1
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Yuan Y, Al Bulushi T, Sastry AV, Sancar C, Szubin R, Golden SS, Palsson BO. Machine learning reveals the transcriptional regulatory network and circadian dynamics of Synechococcus elongatus PCC 7942. Proc Natl Acad Sci U S A 2024; 121:e2410492121. [PMID: 39269777 PMCID: PMC11420160 DOI: 10.1073/pnas.2410492121] [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: 05/26/2024] [Accepted: 08/05/2024] [Indexed: 09/15/2024] Open
Abstract
Synechococcus elongatus is an important cyanobacterium that serves as a versatile and robust model for studying circadian biology and photosynthetic metabolism. Its transcriptional regulatory network (TRN) is of fundamental interest, as it orchestrates the cell's adaptation to the environment, including its response to sunlight. Despite the previous characterization of constituent parts of the S. elongatus TRN, a comprehensive layout of its topology remains to be established. Here, we decomposed a compendium of 300 high-quality RNA sequencing datasets of the model strain PCC 7942 using independent component analysis. We obtained 57 independently modulated gene sets, or iModulons, that explain 67% of the variance in the transcriptional response and 1) accurately reflect the activity of known transcriptional regulations, 2) capture functional components of photosynthesis, 3) provide hypotheses for regulon structures and functional annotations of poorly characterized genes, and 4) describe the transcriptional shifts under dynamic light conditions. This transcriptome-wide analysis of S. elongatus provides a quantitative reconstruction of the TRN and presents a knowledge base that can guide future investigations. Our systems-level analysis also provides a global TRN structure for S. elongatus PCC 7942.
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Affiliation(s)
- Yuan Yuan
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
| | - Tahani Al Bulushi
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
| | - Anand V Sastry
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
| | - Cigdem Sancar
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093
| | - Richard Szubin
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
| | - Susan S Golden
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093
| | - Bernhard O Palsson
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens, Lyngby 2800, Denmark
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2
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Nishanth S, Kokila V, Prasanna R. Metabolite profiling of plant growth promoting cyanobacteria- Anabaena laxa and Calothrix elenkinii, using untargeted metabolomics. 3 Biotech 2024; 14:35. [PMID: 38213508 PMCID: PMC10776517 DOI: 10.1007/s13205-023-03902-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/20/2023] [Indexed: 01/13/2024] Open
Abstract
The metabolite profiles of two plant growth promoting cyanobacteria-Anabaena laxa and Calothrix elenkinii, which serve as promising biofertilizers, and biocontrol agents were generated to investigate their agriculturally beneficial activities. Preliminary biochemical analyses, in terms of total chlorophyll, total proteins, and IAA were highest at 14 days after inoculation (DAI). In A. laxa 20-25% higher values of reducing sugars, than C. elenkinii at both 14 and 21 DAI were recorded. Carbon and nitrogen assimilating enzyme activities-phosphoenol pyruvate carboxylase (PEPC), carbonic anhydrase (CA), and glutamine synthetase (GS) were highest at 14 DAI, albeit, nitrate reductase (NR) activity was higher by 0.73-0.84-fold at 21 DAI. Untargeted GC-MS (Gas chromatography-Mass spectrometric) analysis of metabolite profiles of 21d-old cyanobacterial cultures and characterization using NIST mass spectral library illustrated that A. laxa recorded highest number of metabolite hits in three chemical classes namely amino acid and peptides, nucleotides, nucleosides and analogues, besides other organic compounds. Based on the pathway analysis of identified metabolites, both A. laxa, and C. elenkinii were enriched in metabolites involved in aminoacyl-tRNA biosynthesis, and amino acid metabolism pathways, particularly lactose and glutamic acid, which are important players in plant-microbe interactions. Correlation-based metabolite network illustrated distinct and significant differences in the metabolic machinery of A. laxa and C. elenkinii, highlighting their novel identity and enrichment in C-N rich metabolites, as factors underlying their plant growth and soil fertility enhancing attributes, which make them valuable as inoculants. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03902-7.
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Affiliation(s)
- Sekar Nishanth
- Division of Microbiology, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012 India
| | - Venkatesh Kokila
- Division of Microbiology, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012 India
| | - Radha Prasanna
- Division of Microbiology, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012 India
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3
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Melis A, Hidalgo Martinez DA, Betterle N. Perspectives of cyanobacterial cell factories. PHOTOSYNTHESIS RESEARCH 2023:10.1007/s11120-023-01056-4. [PMID: 37966575 DOI: 10.1007/s11120-023-01056-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/13/2023] [Indexed: 11/16/2023]
Abstract
Cyanobacteria are prokaryotic photosynthetic microorganisms that can generate, in addition to biomass, useful chemicals and proteins/enzymes, essentially from sunlight, carbon dioxide, and water. Selected aspects of cyanobacterial production (isoprenoids and high-value proteins) and scale-up methods suitable for product generation and downstream processing are addressed in this review. The work focuses on the challenge and promise of specialty chemicals and proteins production, with isoprenoid products and biopharma proteins as study cases, and the challenges encountered in the expression of recombinant proteins/enzymes, which underline the essence of synthetic biology with these microorganisms. Progress and the current state-of-the-art in these targeted topics are emphasized.
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Affiliation(s)
- Anastasios Melis
- Department of Plant and Microbial Biology, University of California, MC-3102, Berkeley, CA, 94720-3102, USA.
| | - Diego Alberto Hidalgo Martinez
- Department of Biology, Healthcare and the Environment, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Nico Betterle
- SoLELab, Department of Biotechnology, University of Verona, 37134, Verona, Italy
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4
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Cheng J, Zhang C, Zhang K, Li J, Hou Y, Xin J, Sun Y, Xu C, Xu W. Cyanobacteria-Mediated Light-Driven Biotransformation: The Current Status and Perspectives. ACS OMEGA 2023; 8:42062-42071. [PMID: 38024730 PMCID: PMC10653055 DOI: 10.1021/acsomega.3c05407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/29/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023]
Abstract
Most chemicals are manufactured by traditional chemical processes but at the expense of toxic catalyst use, high energy consumption, and waste generation. Biotransformation is a green, sustainable, and cost-effective process. As cyanobacteria can use light as the energy source to power the synthesis of NADPH and ATP, using cyanobacteria as the chassis organisms to design and develop light-driven biotransformation platforms for chemical synthesis has been gaining attention, since it can provide a theoretical and practical basis for the sustainable and green production of chemicals. Meanwhile, metabolic engineering and genome editing techniques have tremendous prospects for further engineering and optimizing chassis cells to achieve efficient light-driven systems for synthesizing various chemicals. Here, we display the potential of cyanobacteria as a promising light-driven biotransformation platform for the efficient synthesis of green chemicals and current achievements of light-driven biotransformation processes in wild-type or genetically modified cyanobacteria. Meanwhile, future perspectives of one-pot enzymatic cascade biotransformation from biobased materials in cyanobacteria have been proposed, which could provide additional research insights for green biotransformation and accelerate the advancement of biomanufacturing industries.
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Affiliation(s)
- Jie Cheng
- School
of Life Sciences, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Chaobo Zhang
- School
of Life Sciences, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Kaidian Zhang
- State
Key Laboratory of Marine Resource Utilization in the South China Sea,
School of Marine Biology and Aquaculture, Hainan University, Haikou, Hainan 570100, China
- Xiamen
Key Laboratory of Urban Sea Ecological Conservation and Restoration,
State Key Laboratory of Marine Environmental Science, College of Ocean
and Earth Sciences, Xiamen University, Xiamen, Fujian 361005, China
| | - Jiashun Li
- Xiamen
Key Laboratory of Urban Sea Ecological Conservation and Restoration,
State Key Laboratory of Marine Environmental Science, College of Ocean
and Earth Sciences, Xiamen University, Xiamen, Fujian 361005, China
| | - Yuyong Hou
- Key
Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotech-nology, Chinese
Academy of Sciences, Tianjin 300308, China
| | - Jiachao Xin
- School
of Life Sciences, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Yang Sun
- School
of Life Sciences, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Chengshuai Xu
- School
of Life Sciences, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Wei Xu
- School
of Life Sciences, Liaocheng University, Liaocheng, Shandong 252000, China
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5
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Krings S, Chen Y, Keddie JL, Hingley-Wilson S. Oxygen evolution from extremophilic cyanobacteria confined in hard biocoatings. Microbiol Spectr 2023; 11:e0187023. [PMID: 37747195 PMCID: PMC10580922 DOI: 10.1128/spectrum.01870-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/04/2023] [Indexed: 09/26/2023] Open
Abstract
Biocoatings, in which viable bacteria are immobilized within a waterborne polymer coating for a wide range of potential applications, have garnered greater interest in recent years. In bioreactors, biocoatings can be ready-to-use alternatives for carbon capture or biofuel production that could be reused multiple times. Here, we have immobilized cyanobacteria in mechanically hard biocoatings, which were deposited from polymer colloids in water (i.e., latex). The biocoatings are formed upon heating to 37°C and fully dried before rehydrating. The viability and oxygen evolution of three cyanobacterial species within the biocoatings were compared. Synechococcus sp. PCC 7002 was non-viable inside the biocoatings immediately after drying, whereas Synechocystis sp. PCC 6803 survived the coating formation, as shown by an adenosine triphosphate (ATP) assay. Synechocystis sp. PCC 6803 consumed oxygen (by cell respiration) for up to 5 days, but was unable to perform photosynthesis, as indicated by a lack of oxygen evolution. However, Chroococcidiopsis cubana PCC 7433, a strain of desiccation-resistant extremophilic cyanobacteria, survived and performed photosynthesis and carbon capture within the biocoating, with specific rates of oxygen evolution up to 0.4 g of oxygen/g of biomass per day. Continuous measurements of dissolved oxygen were carried out over a month and showed no sign of decreasing activity. Extremophilic cyanobacteria are viable in a variety of environments, making them ideal candidates for use in biocoatings and other biotechnology. IMPORTANCE As water has become a precious resource, there is a growing need for less water-intensive use of microorganisms, while avoiding desiccation stress. Mechanically robust, ready-to-use biocoatings or "living paints" (a type of artificial biofilm consisting of a synthetic matrix containing functional bacteria) represent a novel way to address these issues. Here, we describe the revolutionary, first-ever use of an extremophilic cyanobacterium (Chroococcidiopsis cubana PCC 7433) in biocoatings, which were able to produce high levels of oxygen and carbon capture for at least 1 month despite complete desiccation and subsequent rehydration. Beyond culturing viable bacteria with reduced water resources, this pioneering use of extremophiles in biocoatings could be further developed for a variety of applications, including carbon capture, wastewater treatment and biofuel production.
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Affiliation(s)
- Simone Krings
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Yuxiu Chen
- School of Mathematics and Physics, University of Surrey, Guildford, Surrey, United Kingdom
| | - Joseph L. Keddie
- School of Mathematics and Physics, University of Surrey, Guildford, Surrey, United Kingdom
| | - Suzanne Hingley-Wilson
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, Surrey, United Kingdom
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6
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Kageyama H, Waditee-Sirisattha R. Halotolerance mechanisms in salt‑tolerant cyanobacteria. ADVANCES IN APPLIED MICROBIOLOGY 2023; 124:55-117. [PMID: 37597948 DOI: 10.1016/bs.aambs.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/21/2023]
Abstract
Cyanobacteria are ubiquitously distributed in nature and are the most abundant photoautotrophs on Earth. Their long evolutionary history reveals that cyanobacteria have a remarkable capacity and strong adaptive tendencies to thrive in a variety of conditions. Thus, they can survive successfully, especially in harsh environmental conditions such as salty environments, high radiation, or extreme temperatures. Among others, salt stress because of excessive salt accumulation in salty environments, is the most common abiotic stress in nature and hampers agricultural growth and productivity worldwide. These detrimental effects point to the importance of understanding the molecular mechanisms underlying the salt stress response. While it is generally accepted that the stress response mechanism is a complex network, fewer efforts have been made to represent it as a network. Substantial evidence revealed that salt-tolerant cyanobacteria have evolved genomic specific mechanisms and high adaptability in response to environmental changes. For example, extended gene families and/or clusters of genes encoding proteins involved in the adaptation to high salinity have been collectively reported. This chapter focuses on recent advances and provides an overview of the molecular basis of halotolerance mechanisms in salt‑tolerant cyanobacteria as well as multiple regulatory pathways. We elaborate on the major protective mechanisms, molecular mechanisms associated with halotolerance, and the global transcriptional landscape to provide a gateway to uncover gene regulation principles. Both knowledge and omics approaches are utilized in this chapter to decipher the mechanistic insights into halotolerance. Collectively, this chapter would have a profound impact on providing a comprehensive understanding of halotolerance in salt‑tolerant cyanobacteria.
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Affiliation(s)
- Hakuto Kageyama
- Graduate School of Environmental and Human Sciences, Meijo University, Nagoya, Japan; Department of Chemistry, Faculty of Science and Technology, Meijo University, Nagoya, Japan.
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7
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Su H, Lin J. Biosynthesis pathways of expanding carbon chains for producing advanced biofuels. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:109. [PMID: 37400889 DOI: 10.1186/s13068-023-02340-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/11/2023] [Indexed: 07/05/2023]
Abstract
Because the thermodynamic property is closer to gasoline, advanced biofuels (C ≥ 6) are appealing for replacing non-renewable fossil fuels using biosynthesis method that has presented a promising approach. Synthesizing advanced biofuels (C ≥ 6), in general, requires the expansion of carbon chains from three carbon atoms to more than six carbon atoms. Despite some specific biosynthesis pathways that have been developed in recent years, adequate summary is still lacking on how to obtain an effective metabolic pathway. Review of biosynthesis pathways for expanding carbon chains will be conducive to selecting, optimizing and discovering novel synthetic route to obtain new advanced biofuels. Herein, we first highlighted challenges on expanding carbon chains, followed by presentation of two biosynthesis strategies and review of three different types of biosynthesis pathways of carbon chain expansion for synthesizing advanced biofuels. Finally, we provided an outlook for the introduction of gene-editing technology in the development of new biosynthesis pathways of carbon chain expansion.
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Affiliation(s)
- Haifeng Su
- Key Laboratory of Degraded and Unused Land Consolidation Engineering, The Ministry of Natural and Resources, Xian, 710075, Shanxi, China
| | - JiaFu Lin
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, China.
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8
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Barone GD, Cernava T, Ullmann J, Liu J, Lio E, Germann AT, Nakielski A, Russo DA, Chavkin T, Knufmann K, Tripodi F, Coccetti P, Secundo F, Fu P, Pfleger B, Axmann IM, Lindblad P. Recent developments in the production and utilization of photosynthetic microorganisms for food applications. Heliyon 2023; 9:e14708. [PMID: 37151658 PMCID: PMC10161259 DOI: 10.1016/j.heliyon.2023.e14708] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 05/09/2023] Open
Abstract
The growing use of photosynthetic microorganisms for food and food-related applications is driving related biotechnology research forward. Increasing consumer acceptance, high sustainability, demand of eco-friendly sources for food, and considerable global economic concern are among the main factors to enhance the focus on the novel foods. In the cases of not toxic strains, photosynthetic microorganisms not only provide a source of sustainable nutrients but are also potentially healthy. Several published studies showed that microalgae are sources of accessible protein and fatty acids. More than 400 manuscripts were published per year in the last 4 years. Furthermore, industrial approaches utilizing these microorganisms are resulting in new jobs and services. This is in line with the global strategy for bioeconomy that aims to support sustainable development of bio-based sectors. Despite the recognized potential of the microalgal biomass value chain, significant knowledge gaps still exist especially regarding their optimized production and utilization. This review highlights the potential of microalgae and cyanobacteria for food and food-related applications as well as their market size. The chosen topics also include advanced production as mixed microbial communities, production of high-value biomolecules, photoproduction of terpenoid flavoring compounds, their utilization for sustainable agriculture, application as source of nutrients in space, and a comparison with heterotrophic microorganisms like yeast to better evaluate their advantages over existing nutrient sources. This comprehensive assessment should stimulate further interest in this highly relevant research topic.
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Affiliation(s)
- Giovanni D. Barone
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
- Corresponding author.
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010, Graz, Austria
| | - Jörg Ullmann
- Roquette Klötze GmbH & Co. KG, Lockstedter Chaussee 1, D-38486, Klötze, Germany
| | - Jing Liu
- State Key Laboratory of Marine Resource Utilization in South China Sea Hainan University, 58 Renmin Avenue, Meilan District, Haikou, Hainan Province, 570228, PR China
| | - Elia Lio
- Institute of Chemical Sciences and Technologies (SCITEC) “Giulio Natta” Italian National Research Council (CNR), via Mario Bianco 9, 20131, Milan, Italy
| | - Anna T. Germann
- Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Andreas Nakielski
- Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - David A. Russo
- Friedrich Schiller University Jena, Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Lessingstr. 8, D-07743, Jena, Germany
| | - Ted Chavkin
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Farida Tripodi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milano, Italy
| | - Paola Coccetti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milano, Italy
| | - Francesco Secundo
- Institute of Chemical Sciences and Technologies (SCITEC) “Giulio Natta” Italian National Research Council (CNR), via Mario Bianco 9, 20131, Milan, Italy
| | - Pengcheng Fu
- State Key Laboratory of Marine Resource Utilization in South China Sea Hainan University, 58 Renmin Avenue, Meilan District, Haikou, Hainan Province, 570228, PR China
| | - Brian Pfleger
- Knufmann GmbH, Bergstraße 23, D-38486, Klötze, Germany
| | - Ilka M. Axmann
- Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, D-40001, Düsseldorf, Germany
- Corresponding author. Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany.
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry–Ångström, Uppsala University, Box 523, SE-75120, Uppsala, Sweden
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9
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Dallo T, Krishnakumar R, Kolker SD, Ruffing AM. High-Density Guide RNA Tiling and Machine Learning for Designing CRISPR Interference in Synechococcus sp. PCC 7002. ACS Synth Biol 2023; 12:1175-1186. [PMID: 36893454 DOI: 10.1021/acssynbio.2c00653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
While CRISPRi was previously established in Synechococcus sp. PCC 7002 (hereafter 7002), the design principles for guide RNA (gRNA) effectiveness remain largely unknown. Here, 76 strains of 7002 were constructed with gRNAs targeting three reporter systems to evaluate features that impact gRNA efficiency. Correlation analysis of the data revealed that important features of gRNA design include the position relative to the start codon, GC content, protospacer adjacent motif (PAM) site, minimum free energy, and targeted DNA strand. Unexpectedly, some gRNAs targeting upstream of the promoter region showed small but significant increases in reporter expression, and gRNAs targeting the terminator region showed greater repression than gRNAs targeting the 3' end of the coding sequence. Machine learning algorithms enabled prediction of gRNA effectiveness, with Random Forest having the best performance across all training sets. This study demonstrates that high-density gRNA data and machine learning can improve gRNA design for tuning gene expression in 7002.
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Affiliation(s)
- Tessa Dallo
- Molecular and Microbiology, Sandia National Laboratories, P.O. Box 5800, MS 1413, Albuquerque, New Mexico 87185, United States
| | - Raga Krishnakumar
- Systems Biology, Sandia National Laboratories, P.O. Box 969, MS 9292, Livermore, California 94551, United States
| | - Stephanie D Kolker
- Molecular and Microbiology, Sandia National Laboratories, P.O. Box 5800, MS 1413, Albuquerque, New Mexico 87185, United States
| | - Anne M Ruffing
- Molecular and Microbiology, Sandia National Laboratories, P.O. Box 5800, MS 1413, Albuquerque, New Mexico 87185, United States
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10
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Vamsi Bharadwaj S, Tiwari DS, Ghosh T, Mishra S. Construction of pSM201v: A broad host range replicative vector based on shortening of RSF1010. Heliyon 2023; 9:e14637. [PMID: 37025788 PMCID: PMC10070531 DOI: 10.1016/j.heliyon.2023.e14637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/06/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
Despite possessing attractive features such as autotrophic growth on minimal media, industrial applications of cyanobacteria are hindered by a lack of genetic manipulative tools. There are two important features that are important for an effective manipulation: a vector which can carry the gene, and an induction system activated through external stimuli, giving us control over the expression. In this study, we describe the construction of an improved RSF1010-based vector as well as a temperature-inducible RNA thermometer. RSF1010 is a well-studied incompatibility group Q (IncQ) vector, capable of replication in most Gram negative, and some Gram positive bacteria. Our designed vector, named pSM201v, can be used as an expression vector in some Gram positive and a wide range of Gram negative bacteria including cyanobacteria. An induction system activated via physical external stimuli such as temperature, allows precise control of overexpression. pSM201v addresses several drawbacks of the RSF1010 plasmid; it has a reduced backbone size of 5189 bp compared to 8684 bp of the original plasmid, which provides more space for cloning and transfer of cargo DNA into the host organism. The mobilization function, required for plasmid transfer into several cyanobacterial strains, is reduced to a 99 bp region, as a result that mobilization of this plasmid is no longer linked to the plasmid replication. The RNA thermometer, named DTT1, is based on a RNA hairpin strategy that prevents expression of downstream genes at temperatures below 30 °C. Such RNA elements are expected to find applications in biotechnology to economically control gene expression in a scalable manner.
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11
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Zhang H, Liu Q, Liang Q, Wang B, Chen Z, Wang J. Expression of tardigrade disordered proteins impacts the tolerance to biofuels in a model cyanobacterium Synechocystis sp. PCC 6803. Front Microbiol 2023; 13:1091502. [PMID: 36687595 PMCID: PMC9845703 DOI: 10.3389/fmicb.2022.1091502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/12/2022] [Indexed: 01/05/2023] Open
Abstract
Tardigrades, known colloquially as water bears or moss piglets, are diminutive animals capable of surviving many extreme environments, even been exposed to space in low Earth orbit. Recently termed tardigrade disordered proteins (TDPs) include three families as cytoplasmic-(CAHS), secreted-(SAHS), and mitochondrial-abundant heat soluble (MAHS) proteins. How these tiny animals survive these stresses has remained relatively mysterious. Cyanobacteria cast attention as a "microbial factory" to produce biofuels and high-value-added chemicals due to their ability to photosynthesis and CO2 sequestration. We explored a lot about biofuel stress and related mechanisms in Synechocystis sp. PCC 6803. The previous studies show that CAHS protein heterogenous expression in bacteria, yeast, and human cells increases desiccation tolerance in these hosts. In this study, the expression of three CAHS proteins in cyanobacterium was found to affect the tolerance to biofuels, while the tolerance to Cd2+ and Zn2+ were slightly affected in several mutants. A quantitative transcriptomics approach was applied to decipher response mechanisms at the transcriptional level further.
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Affiliation(s)
- Heao Zhang
- Whittle School and Studios, Shenzhen, Guangdong, China
| | - Qingyang Liu
- Whittle School and Studios, Shenzhen, Guangdong, China
| | - Qing Liang
- Shenzhen Link Spider Technology Co., Ltd., Shenzhen, China
| | - Boxiang Wang
- Shenzhen Link Spider Technology Co., Ltd., Shenzhen, China,*Correspondence: Boxiang Wang, Zixi Chen
| | - Zixi Chen
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China,*Correspondence: Boxiang Wang, Zixi Chen
| | - Jiangxin Wang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
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12
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Shu L, Gu J, Wang Q, Sun S, Cui Y, Fell J, Mak WS, Siegel JB, Shi J, Lye GJ, Baganz F, Hao J. The pyruvate decarboxylase activity of IpdC is a limitation for isobutanol production by Klebsiella pneumoniae. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:41. [PMID: 35501883 PMCID: PMC9063327 DOI: 10.1186/s13068-022-02144-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 04/17/2022] [Indexed: 11/15/2022]
Abstract
Background Klebsiella pneumoniae contains an endogenous isobutanol synthesis pathway. The ipdC gene annotated as an indole-3-pyruvate decarboxylase (Kp-IpdC), was identified to catalyze the formation of isobutyraldehyde from 2-ketoisovalerate. Results Compared with 2-ketoisovalerate decarboxylase from Lactococcus lactis (KivD), a decarboxylase commonly used in artificial isobutanol synthesis pathways, Kp-IpdC has an 2.8-fold lower Km for 2-ketoisovalerate, leading to higher isobutanol production without induction. However, expression of ipdC by IPTG induction resulted in a low isobutanol titer. In vitro enzymatic reactions showed that Kp-IpdC exhibits promiscuous pyruvate decarboxylase activity, which adversely consume the available pyruvate precursor for isobutanol synthesis. To address this, we have engineered Kp-IpdC to reduce pyruvate decarboxylase activity. From computational modeling, we identified 10 amino acid residues surrounding the active site for mutagenesis. Ten designs consisting of eight single-point mutants and two double-point mutants were selected for exploration. Mutants L546W and T290L that showed only 5.1% and 22.1% of catalytic efficiency on pyruvate compared to Kp-IpdC, were then expressed in K. pneumoniae for in vivo testing. Isobutanol production by K. pneumoniae T290L was 25% higher than that of the control strain, and a final titer of 5.5 g/L isobutanol was obtained with a substrate conversion ratio of 0.16 mol/mol glucose. Conclusions This research provides a new way to improve the efficiency of the biological route of isobutanol production. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02144-8. Kp-IpdC is more efficient than KivD for 2-ketoisovalerate decarboxylation. Pyruvate decarboxylase activity is a limitation of Kp-IpdC. T290L variant exhibits a decreased pyruvate decarboxylase activity. Isobutanol production by K. pneumoniae T290L was improved.
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Kim SM, Bae EH, Kim JY, Kang JS, Choi YE. Mixotrophic Cultivation of a Native Cyanobacterium, Pseudanabaena mucicola GO0704, to Produce Phycobiliprotein and Biodiesel. J Microbiol Biotechnol 2022; 32:1325-1334. [PMID: 36224760 PMCID: PMC9668097 DOI: 10.4014/jmb.2207.07008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 12/15/2022]
Abstract
Global warming has accelerated in recent decades due to the continuous consumption of petroleum-based fuels. Cyanobacteria-derived biofuels are a promising carbon-neutral alternative to fossil fuels that may help achieve a cleaner environment. Here, we propose an effective strategy based on the large-scale cultivation of a newly isolated cyanobacterial strain to produce phycobiliprotein and biodiesel, thus demonstrating the potential commercial applicability of the isolated microalgal strain. A native cyanobacterium was isolated from Goryeong, Korea, and identified as Pseudanabaena mucicola GO0704 through 16s RNA analysis. The potential exploitation of P. mucicola GO0704 was explored by analyzing several parameters for mixotrophic culture, and optimal growth was achieved through the addition of sodium acetate (1 g/l) to the BG-11 medium. Next, the cultures were scaled up to a stirred-tank bioreactor in mixotrophic conditions to maximize the productivity of biomass and metabolites. The biomass, phycobiliprotein, and fatty acids concentrations in sodium acetate-treated cells were enhanced, and the highest biodiesel productivity (8.1 mg/l/d) was achieved at 96 h. Finally, the properties of the fuel derived from P. mucicola GO0704 were estimated with converted biodiesels according to the composition of fatty acids. Most of the characteristics of the final product, except for the cloud point, were compliant with international biodiesel standards [ASTM 6761 (US) and EN 14214 (Europe)].
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Affiliation(s)
- Shin Myung Kim
- Division of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Eun Hee Bae
- Research Division of Microorganisms, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Jee Young Kim
- Division of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Jae-Shin Kang
- Research Division of Microorganisms, National Institute of Biological Resources, Incheon 22689, Republic of Korea,Research Division of Plants, National Institute of Biological Resources, Incheon, Republic of Korea (present address),Corresponding authors J.S. Kang Phone: +82-2-3290-3042 Fax: +82-2-3290-3040 E-mail:
| | - Yoon-E Choi
- Division of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea,
Y.E. Choi E-mail:
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Mehdizadeh Allaf M, Fadlallah H, Jarrahi M, Peerhossaini H. Growth and pigment production of
Synechocystis
sp.
PCC
6803 under shear stress. CAN J CHEM ENG 2022. [DOI: 10.1002/cjce.24546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Malihe Mehdizadeh Allaf
- Mechanics of Active Fluids and Bacterial Physics Lab, Department of Civil and Environmental Engineering Western University London ON Canada
| | - Hadi Fadlallah
- Laboratoire AstroParticules et Cosmologie (APC) ‐ CNRS Université de Paris Paris France
| | | | - Hassan Peerhossaini
- Mechanics of Active Fluids and Bacterial Physics Lab, Department of Civil and Environmental Engineering Western University London ON Canada
- Laboratoire AstroParticules et Cosmologie (APC) ‐ CNRS Université de Paris Paris France
- Department of Mechanical & Materials Engineering Western University London ON Canada
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15
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Agarwal P, Soni R, Kaur P, Madan A, Mishra R, Pandey J, Singh S, Singh G. Cyanobacteria as a Promising Alternative for Sustainable Environment: Synthesis of Biofuel and Biodegradable Plastics. Front Microbiol 2022; 13:939347. [PMID: 35903468 PMCID: PMC9325326 DOI: 10.3389/fmicb.2022.939347] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
With the aim to alleviate the increasing plastic burden and carbon footprint on Earth, the role of certain microbes that are capable of capturing and sequestering excess carbon dioxide (CO2) generated by various anthropogenic means was studied. Cyanobacteria, which are photosynthetic prokaryotes, are promising alternative for carbon sequestration as well as biofuel and bioplastic production because of their minimal growth requirements, higher efficiency of photosynthesis and growth rates, presence of considerable amounts of lipids in thylakoid membranes, and cosmopolitan nature. These microbes could prove beneficial to future generations in achieving sustainable environmental goals. Their role in the production of polyhydroxyalkanoates (PHAs) as a source of intracellular energy and carbon sink is being utilized for bioplastic production. PHAs have emerged as well-suited alternatives for conventional plastics and are a parallel competitor to petrochemical-based plastics. Although a lot of studies have been conducted where plants and crops are used as sources of energy and bioplastics, cyanobacteria have been reported to have a more efficient photosynthetic process strongly responsible for increased production with limited land input along with an acceptable cost. The biodiesel production from cyanobacteria is an unconventional choice for a sustainable future as it curtails toxic sulfur release and checks the addition of aromatic hydrocarbons having efficient oxygen content, with promising combustion potential, thus making them a better choice. Here, we aim at reporting the application of cyanobacteria for biofuel production and their competent biotechnological potential, along with achievements and constraints in its pathway toward commercial benefits. This review article also highlights the role of various cyanobacterial species that are a source of green and clean energy along with their high potential in the production of biodegradable plastics.
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16
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Vamsi Krishna K, Bharathi N, George Shiju S, Alagesan Paari K, Malaviya A. An updated review on advancement in fermentative production strategies for biobutanol using Clostridium spp. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:47988-48019. [PMID: 35562606 DOI: 10.1007/s11356-022-20637-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 04/30/2022] [Indexed: 06/15/2023]
Abstract
A significant concern of our fuel-dependent era is the unceasing exhaustion of petroleum fuel supplies. In parallel to this, environmental issues such as the greenhouse effect, change in global climate, and increasing global temperature must be addressed on a priority basis. Biobutanol, which has fuel characteristics comparable to gasoline, has attracted global attention as a viable green fuel alternative among the many biofuel alternatives. Renewable biomass could be used for the sustainable production of biobutanol by the acetone-butanol-ethanol (ABE) pathway. Non-extinguishable resources, such as algal and lignocellulosic biomass, and starch are some of the most commonly used feedstock for fermentative production of biobutanol, and each has its particular set of advantages. Clostridium, a gram-positive endospore-forming bacterium that can produce a range of compounds, along with n-butanol is traditionally known for its biobutanol production capabilities. Clostridium fermentation produces biobased n-butanol through ABE fermentation. However, low butanol titer, a lack of suitable feedstock, and product inhibition are the primary difficulties in biobutanol synthesis. Critical issues that are essential for sustainable production of biobutanol include (i) developing high butanol titer producing strains utilizing genetic and metabolic engineering approaches, (ii) renewable biomass that could be used for biobutanol production at a larger scale, and (iii) addressing the limits of traditional batch fermentation by integrated bioprocessing technologies with effective product recovery procedures that have increased the efficiency of biobutanol synthesis. Our paper reviews the current progress in all three aspects of butanol production and presents recent data on current practices in fermentative biobutanol production technology.
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Affiliation(s)
- Kondapalli Vamsi Krishna
- Applied and Industrial Biotechnology Laboratory, CHRIST (Deemed-to-Be University), Hosur road, Bangalore, Karnataka, India
| | - Natarajan Bharathi
- Department of Life Sciences, CHRIST (Deemed to Be University), Bengaluru, India
| | - Shon George Shiju
- Applied and Industrial Biotechnology Laboratory, CHRIST (Deemed-to-Be University), Hosur road, Bangalore, Karnataka, India
| | | | - Alok Malaviya
- Applied and Industrial Biotechnology Laboratory, CHRIST (Deemed-to-Be University), Hosur road, Bangalore, Karnataka, India.
- Department of Life Sciences, CHRIST (Deemed to Be University), Bengaluru, India.
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17
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Kim S, Lee SH, Kim IK, Seo H, Kim KJ. Structural insight into a molecular mechanism of methenyltetrahydrofolate cyclohydrolase from Methylobacterium extorquens AM1. Int J Biol Macromol 2022; 202:234-240. [PMID: 35051495 DOI: 10.1016/j.ijbiomac.2022.01.072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/06/2022] [Accepted: 01/10/2022] [Indexed: 11/28/2022]
Abstract
Bioconversion of the C1 compounds into value-added products is one of the CO2-reducing strategies. In particular, because CO2 can be easily converted into formate, the efficient and direct bioconversion of CO2 through formate assimilation is attracting attention. The tetrahydrofolate (THF) cycle is the highly efficient reconstructed formate assimilation pathway, and 5,10-methenyltetrahydrofolate cyclohydrolase (FchA) is an essential enzyme involved in the THF cycle. In this study, a kinetic analysis of FchA from Methylobacterium extorquens AM1 (MeFchA) was performed and revealed that the enzyme has much higher cyclization than hydrolyzation activity, making it an optimal enzyme for formate assimilation. The crystal structure of MeFchA in the apo- and the THF-complexed forms was also determined, revealing that the substrate-binding site of the enzyme has three differently charged regions to stabilize the three differently charged moieties of the formyl-THF substrate. The residues involved in the substrate binding were also verified through site-directed mutagenesis. This study provides a biochemical and structural basis for the molecular mechanism underlying formate assimilation.
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Affiliation(s)
- Seongmin Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Seul Hoo Lee
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Il-Kwon Kim
- KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Hogyun Seo
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea; Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Kyoung-Jin Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea.
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18
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Chen H, Wang Q. Microalgae-Based Green Bio-Manufacturing—How Far From Us. Front Microbiol 2022; 13:832097. [PMID: 35250947 PMCID: PMC8891535 DOI: 10.3389/fmicb.2022.832097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/26/2022] [Indexed: 02/04/2023] Open
Affiliation(s)
- Hui Chen
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Qiang Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
- Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, China
- *Correspondence: Qiang Wang
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19
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Kollmen J, Strieth D. The Beneficial Effects of Cyanobacterial Co-Culture on Plant Growth. Life (Basel) 2022; 12:life12020223. [PMID: 35207509 PMCID: PMC8879750 DOI: 10.3390/life12020223] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/21/2022] [Accepted: 01/30/2022] [Indexed: 11/16/2022] Open
Abstract
Cyanobacteria are ubiquitous phototrophic prokaryotes that find a wide range of applications in industry due to their broad product spectrum. In this context, the application of cyanobacteria as biofertilizers and thus as an alternative to artificial fertilizers has emerged in recent decades. The benefit is mostly based on the ability of cyanobacteria to fix elemental nitrogen and make it available to the plants in a usable form. However, the positive effects of co-cultivating plants with cyanobacteria are not limited to the provision of nitrogen. Cyanobacteria produce numerous secondary metabolites that can be useful for plants, for example, they can have growth-promoting effects or increase resistance to plant diseases. The effects of biotic and abiotic stress can as well be reduced by many secondary metabolites. Furthermore, the biofilms formed by the cyanobacteria can lead to improved soil conditions, such as increased water retention capacity. To exchange the substances mentioned, cyanobacteria form symbioses with plants, whereby the strength of the symbiosis depends on both partners, and not every plant can form symbiosis with every cyanobacterium. Not only the plants in symbiosis benefit from the cyanobacteria, but also vice versa. This review summarizes the beneficial effects of cyanobacterial co-cultivation on plants, highlighting the substances exchanged and the strength of cyanobacterial symbioses with plants. A detailed explanation of the mechanism of nitrogen fixation in cyanobacterial heterocysts is given. Finally, a summary of possible applications of co-cultivation in the (agrar-)industry is given.
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20
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Banerjee R, Srinivas V, Lebrette H. Ferritin-Like Proteins: A Conserved Core for a Myriad of Enzyme Complexes. Subcell Biochem 2022; 99:109-153. [PMID: 36151375 DOI: 10.1007/978-3-031-00793-4_4] [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] [Indexed: 06/16/2023]
Abstract
Ferritin-like proteins share a common fold, a four α-helix bundle core, often coordinating a pair of metal ions. Although conserved, the ferritin fold permits a diverse set of reactions, and is central in a multitude of macromolecular enzyme complexes. Here, we emphasize this diversity through three members of the ferritin-like superfamily: the soluble methane monooxygenase, the class I ribonucleotide reductase and the aldehyde deformylating oxygenase. They all rely on dinuclear metal cofactors to catalyze different challenging oxygen-dependent reactions through the formation of multi-protein complexes. Recent studies using cryo-electron microscopy, serial femtosecond crystallography at an X-ray free electron laser source, or single-crystal X-ray diffraction, have reported the structures of the active protein complexes, and revealed unprecedented insights into the molecular mechanisms of these three enzymes.
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Affiliation(s)
- Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse, France.
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21
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Beattie A, Vermaas W, Darzins A, Holland SC, Li S, McGowen J, Nielsen D, Quinn JC. A probabilistic economic and environmental impact assessment of a cyanobacteria-based biorefinery. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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22
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Ravanipour M, Hamidi A, Mahvi AH. Microalgae biodiesel: A systematic review in Iran. RENEWABLE & SUSTAINABLE ENERGY REVIEWS 2021. [DOI: 10.1016/j.rser.2021.111426] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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23
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Wu KC, Ho KC, Tang CC, Yau YH. The potential of foodwaste leachate as a phycoremediation substrate for microalgal CO 2 fixation and biodiesel production. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:40724-40734. [PMID: 29504078 DOI: 10.1007/s11356-018-1242-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 01/08/2018] [Indexed: 06/08/2023]
Abstract
Foodwaste leachate (FWL) is often generated during foodwaste treatment processes. Owing to its high nutrient content, FWL has high potential for phycoremediation, a microalgal technology application for water treatment while acting as CO2 fixation tank. Additionally, the end product of microalgal from phycoremediation can be potentially used for biodiesel production. Therefore, the phycoremediation has drawn a lot of attention in recent decades. This study evaluates the performance of microalgal foodwaste leachate treatment and the potential of utilizing FWL as medium for microalgal biodiesel production. Two microalgal species, Dunaliella tertiolecta and Cyanobacterium aponinum, were selected. For each species, two experimental levels of diluted FWL were used: 5 and 10% FWL. The partial inhibition growth model indicates that some inhibit factors such as ammonia; total suspended solids and oil and grease (O&G) content suppress the microalgal growth. Most of the nutrient such as nitrogen and phosphorus (> 80%) can be removed in the last day of phycoremediation by D. tertiolecta. C. aponinum also show considerable removal rate on total nitrogen ammonia and nitrate (> 60%). Biomass (0.4-0.5 g/L/day) of D. tertiolecta and C. aponinum can be produced though cultivated in diluted FWL. The bio-CO2 fixation rates of the two species were 610.7 and 578.3 mg/L/day of D. tertiolecta and C. aponinum. The strains contain high content of saturated fatty acid such as C16 and C18 making them having potential for producing good quality biodiesel.
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Affiliation(s)
- Kam-Chau Wu
- School of Science and Technology, The Open University of Hong Kong, Hong Kong, China
| | - Kin-Chung Ho
- School of Science and Technology, The Open University of Hong Kong, Hong Kong, China
| | - Chin-Cheung Tang
- School of Science and Technology, The Open University of Hong Kong, Hong Kong, China
| | - Yiu-Hung Yau
- School of Science and Technology, The Open University of Hong Kong, Hong Kong, China.
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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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25
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Mavrommati M, Daskalaki A, Papanikolaou S, Aggelis G. Adaptive laboratory evolution principles and applications in industrial biotechnology. Biotechnol Adv 2021; 54:107795. [PMID: 34246744 DOI: 10.1016/j.biotechadv.2021.107795] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/11/2021] [Accepted: 07/05/2021] [Indexed: 12/20/2022]
Abstract
Adaptive laboratory evolution (ALE) is an innovative approach for the generation of evolved microbial strains with desired characteristics, by implementing the rules of natural selection as presented in the Darwinian Theory, on the laboratory bench. New as it might be, it has already been used by several researchers for the amelioration of a variety of characteristics of widely used microorganisms in biotechnology. ALE is used as a tool for the deeper understanding of the genetic and/or metabolic pathways of evolution. Another important field targeted by ALE is the manufacturing of products of (high) added value, such as ethanol, butanol and lipids. In the current review, we discuss the basic principles and techniques of ALE, and then we focus on studies where it has been applied to bacteria, fungi and microalgae, aiming to improve their performance to biotechnological procedures and/or inspect the genetic background of evolution. We conclude that ALE is a promising and efficacious method that has already led to the acquisition of useful new microbiological strains in biotechnology and could possibly offer even more interesting results in the future.
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Affiliation(s)
- Maria Mavrommati
- Unit of Microbiology, Department of Biology, Division of Genetics, Cell Biology and Development, University of Patras, 26504 Patras, Greece; Laboratory of Food Microbiology and Biotechnology, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece
| | - Alexandra Daskalaki
- Unit of Microbiology, Department of Biology, Division of Genetics, Cell Biology and Development, University of Patras, 26504 Patras, Greece
| | - Seraphim Papanikolaou
- Laboratory of Food Microbiology and Biotechnology, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece
| | - George Aggelis
- Unit of Microbiology, Department of Biology, Division of Genetics, Cell Biology and Development, University of Patras, 26504 Patras, Greece.
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Iyyappan J, Bharathiraja B, Vaishnavi A, Prathiba S. Overview of Current Developments in Biobutanol Production Methods and Future Perspectives. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2290:3-21. [PMID: 34009579 DOI: 10.1007/978-1-0716-1323-8_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Renewable biobutanol production is receiving more attention toward substituting fossil-based nonrenewable fuels. Biobutanol is recognized as the top most biofuel with extraordinary properties as compared with gasoline. The demand for biobutanol production is increasing enormously due to application in various industries as chemical substituent. Biobutanol production technology has attracted many researchers toward implementation of replacing cost-effective substrate and easy method to recover from the fermentation broth. Sugarcane bagasse, algal biomass, crude glycerol, and lignocellulosic biomass are potential cost-effective substrates which could replace consistent glucose-based substrates. The advantages and limitations of these substrates have been discussed in this chapter. Moreover, finding the integrated biobutanol recovery methods is an important factor parameter in production of biobutanol. This chapter also concentrated on possibilities and drawbacks of obtainable integrated biobutanol recovery methods. Thus, successful process involving cost-effective substrate and biobutanol recovery methods could help to implementation of biobutanol production industry. Overall, this chapter has endeavored to increase the viability of industrial production of biobutanol.
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Affiliation(s)
- J Iyyappan
- Vel Tech High Tech Dr. Rangarajan Dr. Sakunthala Engineering College, Chennai, India
| | - B Bharathiraja
- Vel Tech High Tech Dr. Rangarajan Dr. Sakunthala Engineering College, Chennai, India.
| | - A Vaishnavi
- Vel Tech High Tech Dr. Rangarajan Dr. Sakunthala Engineering College, Chennai, India
| | - S Prathiba
- Vel Tech High Tech Dr. Rangarajan Dr. Sakunthala Engineering College, Chennai, India
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Pancha I, Takaya K, Tanaka K, Imamura S. The Unicellular Red Alga Cyanidioschyzon merolae, an Excellent Model Organism for Elucidating Fundamental Molecular Mechanisms and Their Applications in Biofuel Production. PLANTS 2021; 10:plants10061218. [PMID: 34203949 PMCID: PMC8232737 DOI: 10.3390/plants10061218] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/11/2021] [Accepted: 06/11/2021] [Indexed: 11/16/2022]
Abstract
Microalgae are considered one of the best resources for the production of biofuels and industrially important compounds. Various models have been developed to understand the fundamental mechanism underlying the accumulation of triacylglycerols (TAGs)/starch and to enhance its content in cells. Among various algae, the red alga Cyanidioschyzonmerolae has been considered an excellent model system to understand the fundamental mechanisms behind the accumulation of TAG/starch in the microalga, as it has a smaller genome size and various biotechnological methods are available for it. Furthermore, C. merolae can grow and survive under high temperature (40 °C) and low pH (2–3) conditions, where most other organisms would die, thus making it a choice alga for large-scale production. Investigations using this alga has revealed that the target of rapamycin (TOR) kinase is involved in the accumulation of carbon-reserved molecules, TAGs, and starch. Furthermore, detailed molecular mechanisms of the role of TOR in controlling the accumulation of TAGs and starch were uncovered via omics analyses. Based on these findings, genetic engineering of the key gene and proteins resulted in a drastic increment of the amount of TAGs and starch. In addition to these studies, other trials that attempted to achieve the TAG increment in C. merolae have been summarized in this article.
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Affiliation(s)
- Imran Pancha
- Department of Biological Sciences, SRM University-AP, Amaravati, Andhra Pradesh 522502, India
- Correspondence: (I.P.); (S.I.); Tel.: +81-422-59-6179 (S.I.)
| | - Kazuhiro Takaya
- NTT Space Environment and Energy Laboratories, Nippon Telegraph and Telephone Corporation, 3-9-11 Midori-cho, Musashino-shi, Tokyo 180-8585, Japan;
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259-R1-29 Nagatsuta, Midori-ku, Yokohama-shi, Kanagawa 226-8503, Japan;
| | - Sousuke Imamura
- NTT Space Environment and Energy Laboratories, Nippon Telegraph and Telephone Corporation, 3-9-11 Midori-cho, Musashino-shi, Tokyo 180-8585, Japan;
- Correspondence: (I.P.); (S.I.); Tel.: +81-422-59-6179 (S.I.)
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Bagha UK, Satpathy JK, Mukherjee G, Sastri CV, de Visser SP. A comprehensive insight into aldehyde deformylation: mechanistic implications from biology and chemistry. Org Biomol Chem 2021; 19:1879-1899. [PMID: 33406196 DOI: 10.1039/d0ob02204g] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aldehyde deformylation is an important reaction in biology, organic chemistry and inorganic chemistry and the process has been widely applied and utilized. For instance, in biology, the aldehyde deformylation reaction has wide differences in biological function, whereby cyanobacteria convert aldehydes into alkanes or alkenes, which are used as natural products for, e.g., defense mechanisms. By contrast, the cytochromes P450 catalyse the biosynthesis of hormones, such as estrogen, through an aldehyde deformylation reaction step. In organic chemistry, the aldehyde deformylation reaction is a common process for replacing functional groups on a molecule, and as such, many different synthetic methods and procedures have been reported that involve an aldehyde deformylation step. In bioinorganic chemistry, a variety of metal(iii)-peroxo complexes have been synthesized as biomimetic models and shown to react efficiently with aldehydes through deformylation reactions. This review paper provides an overview of the various aldehyde deformylation reactions in organic chemistry, biology and biomimetic model systems, and shows a broad range of different chemical reaction mechanisms for this process. Although a nucleophilic attack at the carbonyl centre is the consensus reaction mechanism, several examples of an alternative electrophilic reaction mechanism starting with hydrogen atom abstraction have been reported as well. There is still much to learn and to discover on aldehyde deformylation reactions, as deciphered in this review paper.
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Affiliation(s)
- Umesh Kumar Bagha
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam 781039, India.
| | | | - Gourab Mukherjee
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam 781039, India.
| | - Chivukula V Sastri
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam 781039, India.
| | - Sam P de Visser
- Manchester Institute of Biotechnology and the Department of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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From CO2 to Value-Added Products: A Review about Carbon-Based Materials for Electro-Chemical CO2 Conversion. Catalysts 2021. [DOI: 10.3390/catal11030351] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The global warming and the dangerous climate change arising from the massive emission of CO2 from the burning of fossil fuels have motivated the search for alternative clean and sustainable energy sources. However, the industrial development and population necessities make the decoupling of economic growth from fossil fuels unimaginable and, consequently, the capture and conversion of CO2 to fuels seems to be, nowadays, one of the most promising and attractive solutions in a world with high energy demand. In this respect, the electrochemical CO2 conversion using renewable electricity provides a promising solution. However, faradaic efficiency of common electro-catalysts is low, and therefore, the design of highly selective, energy-efficient, and cost-effective electrocatalysts is critical. Carbon-based materials present some advantages such as relatively low cost and renewability, excellent electrical conductivity, and tunable textural and chemical surface, which show them as competitive materials for the electro-reduction of CO2. In this review, an overview of the recent progress of carbon-based electro-catalysts in the conversion of CO2 to valuable products is presented, focusing on the role of the different carbon properties, which provides a useful understanding for the materials design progress in this field. Development opportunities and challenges in the field are also summarized.
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Sharafi H, Fooladi J, Tabatabaei M, Momhed Heravi M, Rajabi Memari H. Lipid Production Capacity of a Newly Characterized Cyanobacterial Strain Synechocystissp. MH01: A Comparative Performance Evaluation of Cyanobacterial Lipid-Based Biodiesel. IRANIAN JOURNAL OF BIOTECHNOLOGY 2021; 19:e2313. [PMID: 34179185 PMCID: PMC8217539 DOI: 10.30498/ijb.2021.2313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Background: Cyanobacteria have been the focus of extensive researches because of their high potential for the development of new generations
of useful natural compounds with vast applications. For the entire last ten years, a lot of attention has been dedicated to the
cyanobacterial lipids as a main source of valuable materials for clean energy production. Objectives: As there is a direct relationship between biofuel properties and compositional characteristics of fatty acids, a selected
lipid-producing cyanobacterial strain was examined and analyzed in terms of fatty acid composition. The biodiesel quality parameters
were carefully examined as well. Materials and Methods: A cyanobacterial strain was isolated from waterfalls in the northern part of Iran and identified as Synechocystis
sp. MH01. The fatty acids profile of the selected strain, as tested in various culture conditions, was analyzed by gas chromatography
(GC) and compared with control subjects to further validating the biodiesel quality parameters. Results: The autotrophic cultivation of Synechocystissp. MH01 resulted in biomass and lipid productivity of
109 mg.L-1 day-1 and 22.89 mg.L-1 day-1, respectively.
The mixotrophic cultivation of MH01 strain in sucrose-containing medium led to an approximately 1.8 and 1.22 fold increase
in biomass and lipid productivity compared with the autotrophic condition. The addition of glycine to BG11 medium caused
up to ~1.3 and ~1.18 fold increase in biomass and lipid productivity compared with control subjects.
The analysis of qualitative parameters of the biodiesel, as derived from the lipids, indicated that Synechocystis sp. MH01 has a high
ability for lipid production under optimal culture conditions Conclusions: It seems feasible to evolve the Synechocystissp. MH01 further particularly for more lipid production as a promising primary
raw material for biofuel production through fine-tuning of medium composition
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Affiliation(s)
- Hakimeh Sharafi
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Vanak Village Street, Tehran, Iran
| | - Jamshid Fooladi
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Vanak Village Street, Tehran, Iran
| | - Meisam Tabatabaei
- Biofuel Research Team (BRTeam), Microbial Biotechnology and Biosafety Department, Agricultural Biotechnology Research Institute of Iran (ABRII), Karaj, Iran
| | - Majid Momhed Heravi
- Department of Chemistry, Faculty of Science, Alzahra University, Vanak Village Street, Tehran, Iran
| | - Hamid Rajabi Memari
- Shahid Chamran University of Ahvaz, Faculty of Agronomy and Plant Breeding, Ahvaz, Iran
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Zhu Z, Jiang J, Fa Y. Overcoming the Biological Contamination in Microalgae and Cyanobacteria Mass Cultivations for Photosynthetic Biofuel Production. Molecules 2020; 25:molecules25225220. [PMID: 33182530 PMCID: PMC7698126 DOI: 10.3390/molecules25225220] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 02/08/2023] Open
Abstract
Microalgae and cyanobacteria have shown significant potential for the development of the next biofuels innovation because of their own characteristics as photosynthetic microorganisms. However, it is confronted with a lot of severe challenges on the economic scaling-up of the microalgae- and cyanobacteria-based biofuels production. One of these major challenges is the lack of a reliable preventing and controlling culture system of biological contamination, which can attack the cell growth or product accumulation causing crashing effects. To increase the commercial viability of microalgae- and cyanobacteria-based biofuels production, overcoming the biological contaminations should be at the top of the priority list. Here, we highlight the importance of two categories of biological contaminations and their controlling strategies in the mass cultivations of microalgae and cyanobacteria, and outline the directions that should be exploited in the future.
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Affiliation(s)
- Zhi Zhu
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province and School of Life Science, Jiangsu Normal University, Xuzhou 221116, China;
| | - Jihong Jiang
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province and School of Life Science, Jiangsu Normal University, Xuzhou 221116, China;
- Correspondence: (J.J.); (Y.F.)
| | - Yun Fa
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Correspondence: (J.J.); (Y.F.)
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Kim S, Lee SH, Seo H, Kim KJ. Biochemical properties and crystal structure of formate-tetrahydrofolate ligase from Methylobacterium extorquens CM4. Biochem Biophys Res Commun 2020; 528:426-431. [PMID: 32505353 DOI: 10.1016/j.bbrc.2020.05.198] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 05/26/2020] [Indexed: 11/28/2022]
Abstract
Methylobacterium extorquens is a methylotroph model organism that has the ability to assimilate formate using the tetrahydrofolate (THF) pathway. The formate-tetrahydrofolate ligase from M. extorquens (MeFtfL) is an enzyme involved in the THF pathway that catalyzes the conversion of formate, THF, and ATP into formyltetrahydrofolate and ADP. To investigate the biochemical properties of MeFtfL, we evaluated the metal usage and enzyme kinetics of the enzyme. MeFtfL uses the Mg ion for catalytic activity, but also has activity for Mn and Ca ions. The enzyme kinetics analysis revealed that Km value of farmate was much higher than THF and ATP, which shows that the ligation activity of MeFtfL is highly dependent on formation concentration. We also determined the crystal structure of MeFtfL at 2.8 Å resolution. MeFtfL functions as a tetramer, and each monomer consists of three domains. The structural superposition of MeFtfL with FtfL from Moorella thermoacetica allowed us to predict the substrate binding site of the enzyme.
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Affiliation(s)
- Seongmin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Seul Hoo Lee
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Hogyun Seo
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea; Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea.
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Sacko O, Barnes CL, Greene LH, Lee JW. Survivability of Wild-Type and Genetically Engineered Thermosynechococcus elongatus BP1 with Different Temperature Conditions. APPLIED BIOSAFETY 2020; 25:104-117. [DOI: 10.1177/1535676019896640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Oumar Sacko
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
- Authors Oumar Sacko and Cherrelle L. Barnes contributed equally to this article
| | - Cherrelle L. Barnes
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
- Authors Oumar Sacko and Cherrelle L. Barnes contributed equally to this article
| | - Lesley H. Greene
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
| | - James W. Lee
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
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34
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Wiltschi B, Cernava T, Dennig A, Galindo Casas M, Geier M, Gruber S, Haberbauer M, Heidinger P, Herrero Acero E, Kratzer R, Luley-Goedl C, Müller CA, Pitzer J, Ribitsch D, Sauer M, Schmölzer K, Schnitzhofer W, Sensen CW, Soh J, Steiner K, Winkler CK, Winkler M, Wriessnegger T. Enzymes revolutionize the bioproduction of value-added compounds: From enzyme discovery to special applications. Biotechnol Adv 2020; 40:107520. [DOI: 10.1016/j.biotechadv.2020.107520] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 10/18/2019] [Accepted: 01/13/2020] [Indexed: 12/11/2022]
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35
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Aketo T, Hoshikawa Y, Nojima D, Yabu Y, Maeda Y, Yoshino T, Takano H, Tanaka T. Selection and characterization of microalgae with potential for nutrient removal from municipal wastewater and simultaneous lipid production. J Biosci Bioeng 2020; 129:565-572. [DOI: 10.1016/j.jbiosc.2019.12.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 01/12/2023]
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36
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Production of polymers by cyanobacteria grown in wastewater: Current status, challenges and future perspectives. N Biotechnol 2020; 55:46-57. [DOI: 10.1016/j.nbt.2019.09.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 09/07/2019] [Accepted: 09/13/2019] [Indexed: 11/20/2022]
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Malek Shahkouhi A, Motamedian E. Reconstruction of a regulated two-cell metabolic model to study biohydrogen production in a diazotrophic cyanobacterium Anabaena variabilis ATCC 29413. PLoS One 2020; 15:e0227977. [PMID: 31978122 PMCID: PMC6980584 DOI: 10.1371/journal.pone.0227977] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 01/03/2020] [Indexed: 12/21/2022] Open
Abstract
Anabaena variabilis is a diazotrophic filamentous cyanobacterium that differentiates to heterocysts and produces hydrogen as a byproduct. Study on metabolic interactions of the two differentiated cells provides a better understanding of its metabolism especially for improving hydrogen production. To this end, a genome-scale metabolic model for Anabaena variabilis ATCC 29413, iAM957, was reconstructed and evaluated in this research. Then, the model and transcriptomic data of the vegetative and heterocyst cells were applied to construct a regulated two-cell metabolic model. The regulated model improved prediction for biomass in high radiation levels. The regulated model predicts that heterocysts provide an oxygen-free environment and then, this model was used to find strategies for improving hydrogen production in heterocysts. The predictions indicate that the removal of uptake hydrogenase improves hydrogen production which is consistent with previous empirical research. Furthermore, the regulated model proposed activation of some reactions to provide redox cofactors which are required for improving hydrogen production up to 60% by bidirectional hydrogenase.
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Affiliation(s)
- Ali Malek Shahkouhi
- Department of Biotechnology, Faculty of Chemical Engineering, Tarbiat Modares University, Tehran, Iran
| | - Ehsan Motamedian
- Department of Biotechnology, Faculty of Chemical Engineering, Tarbiat Modares University, Tehran, Iran
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Wessendorf RL, Lu Y. Photosynthetic characterization of transgenic Synechocystis expressing a plant thiol/disulfide-modulating protein. PLANT SIGNALING & BEHAVIOR 2019; 15:1709708. [PMID: 31889463 PMCID: PMC7053882 DOI: 10.1080/15592324.2019.1709708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/18/2019] [Accepted: 12/22/2019] [Indexed: 06/10/2023]
Abstract
A previous study showed that introducing an Arabidopsis thaliana thiol/disulfide-modulating protein, Low Quantum Yield of Photosystem II 1 (LQY1), into the cyanobacterium Synechocystis sp. PCC6803 increased the efficiency of Photosystem II (PSII) photochemistry. In the present study, the authors provided additional evidence for the role of AtLQY1 in improving PSII photochemical efficiency and cell growth. Light response curve analysis showed that AtLQY1-expressing Synechocystis grown at a moderate growth light intensity (50 µmol photons m-2 s-1) had higher minimal, maximal, and variable fluorescence than the empty-vector control, under a wide range of actinic light intensities. Light induction and dark recovery curves demonstrated that AtLQY1-expressing Synechocystis grown at the moderate growth light intensity had higher effective PSII quantum yield, higher photochemical quenching, lower regulated heat dissipation (non-photochemical quenching), low amounts of reduced plastoquinone, and higher amounts of oxidized plastoquinone than the empty-vector control. Furthermore, growth curve analysis indicated that AtLQY1-expressing Synechocystis grew faster than the empty-vector control at the moderate growth light intensity. These results suggest that transgenic expression of AtLQY1 in Synechocystis significantly improves PSII photochemical efficiency and overall cell growth.
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Affiliation(s)
- Ryan L. Wessendorf
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, USA
| | - Yan Lu
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, USA
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Wessendorf RL, Lu Y. Introducing an Arabidopsis thaliana Thylakoid Thiol/Disulfide-Modulating Protein Into Synechocystis Increases the Efficiency of Photosystem II Photochemistry. FRONTIERS IN PLANT SCIENCE 2019; 10:1284. [PMID: 31681379 PMCID: PMC6805722 DOI: 10.3389/fpls.2019.01284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 09/13/2019] [Indexed: 06/10/2023]
Abstract
Photosynthetic species are subjected to a variety of environmental stresses, including suboptimal irradiance. In oxygenic photosynthetic organisms, a major effect of high light exposure is damage to the Photosystem II (PSII) reaction-center protein D1. This process even happens under low or moderate light. To cope with photodamage to D1, photosynthetic organisms evolved an intricate PSII repair and reassembly cycle, which requires the participation of different auxiliary proteins, including thiol/disulfide-modulating proteins. Most of these auxiliary proteins exist ubiquitously in oxygenic photosynthetic organisms. Due to differences in mobility and environmental conditions, land plants are subject to more extensive high light stress than algae and cyanobacteria. Therefore, land plants evolved additional thiol/disulfide-modulating proteins, such as Low Quantum Yield of PSII 1 (LQY1), to aid in the repair and reassembly cycle of PSII. In this study, we introduced an Arabidopsis thaliana homolog of LQY1 (AtLQY1) into the cyanobacterium Synechocystis sp. PCC6803 and performed a series of biochemical and physiological assays on AtLQY1-expressing Synechocystis. At a moderate growth light intensity (50 µmol photons m-2 s-1), AtLQY1-expressing Synechocystis was found to have significantly higher F v /F m , and lower nonphotochemical quenching and reactive oxygen species levels than the empty-vector control, which is opposite from the loss-of-function Atlqy1 mutant phenotype. Light response curve analysis of PSII operating efficiency and electron transport rate showed that AtLQY1-expressing Synechocystis also outperform the empty-vector control under higher light intensities. The increases in F v /F m , PSII operating efficiency, and PSII electron transport rate in AtLQY1-expressing Synechocystis under such growth conditions most likely come from an increased amount of PSII, because the level of D1 protein was found to be higher in AtLQY1-expressing Synechocystis. These results suggest that introducing AtLQY1 is beneficial to Synechocystis.
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Affiliation(s)
| | - Yan Lu
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, United States
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40
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Yaashikaa P, Senthil Kumar P, Varjani SJ, Saravanan A. A review on photochemical, biochemical and electrochemical transformation of CO2 into value-added products. J CO2 UTIL 2019. [DOI: 10.1016/j.jcou.2019.05.017] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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41
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Metabolic engineering of microorganisms for the production of ethanol and butanol from oxides of carbon. Appl Microbiol Biotechnol 2019; 103:8283-8292. [PMID: 31396679 DOI: 10.1007/s00253-019-10072-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/29/2019] [Accepted: 07/29/2019] [Indexed: 01/23/2023]
Abstract
The utilized biomass is an important consideration for sustainable biofuel production. To avoid competing with food needs, researchers have turned their attention to non-food lignocellulosic biomasses as potential feedstocks for biofuel production. However, the saccharification of a lignocellulosic biomass produces a large amount of lignin as waste. To overcome this hurdle, biomass gasification has been suggested as an alternative to saccharification. During biomass gasification, oxides of carbon (CO, CO2) and hydrogen are produced as a major product. Accordingly, microorganisms capable of utilizing these oxides of carbon have gained attention as hosts for the production of biofuels, such as ethanol and butanol. In this work, we reviewed the Calvin cycle and Wood-Ljungdahl pathway for utilizing oxides of carbon in cyanobacteria and acetogens, respectively, and discussed the metabolic engineering strategies that may be used to produce ethanol and butanol from oxides of carbon through these routes.
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Hirokawa Y, Kubo T, Soma Y, Saruta F, Hanai T. Enhancement of acetyl-CoA flux for photosynthetic chemical production by pyruvate dehydrogenase complex overexpression in Synechococcus elongatus PCC 7942. Metab Eng 2019; 57:23-30. [PMID: 31377410 DOI: 10.1016/j.ymben.2019.07.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 10/26/2022]
Abstract
Genetic manipulation in cyanobacteria enables the direct production of valuable chemicals from carbon dioxide. However, there are still very few reports of the production of highly effective photosynthetic chemicals. Several synthetic metabolic pathways (e.g., isopropanol, acetone, isoprene, and fatty acids) have been constructed by branching from acetyl-CoA and malonyl-CoA, which are key intermediates for photosynthetic chemical production downstream of pyruvate decarboxylation. Recent reports of the absolute determination of cellular metabolites in Synechococcus elongatus PCC 7942 have shown that its acetyl-CoA levels corresponded to about one hundredth of the pyruvate levels. In short, one of the reasons for lower photosynthetic chemical production from acetyl-CoA and malonyl-CoA was the smaller flux to acetyl-CoA. Pyruvate decarboxylation is a primary pathway for acetyl-CoA synthesis from pyruvate and is mainly catalyzed by the pyruvate dehydrogenase complex (PDHc). In this study, we tried to enhance the flux toward acetyl-CoA from pyruvate by overexpressing PDH genes and, thus, catalyzing the conversion of pyruvate to acetyl-CoA via NADH generation. The overexpression of PDH genes cloned from S. elongatus PCC 7942 significantly increased PDHc enzymatic activity and intracellular acetyl-CoA levels in the crude cell extract. Although growth defects were observed in overexpressing strains of PDH genes, the combinational overexpression of PDH genes with the synthetic metabolic pathway for acetate or isopropanol resulted in about 7-fold to 9-fold improvement in its production titer, respectively (9.9 mM, 594.5 mg/L acetate, 4.9 mM, 294.5 mg/L isopropanol). PDH genes overexpression would, therefore, be useful not only for the production of these model chemicals, but also for the production of other chemicals that require acetyl-CoA as a key precursor.
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Affiliation(s)
- Yasutaka Hirokawa
- Laboratory for Bioinformatics, Graduate School of Systems Biosciences, Kyushu University, W5-729, 744, Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Takeshi Kubo
- Laboratory for Bioinformatics, Graduate School of Systems Biosciences, Kyushu University, W5-729, 744, Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yuki Soma
- Laboratory for Bioinformatics, Graduate School of Systems Biosciences, Kyushu University, W5-729, 744, Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Fumiko Saruta
- Laboratory for Bioinformatics, Graduate School of Systems Biosciences, Kyushu University, W5-729, 744, Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Taizo Hanai
- Laboratory for Bioinformatics, Graduate School of Systems Biosciences, Kyushu University, W5-729, 744, Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
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iMet: A graphical user interface software tool to merge metabolic networks. Heliyon 2019; 5:e01766. [PMID: 31286073 PMCID: PMC6587100 DOI: 10.1016/j.heliyon.2019.e01766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 04/10/2019] [Accepted: 05/15/2019] [Indexed: 11/23/2022] Open
Abstract
Nowadays, studying microorganisms has become faster and deeper than the last decades, thanks to the modeling of genome-scale metabolic networks. Completed genome sequencing projects of microorganisms and annotating these sequences have provided a worthwhile platform for reconstructing and modeling genome-scale metabolic networks. The genome-scale metabolic network reconstruction is a laborious and time-consuming task which needs an extensive study and search in different types of databases. Furthermore, it also requires an iterative process of creating and curating the obtained network, particularly with experimental methods. Hence, different types of reconstructions and models of a targeted microorganism can be found with different qualities, as the goal and need of researchers differ. Due to these circumstances, scientists have to continue with only one of the reconstructed metabolic networks of each microorganism and ignore the rest in their in silico works. It is clear that having a tool which merges different metabolic networks of a single organism can be a useful and effective way to study them with minimal cost and time. To meet this need, we have developed iMet, the standalone graphical user interface (GUI) software tool to merge multiple reconstructed metabolic networks of microorganisms. As a case study, we merged three reconstructed metabolic networks of a cyanobacterium using iMet, and then all of them (including the new merged one) became modeled. The results of our evaluations including Flux Balance Analysis (FBA), revealed enhancing metabolic network coverage as well as increasing yield of desired products in the new obtained model.
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Werner A, Broeckling CD, Prasad A, Peebles CAM. A comprehensive time-course metabolite profiling of the model cyanobacterium Synechocystis sp. PCC 6803 under diurnal light:dark cycles. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:379-388. [PMID: 30889309 DOI: 10.1111/tpj.14320] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/06/2019] [Accepted: 03/12/2019] [Indexed: 05/07/2023]
Abstract
Cyanobacteria are a model photoautotroph and a chassis for the sustainable production of fuels and chemicals. Knowledge of photoautotrophic metabolism in the natural environment of day/night cycles is lacking, yet has implications for improved yield from plants, algae and cyanobacteria. Here, a thorough approach to characterizing diverse metabolites-including carbohydrates, lipids, amino acids, pigments, cofactors, nucleic acids and polysaccharides-in the model cyanobacterium Synechocystis sp. PCC 6803 (S. 6803) under sinusoidal diurnal light:dark cycles was developed and applied. A custom photobioreactor and multi-platform mass spectrometry workflow enabled metabolite profiling every 30-120 min across a 24-h diurnal sinusoidal LD ('sinLD') cycle peaking at 1600 μmol photons m-2 sec-1 . We report widespread oscillations across the sinLD cycle with 90%, 94% and 40% of the identified polar/semi-polar, non-polar and polymeric metabolites displaying statistically significant oscillations, respectively. Microbial growth displayed distinct lag, biomass accumulation and cell division phases of growth. During the lag phase, amino acids and nucleic acids accumulated to high levels per cell followed by decreased levels during the biomass accumulation phase, presumably due to protein and DNA synthesis. Insoluble carbohydrates displayed sharp oscillations per cell at the day-to-night transition. Potential bottlenecks in central carbon metabolism are highlighted. Together, this report provides a comprehensive view of photosynthetic metabolite behavior with high temporal resolution, offering insight into the impact of growth synchronization to light cycles via circadian rhythms. Incorporation into computational modeling and metabolic engineering efforts promises to improve industrially relevant strain design.
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Affiliation(s)
- Allison Werner
- Cell and Molecular Biology Program, Colorado State University, 1005 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Corey D Broeckling
- Proteomics and Metabolomics Facility, Colorado State University, 2021 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Ashok Prasad
- Cell and Molecular Biology Program, Colorado State University, 1005 Campus Delivery, Fort Collins, CO, 80523, USA
- Department of Chemical and Biological Engineering, Colorado State University, 1370 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Christie A M Peebles
- Cell and Molecular Biology Program, Colorado State University, 1005 Campus Delivery, Fort Collins, CO, 80523, USA
- Department of Chemical and Biological Engineering, Colorado State University, 1370 Campus Delivery, Fort Collins, CO, 80523, USA
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Optimization of Light Intensity and NaNO 3 Concentration in Amazon Cyanobacteria Cultivation to Produce Biodiesel. Molecules 2019; 24:molecules24122326. [PMID: 31238580 PMCID: PMC6630786 DOI: 10.3390/molecules24122326] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/01/2019] [Accepted: 05/15/2019] [Indexed: 12/27/2022] Open
Abstract
The objective of this study, for the first time, was to optimize Amazonian cyanobacterial culture conditions for improving cell productivity and lipid content, by analyzing the effect of light intensity and nitrogen concentration, for empirically evaluating biodiesel quality parameters. The strains Synechocystis sp. CACIAM05, Microcystis aeruginosa CACIAM08, Pantanalinema rosaneae CACIAM18, and Limnothrix sp. CACIAM25, were previously identified by morphological and molecular analysis (16S rRNA) and were selected based on their production of chlorophyll a and dry cell weight. Then, factorial planning (22) with central points was applied, with light intensity and NaNO3 concentration as independent variables. As response variables, cell productivity and lipid content were determined. Statistical analysis indicated that for all strains, the independent variables were statistically significant for cell productivity. Analysis of the fatty acid composition demonstrated diversity in the composition of the fatty acid profile from the experimental planning assays of each strain. The Biodiesel Analyzer software predicted the biodiesel quality parameters. CACIAM05 and CACIAM25 obtained better parameters with low levels of light intensity and NaNO3 concentration, whereas CACIAM08 and CACIAM18 obtained better parameters with low NaNO3 concentrations and high luminous intensity.
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Tabatabai B, Fathabad SG, Bonyi E, Rajini S, Aslan K, Sitther V. Nanoparticle-mediated Impact on Growth and Fatty Acid Methyl Ester Composition in the Cyanobacterium Fremyella diplosiphon. BIOENERGY RESEARCH 2019; 12:409-418. [PMID: 31984113 PMCID: PMC6980354 DOI: 10.1007/s12155-019-09966-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Insufficient light supply is a major limitation in cultivation of cyanobacteria for scaled up biofuel production and other biotechnological applications, which has driven interest in nanoparticle-mediated enhancement of cellular light capture. In the present study, Fremyella diplosiphon wild type (Fd33) and halotolerant (HSF33-2) strains were grown in solution with 20, 100, and 200 nm-diameter gold nanoparticles (AuNPs) to determine their impact on biomass accumulation, pigmentation, and fatty acid methyl ester (FAME) production. Results revealed a significant increase in growth of Fd33 (0.244 ± 0.006) and HSF33-2 (0.112 ± 0.003) when treated with 200 nm AuNPs. In addition, we observed a significant increase in chlorophyll a accumulation in 200 nm AuNP-treated Fd33 (25.7%) and HSF33-2 (36.3%) indicating that NPs enhanced photosynthetic pigmentation. We did not observe any alteration in FAME composition and biodiesel properties of transesterified F. diplosiphon lipids among all AuNP treatments. Interactions between F. diplosiphon and AuNPs were visualized using scanning electron microscopy. Energy dispersive X-ray spectroscopy confirmed the presence of AuNPs outside cells with aggregation in high cell density locales. Our findings indicate that nanotechnological approaches could significantly enhance growth of the organism with no negative effect on FAME-derived biodiesel properties, thus augmenting F. diplosiphon as a potential biofuel agent.
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Affiliation(s)
- Behnam Tabatabai
- Department of Biology, Morgan State University, 1700 East Cold Spring Lane, Baltimore, Maryland 21251, United States
| | - Somayeh Gharaie Fathabad
- Department of Biology, Morgan State University, 1700 East Cold Spring Lane, Baltimore, Maryland 21251, United States
| | - Enock Bonyi
- Department of Civil Engineering, Morgan State University, 1700 East Cold Spring Lane, Baltimore, Maryland 21251, United States
| | - Sophia Rajini
- Middle East Educational Services, Doha, Qatar, P.O. BOX: 3453
| | - Kadir Aslan
- Department of Civil Engineering, Morgan State University, 1700 East Cold Spring Lane, Baltimore, Maryland 21251, United States
| | - Viji Sitther
- Department of Biology, Morgan State University, 1700 East Cold Spring Lane, Baltimore, Maryland 21251, United States
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Monshupanee T, Chairattanawat C, Incharoensakdi A. Disruption of cyanobacterial γ-aminobutyric acid shunt pathway reduces metabolites levels in tricarboxylic acid cycle, but enhances pyruvate and poly(3-hydroxybutyrate) accumulation. Sci Rep 2019; 9:8184. [PMID: 31160681 PMCID: PMC6547876 DOI: 10.1038/s41598-019-44729-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 05/24/2019] [Indexed: 12/13/2022] Open
Abstract
The photoautotrophic cyanobacterium Synechocystis sp. PCC 6803 assimilates carbon dioxide as the sole carbon source, and a major portion of the assimilated carbon is metabolically consumed by the tricarboxylic acid (TCA) cycle. Effects of partial interference of TCA cycle metabolic activity on other carbon metabolism have yet to be examined. Here, the γ-aminobutyric acid (GABA) shunt, one of the metabolic pathways for completing TCA cycle in Synechocystis, was disrupted via inactivating the glutamate decarboxylase gene (gdc). Under normal photoautotrophic condition, cell growth and the level of the TCA cycle metabolites succinate, malate and citrate were decreased by 25%, 35%, 19% and 28%, respectively, in Δgdc mutant relative to those in the wild type (WT). The cellular levels of glycogen and total lipids of the Δgdc mutant were comparable to those of the WT, but the intracellular levels of pyruvate and bioplastic poly(3-hydroxybutyrate) (PHB) were 1.23- and 2.50-fold higher, respectively, in Δgdc mutant. Thus, disruption of the GABA shunt pathway reduced the TCA cycle metabolites levels, but positively enhanced the bioaccumulation of pyruvate and PHB. The PHB production rate in Δgdc mutant was 2.0-fold higher than in the WT under normal photoautotrophy.
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Affiliation(s)
- Tanakarn Monshupanee
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Chayanee Chairattanawat
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Aran Incharoensakdi
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
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Abstract
The current fossil fuel reserves are not sufficient to meet the increasing demand and very soon will become exhausted. Pollution, global warming, and inflated oil prices have led the quest for renewable energy sources. Algal biofuels represent a potential source of renewable energy. Algae, as the third generation feedstock, are suitable for biodiesel and bioethanol production due to their quick growth, excellent biomass yield, and high lipid and carbohydrate contents. With their huge potential, algae are expected to surpass the first and second generation feedstocks. Only a few thousand algal species have been investigated as possible biofuel sources, and none of them was ideal. This review summarizes the current status of algal biofuels, important steps of algal biofuel production, and the major commercial production challenges.
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Nshogozabahizi J, Aubrey K, Ross J, Thakor N. Applications and limitations of regulatory
RNA
elements in synthetic biology and biotechnology. J Appl Microbiol 2019; 127:968-984. [DOI: 10.1111/jam.14270] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/09/2019] [Accepted: 03/21/2019] [Indexed: 12/13/2022]
Affiliation(s)
- J.C. Nshogozabahizi
- Department of Chemistry and Biochemistry Alberta RNA Research and Training Institute (ARRTI) University of Lethbridge Lethbridge AB Canada
| | - K.L. Aubrey
- Department of Chemistry and Biochemistry Alberta RNA Research and Training Institute (ARRTI) University of Lethbridge Lethbridge AB Canada
| | - J.A. Ross
- Department of Chemistry and Biochemistry Alberta RNA Research and Training Institute (ARRTI) University of Lethbridge Lethbridge AB Canada
| | - N. Thakor
- Department of Chemistry and Biochemistry Alberta RNA Research and Training Institute (ARRTI) University of Lethbridge Lethbridge AB Canada
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Mehta K, Jaiswal D, Nayak M, Prasannan CB, Wangikar PP, Srivastava S. Elevated carbon dioxide levels lead to proteome-wide alterations for optimal growth of a fast-growing cyanobacterium, Synechococcus elongatus PCC 11801. Sci Rep 2019; 9:6257. [PMID: 31000743 PMCID: PMC6472392 DOI: 10.1038/s41598-019-42576-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/29/2019] [Indexed: 12/21/2022] Open
Abstract
The environmental considerations attributing to the escalation of carbon dioxide emissions have raised alarmingly. Consequently, the concept of sequestration and biological conversion of CO2 by photosynthetic microorganisms is gaining enormous recognition. In this study, in an attempt to discern the synergistic CO2 tolerance mechanisms, metabolic responses to increasing CO2 concentrations were determined for Synechococcus elongatus PCC 11801, a fast-growing, novel freshwater strain, using quantitative proteomics. The protein expression data revealed that the organism responded to elevated CO2 by not only regulating the cellular transporters involved in carbon-nitrogen uptake and assimilation but also by inducing photosynthesis, carbon fixation and glycolysis. Several components of photosynthetic machinery like photosystem reaction centers, phycobilisomes, cytochromes, etc. showed a marked up-regulation with a concomitant downshift in proteins involved in photoprotection and redox maintenance. Additionally, enzymes belonging to the TCA cycle and oxidative pentose phosphate pathway exhibited a decline in their expression, further highlighting that the demand for reduced cofactors was fulfilled primarily through photosynthesis. The present study brings the first-ever comprehensive assessment of intricate molecular changes in this novel strain while shifting from carbon-limited to carbon-sufficient conditions and may pave the path for future host and pathway engineering for production of sustainable fuels through efficient CO2 capture.
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Affiliation(s)
- Kanika Mehta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Damini Jaiswal
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Monalisha Nayak
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Charulata B Prasannan
- 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
| | - 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
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, 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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