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Chung CW, Ng IS. Tailoring nitrogen and phosphorus levels for tunable glycogen and protein production in halophilic Cyanobacterium aponinum PCC10605. BIORESOURCE TECHNOLOGY 2024; 406:131052. [PMID: 38944314 DOI: 10.1016/j.biortech.2024.131052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Cyanobacteria hold promise for simultaneous carbon capture and chemicals production, but the regulation and effect of nitrogen (N) and phosphorus (P) remains unclear. This study investigates major productions of glycogen, protein, and C-phycocyanin (C-PC) in Cyanobacterium aponinum PCC10605 under different N/P levels, alongside changes in light and CO2. Increasing nitrate (NO3-) from 2 to 6 mM resulted in a 9.7-fold increase in C-PC and reduced glycogen to 8.9 %. On the other hand, elevating phosphorus from 0.1 to 2 mM under limited nitrogen enhanced biomass and glycogen through the upregulation of carbonic anhydrase, ADP-glucose pyrophosphorylase, and glycogen phosphorylase. Changes in phosphorus levels and CO2 inlet concentrations affected metabolites accumulation and carbon capture efficiency, leading to the best condition of 76 % uptake capacity in direct air capture (DAC). All findings underscore the trade-off between glycogen and protein, representing the importance of N/P levels in nutrient modulation of PCC10605.
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Affiliation(s)
- Cheng-Wei Chung
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan.
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2
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Li J, Wang R, Liu Y, Miao X. Role of ERA protein in enhancing glyceroglycolipid synthesis and phosphate starvation tolerance in Synechococcus elongatus PCC 7942. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159431. [PMID: 37977490 DOI: 10.1016/j.bbalip.2023.159431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Glyceroglycolipids are the primary thylakoid membrane lipids in cyanobacteria. Their diverse bioactivities have led to extensive utilization in the biomedical industry. In this study, we elucidated the role of ERA (E. coli Ras-like protein) in augmenting glyceroglycolipid synthesis and bolstering stress resilience in Synechococcus elongatus PCC 7942 during phosphate starvation. Notably, the ERA overexpression strain (ERA OE) outperformed the wild-type (WT) strain under phosphate-starved conditions, displaying an average 13.9 % increase in biomass over WT during the entire growth period, peaking at 0.185 g L-1 of dry cell weight on day 6. Lipidomic analysis using UHPLC-MS/MS techniques revealed that ERA OE exhibited a higher total glyceroglycolipid content compared to WT under phosphate starvation, representing a 7.95 % increase over WT and constituting a maximum of 5.07 % of dry cell weight on day 6. Transcriptomic analysis identified a significant up-regulation of the gldA gene (encoding glycerol dehydrogenase) involved in glycerolipid metabolism due to overexpression of ERA during phosphate starvation. These findings suggest a potential mechanism by which ERA regulates glyceroglycolipid synthesis through the up-regulation of GldA, thereby enhancing phosphate starvation tolerance in S. elongatus PCC 7942. Furthermore, lipidomic analysis revealed that ERA facilitated the production of glyceroglycolipid molecules containing C16:1 and C18:1 fatty acids. Additionally, ERA redirected lipid flux and promoted glyceroglycolipid accumulation while attenuating triacylglycerol production under phosphate starvation. This study represents the first demonstration of pivotal role of ERA in enhancing glyceroglycolipid synthesis and phosphate starvation tolerance in cyanobacteria, offering new insights into the effective utilization of glyceroglycolipids in various applications.
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Affiliation(s)
- Junhao Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; Biomass Energy Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Rui Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; Biomass Energy Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuhong Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; Biomass Energy Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoling Miao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; Biomass Energy Research Center, Shanghai Jiao Tong University, Shanghai 200240, China.
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3
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Noell SE, Hellweger FL, Temperton B, Giovannoni SJ. A Reduction of Transcriptional Regulation in Aquatic Oligotrophic Microorganisms Enhances Fitness in Nutrient-Poor Environments. Microbiol Mol Biol Rev 2023; 87:e0012422. [PMID: 36995249 PMCID: PMC10304753 DOI: 10.1128/mmbr.00124-22] [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] [Indexed: 03/31/2023] Open
Abstract
In this review, we consider the regulatory strategies of aquatic oligotrophs, microbial cells that are adapted to thrive under low-nutrient concentrations in oceans, lakes, and other aquatic ecosystems. Many reports have concluded that oligotrophs use less transcriptional regulation than copiotrophic cells, which are adapted to high nutrient concentrations and are far more common subjects for laboratory investigations of regulation. It is theorized that oligotrophs have retained alternate mechanisms of regulation, such as riboswitches, that provide shorter response times and smaller amplitude responses and require fewer cellular resources. We examine the accumulated evidence for distinctive regulatory strategies in oligotrophs. We explore differences in the selective pressures copiotrophs and oligotrophs encounter and ask why, although evolutionary history gives copiotrophs and oligotrophs access to the same regulatory mechanisms, they might exhibit distinctly different patterns in how these mechanisms are used. We discuss the implications of these findings for understanding broad patterns in the evolution of microbial regulatory networks and their relationships to environmental niche and life history strategy. We ask whether these observations, which have emerged from a decade of increased investigation of the cell biology of oligotrophs, might be relevant to recent discoveries of many microbial cell lineages in nature that share with oligotrophs the property of reduced genome size.
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Affiliation(s)
- Stephen E. Noell
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | | | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, United Kingdom
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Lee M, Heo YB, Woo HM. Cytosine base editing in cyanobacteria by repressing archaic Type IV uracil-DNA glycosylase. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:610-625. [PMID: 36565011 DOI: 10.1111/tpj.16074] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Base editing enables precise gene editing without requiring donor DNA or double-stranded breaks. To facilitate base editing tools, a uracil DNA glycosylase inhibitor (UGI) was fused to cytidine deaminase-Cas nickase to inhibit uracil DNA glycosylase (UDG). Herein, we revealed that the bacteriophage PBS2-derived UGI of the cytosine base editor (CBE) could not inhibit archaic Type IV UDG in oligoploid cyanobacteria. To overcome the limitation of the CBE, dCas12a-assisted gene repression of the udg allowed base editing at the desired targets with up to 100% mutation frequencies, and yielded correct phenotypes of desired mutants in cyanobacteria. Compared with the original CBE (BE3), base editing was analyzed within a broader C4-C16 window with a strong TC-motif preference. Using multiplexed CyanoCBE, while udg was repressed, simultaneous base editing at two different sites was achieved with lower mutation frequencies than single CBE. Our discovery of a Type IV UDG that is not inhibited by the UGI of the CBE in cyanobacteria and the development of dCas12a-mediated base editing should facilitate the application of base editing not only in cyanobacteria, but also in archaea and green algae that possess Type IV UDGs. We revealed the bacteriophage-derived UGI of the base editor did not repress Type IV UDG in cyanobacteria. To overcome the limitation, orthogonal dCas12a interference was successfully applied to repress the UDG gene expression in cyanobacteria during base editing occurred, yielding a premature translational termination at desired targets. This study will open a new opportunity to perform base editing with Type IV UDGs in archaea and green algae.
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Affiliation(s)
- Mieun Lee
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
- BioFoundry Research Center, Institute of Biotechnology and Bioengineering, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
| | - Yu Been Heo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
- BioFoundry Research Center, Institute of Biotechnology and Bioengineering, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
| | - Han Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
- BioFoundry Research Center, Institute of Biotechnology and Bioengineering, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
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Chinchusak N, Incharoensakdi A, Phunpruch S. Dark fermentative hydrogen production and transcriptional analysis of genes involved in the unicellular halotolerant cyanobacterium Aphanothece halophytica under nitrogen and potassium deprivation. Front Bioeng Biotechnol 2023; 10:1028151. [PMID: 36686224 PMCID: PMC9852855 DOI: 10.3389/fbioe.2022.1028151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/19/2022] [Indexed: 01/09/2023] Open
Abstract
The unicellular halotolerant cyanobacterium Aphanothece halophytica is known as a potential hydrogen (H2) producer. This study aimed to investigate the enhancement of H2 production under nutrient deprivation. The results showed that nitrogen and potassium deprivation induced dark fermentative H2 production by A. halophytica, while no differences in H2 production were found under sulfur and phosphorus deprivation. In addition, deprivation of nitrogen and potassium resulted in the highest H2 production in A. halophytica due to the stimulation of hydrogenase activity. The effect of adaptation time under nitrogen and potassium deprivation on H2 production was investigated. The results showed that the highest H2 accumulation of 1,261.96 ± 96.99 µmol H2 g dry wt-1 and maximum hydrogenase activity of 179.39 ± 8.18 µmol H2 g dry wt-1 min-1 were obtained from A. halophytica cells adapted in the nitrogen- and potassium-deprived BG11 medium supplemented with Turk Island salt solution (BG110-K) for 48 h. An increase in hydrogenase activity was attributed to the decreased O2 concentration in the system, due to a reduction of photosynthetic O2 evolution rate and a promotion of dark respiration rate. Moreover, nitrogen and potassium deprivation stimulated glycogen accumulation and decreased specific activity of pyruvate kinase. Transcriptional analysis of genes involved in H2 metabolism using RNA-seq confirmed the above results. Several genes involved in glycogen biosynthesis (glgA, glgB, and glgP) were upregulated under both nitrogen and potassium deprivation, but genes regulating enzymes in the glycolytic pathway were downregulated, especially pyk encoding pyruvate kinase. Interestingly, genes involved in the oxidative pentose phosphate pathway (OPP) were upregulated. Thus, OPP became the favored pathway for glycogen catabolism and the generation of reduced nicotinamide adenine dinucleotide phosphate (NADPH), which resulted in an increase in H2 production under dark anaerobic condition in both nitrogen- and potassium-deprived cells.
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Affiliation(s)
- Nattanon Chinchusak
- Department of Biology, School of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Aran Incharoensakdi
- Laboratory of Cyanobacterial Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand,Academy of Science, Royal Society of Thailand, Bangkok, Thailand
| | - Saranya Phunpruch
- Department of Biology, School of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok, Thailand,Bioenergy Research Unit, School of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok, Thailand,*Correspondence: Saranya Phunpruch,
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6
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Krishnakumar R, Ruffing AM. OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data. PLoS Comput Biol 2022; 18:e1009731. [PMID: 34986143 PMCID: PMC8765615 DOI: 10.1371/journal.pcbi.1009731] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/18/2022] [Accepted: 12/07/2021] [Indexed: 11/19/2022] Open
Abstract
Operon prediction in prokaryotes is critical not only for understanding the regulation of endogenous gene expression, but also for exogenous targeting of genes using newly developed tools such as CRISPR-based gene modulation. A number of methods have used transcriptomics data to predict operons, based on the premise that contiguous genes in an operon will be expressed at similar levels. While promising results have been observed using these methods, most of them do not address uncertainty caused by technical variability between experiments, which is especially relevant when the amount of data available is small. In addition, many existing methods do not provide the flexibility to determine the stringency with which genes should be evaluated for being in an operon pair. We present OperonSEQer, a set of machine learning algorithms that uses the statistic and p-value from a non-parametric analysis of variance test (Kruskal-Wallis) to determine the likelihood that two adjacent genes are expressed from the same RNA molecule. We implement a voting system to allow users to choose the stringency of operon calls depending on whether your priority is high recall or high specificity. In addition, we provide the code so that users can retrain the algorithm and re-establish hyperparameters based on any data they choose, allowing for this method to be expanded as additional data is generated. We show that our approach detects operon pairs that are missed by current methods by comparing our predictions to publicly available long-read sequencing data. OperonSEQer therefore improves on existing methods in terms of accuracy, flexibility, and adaptability. Bacteria and archaea, single-cell organisms collectively known as prokaryotes, live in all imaginable environments and comprise the majority of living organisms on this planet. Prokaryotes play a critical role in the homeostasis of multicellular organisms (such as animals and plants) and ecosystems. In addition, bacteria can be pathogenic and cause a variety of diseases in these same hosts and ecosystems. In short, understanding the biology and molecular functions of bacteria and archaea and devising mechanisms to engineer and optimize their properties are critical scientific endeavors with significant implications in healthcare, agriculture, manufacturing, and climate science among others. One major molecular difference between unicellular and multicellular organisms is the way they express genes–multicellular organisms make individual RNA molecules for each gene while, prokaryotes express operons (i.e., a group of genes coding functionally related proteins) in contiguous polycistronic RNA molecules. Understanding which genes exist within operons is critical for elucidating basic biology and for engineering organisms. In this work, we use a combination of statistical and machine learning-based methods to use next-generation sequencing data to predict operon structure across a range of prokaryotes. Our method provides an easily implemented, robust, accurate, and flexible way to determine operon structure in an organism-agnostic manner using readily available data.
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Affiliation(s)
- Raga Krishnakumar
- Systems Biology Department, Sandia National Laboratories, Livermore, California, United States of America
- * E-mail:
| | - Anne M. Ruffing
- Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, New Mexico, United States of America
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Choi HI, Hwang SW, Kim J, Park B, Jin E, Choi IG, Sim SJ. Augmented CO 2 tolerance by expressing a single H +-pump enables microalgal valorization of industrial flue gas. Nat Commun 2021; 12:6049. [PMID: 34663809 PMCID: PMC8523702 DOI: 10.1038/s41467-021-26325-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 10/01/2021] [Indexed: 12/02/2022] Open
Abstract
Microalgae can accumulate various carbon-neutral products, but their real-world applications are hindered by their CO2 susceptibility. Herein, the transcriptomic changes in a model microalga, Chlamydomonas reinhardtii, in a high-CO2 milieu (20%) are evaluated. The primary toxicity mechanism consists of aberrantly low expression of plasma membrane H+-ATPases (PMAs) accompanied by intracellular acidification. Our results demonstrate that the expression of a universally expressible PMA in wild-type strains makes them capable of not only thriving in acidity levels that they usually cannot survive but also exhibiting 3.2-fold increased photoautotrophic production against high CO2 via maintenance of a higher cytoplasmic pH. A proof-of-concept experiment involving cultivation with toxic flue gas (13 vol% CO2, 20 ppm NOX, and 32 ppm SOX) shows that the production of CO2-based bioproducts by the strain is doubled compared with that by the wild-type, implying that this strategy potentially enables the microalgal valorization of CO2 in industrial exhaust.
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Affiliation(s)
- Hong Il Choi
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Sung-Won Hwang
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Jongrae Kim
- Department of Life Science, Hanyang University, 206, Wangsimni-ro, Seongbuk-gu, Seoul, 04763, Republic of Korea
| | - Byeonghyeok Park
- Department of Biotechnology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - EonSeon Jin
- Department of Life Science, Hanyang University, 206, Wangsimni-ro, Seongbuk-gu, Seoul, 04763, Republic of Korea
| | - In-Geol Choi
- Department of Biotechnology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Sang Jun Sim
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea.
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8
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Muro-Pastor MI, Cutillas-Farray Á, Pérez-Rodríguez L, Pérez-Saavedra J, Vega-de Armas A, Paredes A, Robles-Rengel R, Florencio FJ. CfrA, a Novel Carbon Flow Regulator, Adapts Carbon Metabolism to Nitrogen Deficiency in Cyanobacteria. PLANT PHYSIOLOGY 2020; 184:1792-1810. [PMID: 32900980 PMCID: PMC7723081 DOI: 10.1104/pp.20.00802] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 08/22/2020] [Indexed: 05/03/2023]
Abstract
Cyanobacteria unable to fix atmospheric nitrogen have evolved sophisticated adaptations to survive to long periods of nitrogen starvation. These genetic programs are still largely unknown-as evidenced by the many proteins whose expression is regulated in response to nitrogen availability, but which belong to unknown or hypothetical categories. In Synechocystis sp. PCC 6803, the global nitrogen regulator NtcA activates the expression of the sll0944 gene upon nitrogen deprivation. This gene encodes a protein that is highly conserved in cyanobacteria, but of unknown function. Based on the results described herein, we named the product of sll0944 carbon flow regulator A (CfrA). We analyzed the phenotypes of strains containing different levels of CfrA, including a knock-out strain (ΔcfrA), and two strains overexpressing CfrA from either the constitutive P trc promoter (Ptrc-cfrA) or the arsenite-inducible promoter P arsB (Pars-cfrA). Our results show that the amount of CfrA determines the accumulation of glycogen, and affects the synthesis of protein and photosynthetic pigments as well as amino acid pools. Strains with high levels of CfrA present high levels of glycogen and a decrease in photosynthetic pigments and protein content when nitrogen is available. Possible interactions between CfrA and the pyruvate dehydrogenase complex or PII protein have been revealed. The phenotype associated with CfrA overexpression is also observed in PII-deficient strains; however, it is lethal in this genetic background. Taken together, our results indicate a role for CfrA in the adaptation of carbon flux during acclimation to nitrogen deficiency.
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Affiliation(s)
- M Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla, 41092 Sevilla, Spain
| | - Áureo Cutillas-Farray
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla, 41092 Sevilla, Spain
| | - Laura Pérez-Rodríguez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla, 41092 Sevilla, Spain
| | - Julia Pérez-Saavedra
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla, 41092 Sevilla, Spain
| | - Ana Vega-de Armas
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla, 41092 Sevilla, Spain
| | - Ana Paredes
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla, 41092 Sevilla, Spain
| | - Rocío Robles-Rengel
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla, 41092 Sevilla, Spain
| | - Francisco J Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla, 41092 Sevilla, Spain
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9
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Loofah-based microalgae and cyanobacteria biocomposites for intensifying carbon dioxide capture. J CO2 UTIL 2020. [DOI: 10.1016/j.jcou.2020.101348] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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Jeong Y, Cho SH, Lee H, Choi HK, Kim DM, Lee CG, Cho S, Cho BK. Current Status and Future Strategies to Increase Secondary Metabolite Production from Cyanobacteria. Microorganisms 2020; 8:E1849. [PMID: 33255283 PMCID: PMC7761380 DOI: 10.3390/microorganisms8121849] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/15/2020] [Accepted: 11/23/2020] [Indexed: 12/16/2022] Open
Abstract
Cyanobacteria, given their ability to produce various secondary metabolites utilizing solar energy and carbon dioxide, are a potential platform for sustainable production of biochemicals. Until now, conventional metabolic engineering approaches have been applied to various cyanobacterial species for enhanced production of industrially valued compounds, including secondary metabolites and non-natural biochemicals. However, the shortage of understanding of cyanobacterial metabolic and regulatory networks for atmospheric carbon fixation to biochemical production and the lack of available engineering tools limit the potential of cyanobacteria for industrial applications. Recently, to overcome the limitations, synthetic biology tools and systems biology approaches such as genome-scale modeling based on diverse omics data have been applied to cyanobacteria. This review covers the synthetic and systems biology approaches for advanced metabolic engineering of cyanobacteria.
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Affiliation(s)
- Yujin Jeong
- Department of Biological Sciences and KAIST Institutes for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea; (Y.J.); (S.-H.C.)
| | - Sang-Hyeok Cho
- Department of Biological Sciences and KAIST Institutes for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea; (Y.J.); (S.-H.C.)
| | - Hookeun Lee
- Institute of Pharmaceutical Research, College of Pharmacy, Gachon University, Incheon 21999, Korea;
| | | | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon 34134, Korea;
| | - Choul-Gyun Lee
- Department of Biological Engineering, Inha University, Incheon 22212, Korea;
| | - Suhyung Cho
- Department of Biological Sciences and KAIST Institutes for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea; (Y.J.); (S.-H.C.)
| | - Byung-Kwan Cho
- Department of Biological Sciences and KAIST Institutes for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea; (Y.J.); (S.-H.C.)
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11
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Ko SC, Woo HM. Biosynthesis of the Calorie-Free Sweetener Precursor ent-Kaurenoic Acid from CO 2 Using Engineered Cyanobacteria. ACS Synth Biol 2020; 9:2979-2985. [PMID: 33175492 DOI: 10.1021/acssynbio.0c00523] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
To supply the sustainable calorie-free sweetener stevioside, synthetic photosynthetic bacteria were developed to produce ent-kaurenoic acid as a precursor of stevioside directly from CO2. By the use of a combinatorial and modular approach for gene expression, including a cytochrome P450 and the corresponding reductase, engineered Synechoccous elongatus PCC 7942 as a model cyanobacterium enabled the biosynthesis of ent-kaurenoic acid at 2.9 ± 0.01 mg L-1 from CO2. We found that the order of genes for expression was critical, producing ent-kaurenoic acid by balancing gene expressions and accumulation of the toxic intermediate in a cell. The engineered bacteria allowed the complete biosynthesis of ent-kaurenoic acid, and it will be used for stevioside biosynthesis from CO2 as a controlled fermentation.
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Affiliation(s)
- Sung Cheon Ko
- Department of Food Science and Biotechnology, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Han Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
- BioFoundry Research Center, Institute of Biotechnology and Bioengineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
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12
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Choi SY, Woo HM. CRISPRi-dCas12a: A dCas12a-Mediated CRISPR Interference for Repression of Multiple Genes and Metabolic Engineering in Cyanobacteria. ACS Synth Biol 2020; 9:2351-2361. [PMID: 32379967 DOI: 10.1021/acssynbio.0c00091] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In cyanobacteria, metabolic engineering using synthetic biology tools is limited to build a biosolar cell factory that converts CO2 to value-added chemicals, as repression of essential genes has not been achieved. In this study, we developed a dCas12a-mediated CRISPR interference system (CRISPRi-dCas12a) in cyanobacteria that effectively blocked the transcriptional initiation by means of a CRISPR-RNA (crRNA) and 19-nt direct repeat, resulting in 53-94% gene repression. The repression of multiple genes in a single crRNA array was also successfully achieved without a loss in repression strength. In addition, as a demonstration of the dCas12a-mediated CRISPRi for metabolic engineering, photosynthetic squalene production was improved by repressing the essential genes of either acnB encoding for aconitase or cpcB2 encoding for phycocyanin β-subunit in Synechococcus elongatus PCC 7942. The ability to regulate gene repression will promote the construction of biosolar cell factories to produce value-added chemicals.
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Affiliation(s)
- Sun Young Choi
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
- BioFoundry Research Center, Institute of Biotechnology and Bioengineering, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Han Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
- BioFoundry Research Center, Institute of Biotechnology and Bioengineering, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
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Glyceroglycolipid Metabolism Regulations under Phosphate Starvation Revealed by Transcriptome Analysis in Synechococcus elongatus PCC 7942. Mar Drugs 2020; 18:md18070360. [PMID: 32668657 PMCID: PMC7401256 DOI: 10.3390/md18070360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/04/2020] [Accepted: 07/10/2020] [Indexed: 12/12/2022] Open
Abstract
Glyceroglycolipids, abundant in cyanobacteria's photosynthetic membranes, present bioactivities and pharmacological activities, and can be widely used in the pharmaceutical industry. Environmental factors could alter the contents and compositions of cyanobacteria glyceroglycolipids, but the regulation mechanism remains unclear. Therefore, the glyceroglycolipids contents and the transcriptome in Synechococcus elongatus PCC 7942 were analyzed under phosphate starvation. Under phosphate starvation, the decrease of monogalactosyl diacylglycerol (MGDG) and increases of digalactosyl diacylglycerol (DGDG) and sulfoquinovosyl diacylglycerol (SQDG) led to a decrease in the MGDG/DGDG ratio, from 4:1 to 5:3, after 12 days of cultivation. However, UDP-sulfoquinovose synthase gene sqdB, and the SQDG synthase gene sqdX, were down-regulated, and the decreased MGDG/DGDG ratio was later increased back to 2:1 after 15 days of cultivation, suggesting the regulation of glyceroglycolipids on day 12 was based on the MGDG/DGDG ratio maintaining glyceroglycolipid homeostasis. There are 12 differentially expressed transcriptional regulators that could be potential candidates related to glyceroglycolipid regulation, according to the transcriptome analysis. The transcriptome analysis also suggested post-transcriptional or post-translational regulations in glyceroglycolipid synthesis. This study provides further insights into glyceroglycolipid metabolism, as well as the scientific basis for glyceroglycolipid synthesis optimization and cyanobacteria glyceroglycolipids utilization via metabolic engineering.
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14
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Zhou Y, Li X, Xia Q, Dai R. Transcriptomic survey on the microcystins production and growth of Microcystis aeruginosa under nitrogen starvation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 700:134501. [PMID: 31689655 DOI: 10.1016/j.scitotenv.2019.134501] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/15/2019] [Accepted: 09/15/2019] [Indexed: 06/10/2023]
Abstract
Cyanobacteria are a vital component of freshwater phytoplankton, and many species are recognized for their ability to produce toxins and harmful algal blooms (HABs). Nitrogen is an essential element of all the complex macromolecules in algal cells. However, the underlying molecular mechanism of the changes in transcriptomic patterns and physiological responses in response to N starvation is poorly understood. The transcriptomes were generated via RNA-sequencing (RNA-Seq) technology to study the major metabolic pathway under N starvation. The results shed light on the mechanism of toxin production and physiological adaptations in Microcystis aeruginosa (M. aeruginosa). The cell density gradually increased during the first two days then declined over time and was finally stable at (15.50 ± 0.5) × 105 cell mL-1 after 6 days. The chlorophyll-a content and phycocyanin content of M. aeruginosa increased during the first two days and subsequently decreased markedly over time under N starvation. The variable to maximum chlorophyll fluorescence ratio (Fv/Fm ratio) decreased with time under N starvation. Most photosynthesis genes have similarity decreasing trends with growth physiological changes. The microcystins (MCs) levels generally increased first, reaching a peak value with 1.35 pg cell-1 on the fifth day, and then remained roughly constant. The genes involved in N metabolism-related gene expression were upregulated to maintain normal biological activity, while the genes involved in photosynthesis-related gene expression were downregulated to save energy. All genes encoding algae toxin synthesis were upregulated under N starvation. The observed expression patterns demonstrate that all MCs genes respond similarly to MCs production within the cell. Our results indicate the response mechanism of M. aeruginosa under N starvation and provide a comprehensive understanding of N-controlling cyanobacteria and MCs synthesis.
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Affiliation(s)
- Yanping Zhou
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Xuan Li
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Qiongqiong Xia
- North China Municipal Engineering Design & Research Institute Co. Ltd., Tianjin 300074, China
| | - Ruihua Dai
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China.
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15
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Pattharaprachayakul N, Lee HJ, Incharoensakdi A, Woo HM. Evolutionary Engineering of Cyanobacteria to Enhance the Production of α-Farnesene from CO 2. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:13658-13664. [PMID: 31755253 DOI: 10.1021/acs.jafc.9b06254] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Photosynthetic cyanobacteria can fix CO2 and utilize it as the sole carbon source for cell growth and production of biochemicals. Here, we metabolically engineered Synechococcus elongatus PCC 7942 for an enhanced production of α-farnesene by optimizing the ribosome-binding site (RBS) of the codon-optimized farnesene synthase gene. The production of α-farnesene was found to be enhanced in strains with a low translation initiation rate, resulting in α-farnesene production (0.57 mg/(L day)). Using the RBS variants and random mutations, we performed fluorescence-based analysis of cells grown in 96-well culture plates to screen the α-farnesene-producing strains but could not improve the titers of the RBS-optimized strains. However, evolutionary engineering of the RBS-optimized strains resulted in a twofold increase in α-farnesene production (1.2 mg/(L day)) compared to the previous study. Therefore, combining metabolic and evolutionary engineering might be helpful for enhancing the cellular fitness of cyanobacteria for the production of target chemicals.
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Affiliation(s)
- Napisa Pattharaprachayakul
- Department of Food Science and Biotechnology , Sungkyunkwan University (SKKU) , 2066 Seobu-ro , Jangan-gu, Suwon 16419 , Republic of Korea
- Laboratory of Cyanobacterial Biotechnology, Department of Biochemistry, Faculty of Science , Chulalongkorn University , 254 Phayathai Road , Pathumwan, Bangkok 10330 , Thailand
| | - Hyun Jeong Lee
- Department of Food Science and Biotechnology , Sungkyunkwan University (SKKU) , 2066 Seobu-ro , Jangan-gu, Suwon 16419 , Republic of Korea
| | - Aran Incharoensakdi
- Laboratory of Cyanobacterial Biotechnology, Department of Biochemistry, Faculty of Science , Chulalongkorn University , 254 Phayathai Road , Pathumwan, Bangkok 10330 , Thailand
| | - Han Min Woo
- Department of Food Science and Biotechnology , Sungkyunkwan University (SKKU) , 2066 Seobu-ro , Jangan-gu, Suwon 16419 , Republic of Korea
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16
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Park J, Lee HH, Jung H, Seo YS. Transcriptome analysis to understand the effects of the toxoflavin and tropolone produced by phytopathogenic Burkholderia on Escherichia coli. J Microbiol 2019; 57:781-794. [DOI: 10.1007/s12275-019-9330-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/18/2019] [Accepted: 07/25/2019] [Indexed: 12/13/2022]
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17
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Knoot CJ, Khatri Y, Hohlman RM, Sherman DH, Pakrasi HB. Engineered Production of Hapalindole Alkaloids in the Cyanobacterium Synechococcus sp. UTEX 2973. ACS Synth Biol 2019; 8:1941-1951. [PMID: 31284716 PMCID: PMC6724726 DOI: 10.1021/acssynbio.9b00229] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cyanobacteria produce numerous valuable bioactive secondary metabolites (natural products) including alkaloids, isoprenoids, nonribosomal peptides, and polyketides. However, the genomic organization of the biosynthetic gene clusters, complex gene expression patterns, and low compound yields synthesized by the native producers currently limits access to the vast majority of these valuable molecules for detailed studies. Molecular cloning and expression of such clusters in heterotrophic hosts is often precarious owing to genetic and biochemical incompatibilities. Production of such biomolecules in photoautotrophic hosts analogous to the native producers is an attractive alternative that has been under-explored. Here, we describe engineering of the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973 to produce key compounds of the hapalindole family of indole-isonitrile alkaloids. Engineering of the 42-kbp "fam" hapalindole pathway from the cyanobacterium Fischerella ambigua UTEX 1903 into S2973 was accomplished by rationally reconstructing six to seven core biosynthetic genes into synthetic operons. The resulting Synechococcus strains afforded controllable production of indole-isonitrile biosynthetic intermediates and hapalindoles H and 12-epi-hapalindole U at a titer of 0.75-3 mg/L. Exchanging genes encoding fam cyclase enzymes in the synthetic operons was employed to control the stereochemistry of the resulting product. Establishing a robust expression system provides a facile route to scalable levels of similar natural and new forms of bioactive hapalindole derivatives and its structural relatives (e.g., fischerindoles, welwitindolinones). Moreover, this versatile expression system represents a promising tool for exploring other functional characteristics of orphan gene products that mediate the remarkable biosynthesis of this important family of natural products.
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Affiliation(s)
- Cory J Knoot
- Department of Biology , Washington University , St. Louis , Missouri 63130 , United States
| | - Yogan Khatri
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Robert M Hohlman
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - David H Sherman
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Himadri B Pakrasi
- Department of Biology , Washington University , St. Louis , Missouri 63130 , United States
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18
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Forchhammer K, Schwarz R. Nitrogen chlorosis in unicellular cyanobacteria – a developmental program for surviving nitrogen deprivation. Environ Microbiol 2018; 21:1173-1184. [DOI: 10.1111/1462-2920.14447] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/04/2018] [Accepted: 10/09/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine, University Tübingen Auf der Morgenstelle 28, 72076 Tübingen Germany
| | - Rakefet Schwarz
- The Mina & Everard Goodman Faculty of Life SciencesBar‐Ilan University Ramat‐Gan 5290002 Israel
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19
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Chrismas NAM, Anesio AM, Sánchez-Baracaldo P. The future of genomics in polar and alpine cyanobacteria. FEMS Microbiol Ecol 2018; 94:4904125. [PMID: 29506259 PMCID: PMC5939894 DOI: 10.1093/femsec/fiy032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/23/2018] [Indexed: 01/01/2023] Open
Abstract
In recent years, genomic analyses have arisen as an exciting way of investigating the functional capacity and environmental adaptations of numerous micro-organisms of global relevance, including cyanobacteria. In the extreme cold of Arctic, Antarctic and alpine environments, cyanobacteria are of fundamental ecological importance as primary producers and ecosystem engineers. While their role in biogeochemical cycles is well appreciated, little is known about the genomic makeup of polar and alpine cyanobacteria. In this article, we present ways that genomic techniques might be used to further our understanding of cyanobacteria in cold environments in terms of their evolution and ecology. Existing examples from other environments (e.g. marine/hot springs) are used to discuss how methods developed there might be used to investigate specific questions in the cryosphere. Phylogenomics, comparative genomics and population genomics are identified as methods for understanding the evolution and biogeography of polar and alpine cyanobacteria. Transcriptomics will allow us to investigate gene expression under extreme environmental conditions, and metagenomics can be used to complement tradition amplicon-based methods of community profiling. Finally, new techniques such as single cell genomics and metagenome assembled genomes will also help to expand our understanding of polar and alpine cyanobacteria that cannot readily be cultured.
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Affiliation(s)
- Nathan A M Chrismas
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, UK
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
| | - Alexandre M Anesio
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, UK
| | - Patricia Sánchez-Baracaldo
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, UK
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20
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Rewiring of Cyanobacterial Metabolism for Hydrogen Production: Synthetic Biology Approaches and Challenges. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1080:171-213. [PMID: 30091096 DOI: 10.1007/978-981-13-0854-3_8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
Abstract
With the demand for renewable energy growing, hydrogen (H2) is becoming an attractive energy carrier. Developing H2 production technologies with near-net zero carbon emissions is a major challenge for the "H2 economy." Certain cyanobacteria inherently possess enzymes, nitrogenases, and bidirectional hydrogenases that are capable of H2 evolution using sunlight, making them ideal cell factories for photocatalytic conversion of water to H2. With the advances in synthetic biology, cyanobacteria are currently being developed as a "plug and play" chassis to produce H2. This chapter describes the metabolic pathways involved and the theoretical limits to cyanobacterial H2 production and summarizes the metabolic engineering technologies pursued.
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21
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Tan X, Hou S, Song K, Georg J, Klähn S, Lu X, Hess WR. The primary transcriptome of the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:218. [PMID: 30127850 PMCID: PMC6091082 DOI: 10.1186/s13068-018-1215-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/25/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Cyanobacteria have shown promising potential for the production of various biofuels and chemical feedstocks. Synechococcus elongatus UTEX 2973 is a fast-growing strain with pronounced tolerance to high temperatures and illumination. Hence, this strain appears to be ideal for the development of photosynthetic biotechnology. However, molecular insights on how this strain can rapidly accumulate biomass and carbohydrates under high-light and high-temperature conditions are lacking. RESULTS Differential RNA-Sequencing (dRNA-Seq) enabled the genome-wide identification of 4808 transcription start sites (TSSs) in S. elongatus UTEX 2973 using a background reduction algorithm. High light promoted the transcription of genes associated with central metabolic pathways, whereas the highly induced small RNA (sRNA) PsrR1 likely contributed to the repression of phycobilisome genes and the accelerated glycogen accumulation rates measured under this condition. Darkness caused transcriptome remodeling with a decline in the expression of genes for carbon fixation and other major metabolic pathways and an increase in the expression of genes for glycogen catabolism and Calvin cycle inhibitor CP12. Two of the identified TSSs drive the transcription of highly abundant sRNAs in darkness. One of them is widely conserved throughout the cyanobacterial phylum. Its gene is fused to a protein-coding gene in some species, illustrating the evolutionary origin of sRNAs from an mRNA 3'-end. CONCLUSIONS Our comprehensive set of genome-wide mapped TSSs, sRNAs and promoter activities will be valuable for projects requiring precise information about the control of transcription aimed at metabolic engineering and the elucidation of stress acclimation mechanisms in this promising strain.
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Affiliation(s)
- Xiaoming Tan
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Present Address: College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062 China
| | - Shengwei Hou
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Kuo Song
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Jens Georg
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Stephan Klähn
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Department of Solar Materials, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Xuefeng Lu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, No. 1 Wenhai Road, Qingdao, 266237 China
| | - Wolfgang R. Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Freiburg Institute for Advanced Studies, University of Freiburg, Albertstraße 19, 79104 Freiburg, Germany
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22
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Giner-Lamia J, Robles-Rengel R, Hernández-Prieto MA, Muro-Pastor MI, Florencio FJ, Futschik ME. Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803. Nucleic Acids Res 2017; 45:11800-11820. [PMID: 29036481 PMCID: PMC5714215 DOI: 10.1093/nar/gkx860] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 09/15/2017] [Indexed: 12/22/2022] Open
Abstract
In cyanobacteria, nitrogen homeostasis is maintained by an intricate regulatory network around transcription factor NtcA. Although mechanisms controlling NtcA activity appear to be well understood, its regulon remains poorly defined. To determine the NtcA regulon during the early stages of nitrogen starvation for the model cyanobacterium Synechocystis sp. PCC 6803, we performed chromatin immunoprecipitation, followed by sequencing (ChIP-seq), in parallel with transcriptome analysis (RNA-seq). Through combining these methods, we determined 51 genes activated and 28 repressed directly by NtcA. In addition to genes associated with nitrogen and carbon metabolism, a considerable number of genes without current functional annotation were among direct targets providing a rich reservoir for further studies. The NtcA regulon also included eight non-coding RNAs, of which Ncr1071, Syr6 and NsiR7 were experimentally validated, and their putative targets were computationally predicted. Surprisingly, we found substantial NtcA binding associated with delayed expression changes indicating that NtcA can reside in a poised state controlled by other factors. Indeed, a role of PipX as modulating factor in nitrogen regulation was confirmed for selected NtcA-targets. We suggest that the indicated poised state of NtcA enables a more differentiated response to nitrogen limitation and can be advantageous in native habitats of Synechocystis.
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Affiliation(s)
- Joaquín Giner-Lamia
- Systems Biology and Bioinformatics Laboratory, CBMR, University of Algarve, 8005-139 Faro, Portugal.,Laboratory of Intracellular Bacterial Pathogens, Department of Microbial Biotechnology, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain
| | - Rocío Robles-Rengel
- Instituto de Bioquímica Vegetal y Fotosíntesis. Universidad de Sevilla-CSIC, Av. Américo Vespucio 49, E-41092 Seville, Spain
| | - Miguel A Hernández-Prieto
- Systems Biology and Bioinformatics Laboratory, CBMR, University of Algarve, 8005-139 Faro, Portugal.,ARC Centre of Excellence for Translational Photosynthesis and School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - M Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis. Universidad de Sevilla-CSIC, Av. Américo Vespucio 49, E-41092 Seville, Spain
| | - Francisco J Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis. Universidad de Sevilla-CSIC, Av. Américo Vespucio 49, E-41092 Seville, Spain
| | - Matthias E Futschik
- Systems Biology and Bioinformatics Laboratory, CBMR, University of Algarve, 8005-139 Faro, Portugal.,Centre of Marine Sciences (CCMAR), University of Algarve, 8005-139 Faro, Portugal.,School of Biomedical & Healthcare Sciences, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth PL6 8BU, UK
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23
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Lee HJ, Lee J, Lee SM, Um Y, Kim Y, Sim SJ, Choi JI, Woo HM. Direct Conversion of CO 2 to α-Farnesene Using Metabolically Engineered Synechococcus elongatus PCC 7942. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:10424-10428. [PMID: 29068210 DOI: 10.1021/acs.jafc.7b03625] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Direct conversion of carbon dioxide (CO2) to value-added chemicals by engineering of cyanobacteria has received attention as a sustainable strategy in food and chemical industries. Herein, Synechococcus elongatus PCC 7942, a model cyanobacterium, was engineered to produce α-farnesene from CO2. As a result of the lack of farnesene synthase (FS) activity in the wild-type cyanobacterium, we metabolically engineered S. elongatus PCC 7942 to express heterologous FS from either Norway spruce or apple fruit, resulting in detectable peaks of α-farnesene. To enhance α-farnesene production, an optimized methylerythritol phosphate (MEP) pathway was introduced in the farnesene-producing strain to supply farnesyl diphosphate. Subsequent cyanobacterial culture with a dodecane overlay resulted in photosynthetic production of α-farnesene (4.6 ± 0.4 mg/L in 7 days) from CO2. To the best of our knowledge, this is the first report of the photosynthetic production of α-farnesene from CO2 in the unicellular cyanobacterium S. elongatus PCC 7942.
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Affiliation(s)
| | - Jiwon Lee
- Clean Energy Research Center, Korea Institute of Science and Technology , Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology , Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology , Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Yunje Kim
- Clean Energy Research Center, Korea Institute of Science and Technology , Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Sang Jun Sim
- Department of Chemical and Biological Engineering, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Jong-Il Choi
- Department of Biotechnology and Bioengineering, Chonnam National University , 77 Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea
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24
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Lee HJ, Choi J, Lee SM, Um Y, Sim SJ, Kim Y, Woo HM. Photosynthetic CO 2 Conversion to Fatty Acid Ethyl Esters (FAEEs) Using Engineered Cyanobacteria. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:1087-1092. [PMID: 28128561 DOI: 10.1021/acs.jafc.7b00002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Metabolic engineering of cyanobacteria has received attention as a sustainable strategy to convert carbon dioxide to fatty acid-derived chemicals that are widely used in the food and chemical industries. Herein, Synechococcus elongatus PCC 7942, a model cyanobacterium, was engineered for the first time to produce fatty acid ethyl esters (FAEEs) from CO2. Due to the lack of an endogenous ethanol production pathway and wax ester synthase (AftA) activity in the wild-type cyanobacterium, we metabolically engineered S. elongatus PCC 7942 by expressing heterologous AftA and introducing the ethanol pathway, resulting in detectable peaks of FAEEs. To enhance FAEE production, a heterologous phosphoketolase pathway was introduced in the FAEE-producing strain to supply acetyl-CoA. Subsequent optimization of the cyanobacterial culture with a hexadecane overlay resulted in engineered S. elongatus PCC 7942 that produced photosynthetic FAEEs (10.0 ± 0.7 mg/L/OD730) from CO2. This paper is the first report of photosynthetic production of FAEEs from CO2 in cyanobacteria.
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Affiliation(s)
- Hyun Jeong Lee
- Clean Energy Research Center, Korea Institute of Science and Technology , Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Jaeyeon Choi
- Clean Energy Research Center, Korea Institute of Science and Technology , Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology , Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology , Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Sang Jun Sim
- Department of Chemical and Biological Engineering, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Yunje Kim
- Clean Energy Research Center, Korea Institute of Science and Technology , Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Han Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU) , 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
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