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Swain K, Sharon I, Blackson W, Parrish S, Tekel S, Schmeing TM, Nielsen DR, Nannenga BL. Soluble and stable cyanophycin synthetase expression enhances heterologous cyanophycin production in Escherichia coli. Biochem Eng J 2023. [DOI: 10.1016/j.bej.2023.108916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
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Thiel T. Organization and regulation of cyanobacterial nif gene clusters: implications for nitrogenase expression in plant cells. FEMS Microbiol Lett 2020; 366:5470946. [PMID: 31062027 DOI: 10.1093/femsle/fnz077] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 04/11/2019] [Indexed: 12/16/2022] Open
Abstract
For over 50 years scientists have considered the possibility of engineering a plant with nitrogen fixation capability, freeing farmers from their dependence on nitrogen fertilizers. With the development of the tools of synthetic biology, more progress has been made toward this goal in the last 5 years than in the previous five decades. Most of the effort has focused on nitrogenase genes from Klebsiella oxytoca, which has complex gene regulation. There may be advantages in using nitrogenase genes from cyanobacteria, which comprise large polycistronic gene clusters that may be easier to manipulate and eventually express in a plant. The fact that some diatoms have a cyanobacterial nitrogen fixing organelle further supports the idea that a cyanobacterial nitrogenase gene cluster may function in a newly-engineered, cyanobacterial-based plant organelle, a nitroplast. This review describes recent attempts to express the nif genes from Anabaena variabilis ATCC 29413, Leptolyngbya boryana dg5 and Cyanothece sp. ATCC 51142 in heterologous cyanobacteria in the context of the organization of the nitrogenase genes and their regulation by the transcription factor CnfR via its highly conserved binding sites.
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Affiliation(s)
- Teresa Thiel
- Department of Biology, University of Missouri-St. Louis, One University Blvd., St. Louis, MO 63121, USA
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Transcriptomic data-driven discovery of global regulatory features of rice seeds developing under heat stress. Comput Struct Biotechnol J 2020; 18:2556-2567. [PMID: 33033578 PMCID: PMC7522763 DOI: 10.1016/j.csbj.2020.09.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 11/30/2022] Open
Abstract
Plants respond to abiotic stressors through a suite of strategies including differential regulation of stress-responsive genes. Hence, characterizing the influences of the relevant global regulators or on stress-related transcription factors is critical to understand plant stress response. Rice seed development is highly sensitive to elevated temperatures. To elucidate the extent and directional hierarchy of gene regulation in rice seeds under heat stress, we developed and implemented a robust multi-level optimization-based algorithm called Minimal Regulatory Network identifier (MiReN). MiReN could predict the minimal regulatory relationship between a gene and its potential regulators from our temporal transcriptomic dataset. MiReN predictions for global regulators including stress-responsive gene Slender Rice 1 (SLR1) and disease resistance gene XA21 were validated with published literature. It also predicted novel regulatory influences of other major regulators such as Kinesin-like proteins KIN12C and STD1, and WD repeat-containing protein WD40. Out of the 228 stress-responsive transcription factors identified, we predicted de novo regulatory influences on three major groups (MADS-box M-type, MYB, and bZIP) and investigated their physiological impacts during stress. Overall, MiReN results can facilitate new experimental studies to enhance our understanding of global regulatory mechanisms triggered during heat stress, which can potentially accelerate the development of stress-tolerant cultivars.
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Burén S, Rubio LM. State of the art in eukaryotic nitrogenase engineering. FEMS Microbiol Lett 2019; 365:4733273. [PMID: 29240940 PMCID: PMC5812491 DOI: 10.1093/femsle/fnx274] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/11/2017] [Indexed: 12/27/2022] Open
Abstract
Improving the ability of plants and plant-associated organisms to fix and assimilate atmospheric nitrogen has inspired plant biotechnologists for decades, not only to alleviate negative effects on nature from increased use and availability of reactive nitrogen, but also because of apparent economic benefits and opportunities. The combination of recent advances in synthetic biology and increased knowledge about the biochemistry and biosynthesis of the nitrogenase enzyme has made the seemingly remote and for long unreachable dream more possible. In this review, we will discuss strategies how this could be accomplished using biotechnology, with a special focus on recent progress on engineering plants to express its own nitrogenase.
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Affiliation(s)
- Stefan Burén
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223-Pozuelo de Alarcón, Madrid, Spain
| | - Luis M Rubio
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223-Pozuelo de Alarcón, Madrid, Spain
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Microbial production of cyanophycin: From enzymes to biopolymers. Biotechnol Adv 2019; 37:107400. [PMID: 31095967 DOI: 10.1016/j.biotechadv.2019.05.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 04/30/2019] [Accepted: 05/11/2019] [Indexed: 11/20/2022]
Abstract
Cyanophycin is an attractive biopolymer with chemical and material properties that are suitable for industrial applications in the fields of food, medicine, cosmetics, nutrition, and agriculture. For efficient production of cyanophycin, considerable efforts have been exerted to characterize cyanophycin synthetases (CphAs) and optimize fermentations and downstream processes. In this paper, we review the characteristics of diverse CphAs from cyanobacteria and non-cyanobacteria. Furthermore, strategies for cyanophycin production in microbial strains, including Escherichia coli, Pseudomonas putida, Ralstonia eutropha, Rhizopus oryzae, and Saccharomyces cerevisiae, heterologously expressing different cphA genes are reviewed. Additionally, chemical and material properties of cyanophycin and its derivatives produced through biological or chemical modifications are reviewed in the context of their industrial applications. Finally, future perspectives on microbial production of cyanophycin are provided to improve its cost-effectiveness.
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Behler J, Vijay D, Hess WR, Akhtar MK. CRISPR-Based Technologies for Metabolic Engineering in Cyanobacteria. Trends Biotechnol 2018; 36:996-1010. [DOI: 10.1016/j.tibtech.2018.05.011] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 05/24/2018] [Accepted: 05/29/2018] [Indexed: 12/16/2022]
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Synthetic Gene Regulation in Cyanobacteria. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1080:317-355. [DOI: 10.1007/978-981-13-0854-3_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Jin H, Wang Y, Idoine A, Bhaya D. Construction of a Shuttle Vector Using an Endogenous Plasmid From the Cyanobacterium Synechocystis sp. PCC6803. Front Microbiol 2018; 9:1662. [PMID: 30087668 PMCID: PMC6066503 DOI: 10.3389/fmicb.2018.01662] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 07/04/2018] [Indexed: 12/21/2022] Open
Abstract
To advance synthetic biology in the photosynthetic cyanobacterium Synechocystis sp. PCC6803 (Syn6803), we constructed a shuttle vector with some versatile features. This shuttle vector, pSCB-YFP, consists of a putative replicon identified on the plasmid pCC5.2, the origin of replication of pMB1 from E. coli, as well as the YFP reporter gene and a spectinomycin/streptomycin resistance cassette. pSCB-YFP is stably maintained in Syn6803M (a motile strain that lacks the endogenous pCC5.2) and expresses YFP. In addition, we engineered a fragment into pSCB-YFP that has multiple cloning sites and other features such that this plasmid can also be used as an expression vector (pSCBe). The shuttle vector pSCB-YFP can be stably maintained for at least 50 generations without antibiotic selection. It is a high copy number plasmid and can stably co-exist with the RSF1010-based pPMQAK1-GFP.
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Affiliation(s)
- Haojie Jin
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, United States
| | - Yan Wang
- Department of Neurosurgery and Stanford Stroke Center, Stanford University, Stanford, CA, United States
| | - Adam Idoine
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, United States
| | - Devaki Bhaya
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, United States
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Immethun CM, DeLorenzo DM, Focht CM, Gupta D, Johnson CB, Moon TS. Physical, chemical, and metabolic state sensors expand the synthetic biology toolbox for Synechocystis sp. PCC 6803. Biotechnol Bioeng 2017; 114:1561-1569. [PMID: 28244586 DOI: 10.1002/bit.26275] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 01/19/2017] [Accepted: 02/19/2017] [Indexed: 02/04/2023]
Abstract
Many under-developed organisms possess important traits that can boost the effectiveness and sustainability of microbial biotechnology. Photoautotrophic cyanobacteria can utilize the energy captured from light to fix carbon dioxide for their metabolic needs while living in environments not suited for growing crops. Various value-added compounds have been produced by cyanobacteria in the laboratory; yet, the products' titers and yields are often not industrially relevant and lag behind what have been accomplished in heterotrophic microbes. Genetic tools for biological process control are needed to take advantage of cyanobacteria's beneficial qualities, as tool development also lags behind what has been created in common heterotrophic hosts. To address this problem, we developed a suite of sensors that regulate transcription in the model cyanobacterium Synechocystis sp. PCC 6803 in response to metabolically relevant signals, including light and the cell's nitrogen status, and a family of sensors that respond to the inexpensive chemical, l-arabinose. Increasing the number of available tools enables more complex and precise control of gene expression. Expanding the synthetic biology toolbox for this cyanobacterium also improves our ability to utilize this important under-developed organism in biotechnology. Biotechnol. Bioeng. 2017;114: 1561-1569. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Cheryl M Immethun
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Drew M DeLorenzo
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Caroline M Focht
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Dinesh Gupta
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Charles B Johnson
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
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Identifying the Metabolic Differences of a Fast-Growth Phenotype in Synechococcus UTEX 2973. Sci Rep 2017; 7:41569. [PMID: 28139686 PMCID: PMC5282492 DOI: 10.1038/srep41569] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/21/2016] [Indexed: 11/18/2022] Open
Abstract
The photosynthetic capabilities of cyanobacteria make them interesting candidates for industrial bioproduction. One obstacle to large-scale implementation of cyanobacteria is their limited growth rates as compared to industrial mainstays. Synechococcus UTEX 2973, a strain closely related to Synechococcus PCC 7942, was recently identified as having the fastest measured growth rate among cyanobacteria. To facilitate the development of 2973 as a model organism we developed in this study the genome-scale metabolic model iSyu683. Experimental data were used to define CO2 uptake rates as well as the biomass compositions for each strain. The inclusion of constraints based on experimental measurements of CO2 uptake resulted in a ratio of the growth rates of Synechococcus 2973 to Synechococcus 7942 of 2.03, which nearly recapitulates the in vivo growth rate ratio of 2.13. This identified the difference in carbon uptake rate as the main factor contributing to the divergent growth rates. Additionally four SNPs were identified as possible contributors to modified kinetic parameters of metabolic enzymes and candidates for further study. Comparisons against more established cyanobacterial strains identified a number of differences between the strains along with a correlation between the number of cytochrome c oxidase operons and heterotrophic or diazotrophic capabilities.
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Najib MZM, Ujang Z, Salim MR, Ibrahim Z, Muda K. Reduction and biofixation of carbon dioxide in palm oil mill effluent using developed microbial granules containing photosynthetic pigments. BIORESOURCE TECHNOLOGY 2016; 221:157-164. [PMID: 27639234 DOI: 10.1016/j.biortech.2016.08.119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 08/20/2016] [Accepted: 08/22/2016] [Indexed: 06/06/2023]
Abstract
The developed microbial granules containing photosynthetic pigments had successfully achieved approximately 18-21% of carbon dioxide (CO2) removal in POME for one complete SBR cycle. Also, the granules had reached CO2 removal at 15-29% within 24h and removal of 25% after 5 days. Both results were inconsistent possibly due to the slow mass transfer rate of CO2 from gas to liquid as well as the simultaneous effect of CO2 production and respiration among the microbes. Furthermore, results showed the removal of CO2 from air increases proportionally with the CO2 removed in liquid. The CO2 biofixation of granules attained was approximately 0.23g/L/day for a week. Using the regression model, the removal of CO2 between liquid and gas, CO2 biofixation rate were highly correlated with the treatment time. A statistically significant relationship was obtained between CO2 concentration in liquid, biomass productivity and treatment time for the CO2 biofixation rate of the granules.
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Affiliation(s)
- M Z Mohamed Najib
- Department of Environmental Engineering, Faculty of Civil Engineering, Universiti Teknologi Malaysia (UTM), 81310 Skudai, Johor, Malaysia
| | - Z Ujang
- Centre for Environmental Sustainability and Water Security (IPASA), Research Institute for Sustainable Environment (RISE), Universiti Teknologi Malaysia (UTM), 81310 Skudai, Johor, Malaysia
| | - M R Salim
- Department of Environmental Engineering, Faculty of Civil Engineering, Universiti Teknologi Malaysia (UTM), 81310 Skudai, Johor, Malaysia; Centre for Environmental Sustainability and Water Security (IPASA), Research Institute for Sustainable Environment (RISE), Universiti Teknologi Malaysia (UTM), 81310 Skudai, Johor, Malaysia
| | - Z Ibrahim
- Department of Biosciences and Health Sciences, Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia (UTM), 81310 Skudai, Johor, Malaysia
| | - K Muda
- Department of Environmental Engineering, Faculty of Civil Engineering, Universiti Teknologi Malaysia (UTM), 81310 Skudai, Johor, Malaysia
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