyanobacteria and provide perspectives for economic cyanobacterial oleochemical production in the future.
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Affiliation(s)
- Li Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
| | - Liyuan Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
| | - Xiaoming Tan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
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30
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Benítez-Rangel E, Rodríguez-Hernández A, Velasco-García R. The substrate of the glucose-6-phosphate dehydrogenase of Pseudomonas aeruginosa provides structural stability. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1868:140331. [PMID: 31760039 DOI: 10.1016/j.bbapap.2019.140331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 10/22/2019] [Accepted: 11/20/2019] [Indexed: 01/18/2023]
Abstract
In general, eukaryotic glucose-6-phosphate dehydrogenases (G6PDHs) are structurally stabilized by NADP+. Here we show by spectrofluorometric analysis, thermal and urea denaturation, and trypsin proteolysis, that a different mechanism stabilizes the enzyme from Pseudomonas aeruginosa (PaG6PDH) (EC 1.1.1.363). The spectrofluorometric analysis of the emission of 8-anilino-1-naphthalenesulfonic acid (ANS) indicates that this stabilization is the result of a structural change in the enzyme caused by G6P. The similarity between the Kd values determined for the PaG6PDH-G6P complex (78.0 ± 7.9 μM) and the K0.5 values determined for G6P (57.9 ± 2.5 and 104.5 ± 9.3 μM in the NADP+- and NAD+-dependent reactions, respectively) suggests that the structural changes are the result of G6P binding to the active site of PaG6PDH. Modeling of PaG6PDH indicated the residues that potentially bind the ligand. These results and a phylogenetic analysis of the amino acid sequences of forty-four G6PDHs, suggest that the stabilization observed for PaG6PDH could be a characteristic that distinguishes this and other G6PDHs that use NAD+ and NADP+ from those that use NADP+ only or preferentially, such as those found in eukaryotes. This characteristic could be related to the metabolic roles these enzymes play in the organisms to which they belong.
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Affiliation(s)
- Edaena Benítez-Rangel
- Universidad Nacional Autónoma de México, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Estado de México 54090, Mexico
| | - Annia Rodríguez-Hernández
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad Universitaria, Ciudad de México 04510, Mexico
| | - Roberto Velasco-García
- Universidad Nacional Autónoma de México, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Estado de México 54090, Mexico.
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31
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Luan G, Zhang S, Wang M, Lu X. Progress and perspective on cyanobacterial glycogen metabolism engineering. Biotechnol Adv 2019; 37:771-786. [DOI: 10.1016/j.biotechadv.2019.04.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 03/09/2019] [Accepted: 04/07/2019] [Indexed: 12/20/2022]
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32
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Douchi D, Liang F, Cano M, Xiong W, Wang B, Maness PC, Lindblad P, Yu J. Membrane-Inlet Mass Spectrometry Enables a Quantitative Understanding of Inorganic Carbon Uptake Flux and Carbon Concentrating Mechanisms in Metabolically Engineered Cyanobacteria. Front Microbiol 2019; 10:1356. [PMID: 31293533 PMCID: PMC6604854 DOI: 10.3389/fmicb.2019.01356] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 05/31/2019] [Indexed: 01/04/2023] Open
Abstract
Photosynthesis uses solar energy to drive inorganic carbon (Ci) uptake, fixation, and biomass formation. In cyanobacteria, Ci uptake is assisted by carbon concentrating mechanisms (CCM), and CO2 fixation is catalyzed by RubisCO in the Calvin-Benson-Bassham (CBB) cycle. Understanding the regulation that governs CCM and CBB cycle activities in natural and engineered strains requires methods and parameters that quantify these activities. Here, we used membrane-inlet mass spectrometry (MIMS) to simultaneously quantify Ci concentrating and fixation processes in the cyanobacterium Synechocystis 6803. By comparing cultures acclimated to ambient air conditions to cultures transitioning to high Ci conditions, we show that acclimation to high Ci involves a concurrent decline of Ci uptake and fixation parameters. By varying light input, we show that both CCM and CBB reactions become energy limited under low light conditions. A strain over-expressing the gene for the CBB cycle enzyme fructose-bisphosphate aldolase showed higher CCM and carbon fixation capabilities, suggesting a regulatory link between CBB metabolites and CCM capacity. While the engineering of an ethanol production pathway had no effect on CCM or carbon fixation parameters, additional fructose-bisphosphate aldolase gene over-expression enhanced both activities while simultaneously increasing ethanol productivity. These observations show that MIMS can be a useful tool to study the extracellular Ci flux and how CBB metabolites regulate Ci uptake and fixation.
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Affiliation(s)
- Damien Douchi
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Feiyan Liang
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Uppsala, Sweden
| | - Melissa Cano
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Wei Xiong
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Bo Wang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Pin-Ching Maness
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Uppsala, Sweden
| | - Jianping Yu
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
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33
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Santos-Merino M, Singh AK, Ducat DC. New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering. Front Bioeng Biotechnol 2019; 7:33. [PMID: 30873404 PMCID: PMC6400836 DOI: 10.3389/fbioe.2019.00033] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/05/2019] [Indexed: 01/25/2023] Open
Abstract
Cyanobacteria are promising microorganisms for sustainable biotechnologies, yet unlocking their potential requires radical re-engineering and application of cutting-edge synthetic biology techniques. In recent years, the available devices and strategies for modifying cyanobacteria have been increasing, including advances in the design of genetic promoters, ribosome binding sites, riboswitches, reporter proteins, modular vector systems, and markerless selection systems. Because of these new toolkits, cyanobacteria have been successfully engineered to express heterologous pathways for the production of a wide variety of valuable compounds. Cyanobacterial strains with the potential to be used in real-world applications will require the refinement of genetic circuits used to express the heterologous pathways and development of accurate models that predict how these pathways can be best integrated into the larger cellular metabolic network. Herein, we review advances that have been made to translate synthetic biology tools into cyanobacterial model organisms and summarize experimental and in silico strategies that have been employed to increase their bioproduction potential. Despite the advances in synthetic biology and metabolic engineering during the last years, it is clear that still further improvements are required if cyanobacteria are to be competitive with heterotrophic microorganisms for the bioproduction of added-value compounds.
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Affiliation(s)
- María Santos-Merino
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
| | - Amit K. Singh
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
| | - Daniel C. Ducat
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
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34
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Selão TT, Jebarani J, Ismail NA, Norling B, Nixon PJ. Enhanced Production of D-Lactate in Cyanobacteria by Re-Routing Photosynthetic Cyclic and Pseudo-Cyclic Electron Flow. FRONTIERS IN PLANT SCIENCE 2019; 10:1700. [PMID: 32117327 PMCID: PMC7025493 DOI: 10.3389/fpls.2019.01700] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 12/03/2019] [Indexed: 05/22/2023]
Abstract
Cyanobacteria are promising chassis strains for the photosynthetic production of platform and specialty chemicals from carbon dioxide. Their efficient light harvesting and metabolic flexibility abilities have allowed a wide range of biomolecules, such as the bioplastic polylactate precursor D-lactate, to be produced, though usually at relatively low yields. In order to increase photosynthetic electron flow towards the production of D-lactate, we have generated several strains of the marine cyanobacterium Synechococcus sp. PCC 7002 (Syn7002) with deletions in genes involved in cyclic or pseudo-cyclic electron flow around photosystem I. Using a variant of the Chlamydomonas reinhardtii D-lactate dehydrogenase (LDHSRT, engineered to efficiently utilize NADPH in vivo), we have shown that deletion of either of the two flavodiiron flv homologs (involved in pseudo-cyclic electron transport) or the Syn7002 pgr5 homolog (proposed to be a vital part of the cyclic electron transport pathway) is able to increase D-lactate production in Syn7002 strains expressing LDHSRT and the Escherichia coli LldP (lactate permease), especially at low temperature (25°C) and 0.04% (v/v) CO2, though at elevated temperatures (38°C) and/or high (1%) CO2 concentrations, the effect was less obvious. The Δpgr5 background seemed to be particularly beneficial at 25°C and 0.04% (v/v) CO2, with a nearly 7-fold increase in D-lactate accumulation in comparison to the wild-type background (≈1000 vs ≈150 mg/L) and decreased side effects in comparison to the flv deletion strains. Overall, our results show that manipulation of photosynthetic electron flow is a viable strategy to increase production of platform chemicals in cyanobacteria under ambient conditions.
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Affiliation(s)
- Tiago Toscano Selão
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jasmin Jebarani
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Nurul Aina Ismail
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Birgitta Norling
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Peter Julian Nixon
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Department of Life Sciences, Imperial College London, London, United Kingdom
- *Correspondence: Peter Julian Nixon,
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35
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Ni J, Liu H, Tao F, Wu Y, Xu P. Remodeling of the Photosynthetic Chain Promotes Direct CO
2
Conversion into Valuable Aromatic Compounds. Angew Chem Int Ed Engl 2018; 57:15990-15994. [DOI: 10.1002/anie.201808402] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 09/24/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Jun Ni
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & BiotechnologyShanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Hong‐Yu Liu
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & BiotechnologyShanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Fei Tao
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & BiotechnologyShanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Yu‐Tong Wu
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & BiotechnologyShanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Ping Xu
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & BiotechnologyShanghai Jiao Tong University Shanghai 200240 P. R. China
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36
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Ni J, Liu H, Tao F, Wu Y, Xu P. Remodeling of the Photosynthetic Chain Promotes Direct CO2Conversion into Valuable Aromatic Compounds. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jun Ni
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & BiotechnologyShanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Hong‐Yu Liu
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & BiotechnologyShanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Fei Tao
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & BiotechnologyShanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Yu‐Tong Wu
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & BiotechnologyShanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Ping Xu
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & BiotechnologyShanghai Jiao Tong University Shanghai 200240 P. R. China
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37
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Vavitsas K, Fabris M, Vickers CE. Terpenoid Metabolic Engineering in Photosynthetic Microorganisms. Genes (Basel) 2018; 9:E520. [PMID: 30360565 PMCID: PMC6266707 DOI: 10.3390/genes9110520] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 12/13/2022] Open
Abstract
Terpenoids are a group of natural products that have a variety of roles, both essential and non-essential, in metabolism and in biotic and abiotic interactions, as well as commercial applications such as pharmaceuticals, food additives, and chemical feedstocks. Economic viability for commercial applications is commonly not achievable by using natural source organisms or chemical synthesis. Engineered bio-production in suitable heterologous hosts is often required to achieve commercial viability. However, our poor understanding of regulatory mechanisms and other biochemical processes makes obtaining efficient conversion yields from feedstocks challenging. Moreover, production from carbon dioxide via photosynthesis would significantly increase the environmental and potentially the economic credentials of these processes by disintermediating biomass feedstocks. In this paper, we briefly review terpenoid metabolism, outline some recent advances in terpenoid metabolic engineering, and discuss why photosynthetic unicellular organisms-such as algae and cyanobacteria-might be preferred production platforms for the expression of some of the more challenging terpenoid pathways.
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Affiliation(s)
- Konstantinos Vavitsas
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia.
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia.
| | - Michele Fabris
- Climate Change Cluster, University of Technology Sydney, 15 Broadway, Ultimo, NSW 2007, Australia.
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia.
| | - Claudia E Vickers
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia.
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia.
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38
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Biotechnology of cyanobacterial isoprene production. Appl Microbiol Biotechnol 2018; 102:6451-6458. [DOI: 10.1007/s00253-018-9093-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 05/12/2018] [Indexed: 12/20/2022]
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39
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Sengupta A, Pakrasi HB, Wangikar PP. Recent advances in synthetic biology of cyanobacteria. Appl Microbiol Biotechnol 2018; 102:5457-5471. [PMID: 29744631 DOI: 10.1007/s00253-018-9046-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 04/23/2018] [Accepted: 04/24/2018] [Indexed: 12/11/2022]
Abstract
Cyanobacteria are attractive hosts that can be engineered for the photosynthetic production of fuels, fine chemicals, and proteins from CO2. Moreover, the responsiveness of these photoautotrophs towards different environmental signals, such as light, CO2, diurnal cycle, and metals make them potential hosts for the development of biosensors. However, engineering these hosts proves to be a challenging and lengthy process. Synthetic biology can make the process of biological engineering more predictable through the use of standardized biological parts that are well characterized and tools to assemble them. While significant progress has been made with model heterotrophic organisms, many of the parts and tools are not portable in cyanobacteria. Therefore, efforts are underway to develop and characterize parts derived from cyanobacteria. In this review, we discuss the reported parts and tools with the objective to develop cyanobacteria as cell factories or biosensors. We also discuss the issues related to characterization, tunability, portability, and the need to develop enabling technologies to engineer this "green" chassis.
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Affiliation(s)
- Annesha Sengupta
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Himadri B Pakrasi
- Department of Biology, Washington University, St. Louis, MO, USA.,Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, USA
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India. .,DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India. .,Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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40
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Hu G, Zhou J, Chen X, Qian Y, Gao C, Guo L, Xu P, Chen W, Chen J, Li Y, Liu L. Engineering synergetic CO2-fixing pathways for malate production. Metab Eng 2018; 47:496-504. [DOI: 10.1016/j.ymben.2018.05.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/10/2018] [Accepted: 05/10/2018] [Indexed: 12/11/2022]
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41
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Tailoring cyanobacterial cell factory for improved industrial properties. Biotechnol Adv 2018; 36:430-442. [DOI: 10.1016/j.biotechadv.2018.01.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 01/07/2018] [Accepted: 01/08/2018] [Indexed: 11/20/2022]
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42
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Wang B, Eckert C, Maness PC, Yu J. A Genetic Toolbox for Modulating the Expression of Heterologous Genes in the Cyanobacterium Synechocystis sp. PCC 6803. ACS Synth Biol 2018; 7:276-286. [PMID: 29232504 DOI: 10.1021/acssynbio.7b00297] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cyanobacteria, genetic models for photosynthesis research for decades, have recently become attractive hosts for producing renewable fuels and chemicals, owing to their genetic tractability, relatively fast growth, and their ability to utilize sunlight, fix carbon dioxide, and in some cases, fix nitrogen. Despite significant advances, there is still an urgent demand for synthetic biology tools in order to effectively manipulate genetic circuits in cyanobacteria. In this study, we have compared a total of 17 natural and chimeric promoters, focusing on expression of the ethylene-forming enzyme (EFE) in the cyanobacterium Synechocystis sp. PCC 6803. We report the finding that the E. coli σ70 promoter Ptrc is superior compared to the previously reported strong promoters, such as PcpcB and PpsbA, for the expression of EFE. In addition, we found that the EFE expression level was very sensitive to the 5'-untranslated region upstream of the open reading frame. A library of ribosome binding sites (RBSs) was rationally designed and was built and systematically characterized. We demonstrate a strategy complementary to the RBS prediction software to facilitate the rational design of an RBS library to optimize the gene expression in cyanobacteria. Our results show that the EFE expression level is dramatically enhanced through these synthetic biology tools and is no longer the rate-limiting step for cyanobacterial ethylene production. These systematically characterized promoters and the RBS design strategy can serve as useful tools to tune gene expression levels and to identify and mitigate metabolic bottlenecks in cyanobacteria.
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Affiliation(s)
- Bo Wang
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Carrie Eckert
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
- Renewable
and Sustainable Energy Institute, University of Colorado, Boulder, 4001 Discovery Drive, Boulder, Colorado 80303, United States
| | - Pin-Ching Maness
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Jianping Yu
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
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43
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Zhou J, Meng H, Zhang W, Li Y. Production of Industrial Chemicals from CO 2 by Engineering Cyanobacteria. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1080:97-116. [PMID: 30091093 DOI: 10.1007/978-981-13-0854-3_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
As photosynthetic prokaryotes, cyanobacteria can directly convert CO2 to organic compounds and grow rapidly using sunlight as the sole source of energy. The direct biosynthesis of chemicals from CO2 and sunlight in cyanobacteria is therefore theoretically more attractive than using glucose as carbon source in heterotrophic bacteria. To date, more than 20 different target chemicals have been synthesized from CO2 in cyanobacteria. However, the yield and productivity of the constructed strains is about 100-fold lower than what can be obtained using heterotrophic bacteria, and only a few products reached the gram level. The main bottleneck in optimizing cyanobacterial cell factories is the relative complexity of the metabolism of photoautotrophic bacteria. In heterotrophic bacteria, energy metabolism is integrated with the carbon metabolism, so that glucose can provide both energy and carbon for the synthesis of target chemicals. By contrast, the energy and carbon metabolism of cyanobacteria are separated. First, solar energy is converted into chemical energy and reducing power via the light reactions of photosynthesis. Subsequently, CO2 is reduced to organic compounds using this chemical energy and reducing power. Finally, the reduced CO2 provides the carbon source and chemical energy for the synthesis of target chemicals and cell growth. Consequently, the unique nature of the cyanobacterial energy and carbon metabolism determines the specific metabolic engineering strategies required for these organisms. In this chapter, we will describe the specific characteristics of cyanobacteria regarding their metabolism of carbon and energy, summarize and analyze the specific strategies for the production of chemicals in cyanobacteria, and propose metabolic engineering strategies which may be most suitable for cyanobacteria.
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Affiliation(s)
- Jie Zhou
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hengkai Meng
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Wei Zhang
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yin Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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