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Zhong J, Wang Y, Chen Z, Yalikun Y, He L, Liu T, Ma G. Engineering cyanobacteria as a new platform for producing taxol precursors directly from carbon dioxide. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:99. [PMID: 39014505 PMCID: PMC11253407 DOI: 10.1186/s13068-024-02555-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 07/10/2024] [Indexed: 07/18/2024]
Abstract
Taxol serves as an efficient natural anticancer agent with extensive applications in the treatment of diverse malignancies. Although advances in synthetic biology have enabled the de novo synthesis of taxol precursors in various microbial chassis, the total biosynthesis of taxol remains challengable owing to the restricted oxidation efficiency in heterotrophic microbes. Here, we engineered Synechocystis sp. PCC 6803 with modular metabolic pathways consisting of the methylerythritol phosphate pathway enzymes and taxol biosynthetic enzymes for production of taxadiene-5α-ol (T5α-ol), the key oxygenated intermediate of taxol. The best strain DIGT-P560 produced up to 17.43 mg/L of oxygenated taxanes and 4.32 mg/L of T5α-ol. Moreover, transcriptomic analysis of DIGT-P560 revealed that establishing a oxygenated taxane flux may enhance photosynthetic electron transfer efficiency and central metabolism in the engineered strain to ameliorate the metabolic disturbances triggered by the incorporation of exogenous genes. This is the first demonstration of photosynthetic production of taxadiene-5α-ol from CO2 in cyanobacteria, highlighting the broad prospects of engineered cyanobacteria as bio-solar cell factories for valuable terpenoids production and expanding the ideas for further rational engineering and optimization.
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Affiliation(s)
- Jialing Zhong
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai, 200240, People's Republic of China
| | - Yushu Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai, 200240, People's Republic of China
| | - Zhuoyang Chen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai, 200240, People's Republic of China
| | - Yaliqin Yalikun
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai, 200240, People's Republic of China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai, 200240, People's Republic of China
| | - Tiangang Liu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Gang Ma
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai, 200240, People's Republic of China.
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Bolay P, Dodge N, Janssen K, Jensen PE, Lindberg P. Tailoring regulatory components for metabolic engineering in cyanobacteria. PHYSIOLOGIA PLANTARUM 2024; 176:e14316. [PMID: 38686633 DOI: 10.1111/ppl.14316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/26/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024]
Abstract
The looming climate crisis has prompted an ever-growing interest in cyanobacteria due to their potential as sustainable production platforms for the synthesis of energy carriers and value-added chemicals from CO2 and sunlight. Nonetheless, cyanobacteria are yet to compete with heterotrophic systems in terms of space-time yields and consequently production costs. One major drawback leading to the low production performance observed in cyanobacteria is the limited ability to utilize the full capacity of the photosynthetic apparatus and its associated systems, i.e. CO2 fixation and the directly connected metabolism. In this review, novel insights into various levels of metabolic regulation of cyanobacteria are discussed, including the potential of targeting these regulatory mechanisms to create a chassis with a phenotype favorable for photoautotrophic production. Compared to conventional metabolic engineering approaches, minor perturbations of regulatory mechanisms can have wide-ranging effects.
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Affiliation(s)
- Paul Bolay
- Microbial Chemistry, Department of Chemistry - Ångström, Uppsala University, Uppsala, SE, Sweden
| | - Nadia Dodge
- Plant Based Foods and Biochemistry, Food Analytics and Biotechnology, Department of Food Science, University of Copenhagen, Denmark
| | - Kim Janssen
- Microbial Chemistry, Department of Chemistry - Ångström, Uppsala University, Uppsala, SE, Sweden
| | - Poul Erik Jensen
- Plant Based Foods and Biochemistry, Food Analytics and Biotechnology, Department of Food Science, University of Copenhagen, Denmark
| | - Pia Lindberg
- Microbial Chemistry, Department of Chemistry - Ångström, Uppsala University, Uppsala, SE, Sweden
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Aronsson H, Solymosi K. Diversification of Plastid Structure and Function in Land Plants. Methods Mol Biol 2024; 2776:63-88. [PMID: 38502498 DOI: 10.1007/978-1-0716-3726-5_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: 03/21/2024]
Abstract
Plastids represent a largely diverse group of organelles in plant and algal cells that have several common features but also a broad spectrum of morphological, ultrastructural, biochemical, and physiological differences. Plastids and their structural and metabolic diversity significantly contribute to the functionality and developmental flexibility of the plant body throughout its lifetime. In addition to the multiple roles of given plastid types, this diversity is accomplished in some cases by interconversions between different plastids as a consequence of developmental and environmental signals that regulate plastid differentiation and specialization. In addition to basic plastid structural features, the most important plastid types, the newly characterized peculiar plastids, and future perspectives in plastid biology are also provided in this chapter.
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Affiliation(s)
- Henrik Aronsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Katalin Solymosi
- Department of Plant Anatomy, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary.
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Kwok ACM, Leung SK, Wong JTY. DNA:RNA Hybrids Are Major Dinoflagellate Minicircle Molecular Types. Int J Mol Sci 2023; 24:ijms24119651. [PMID: 37298602 DOI: 10.3390/ijms24119651] [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: 05/19/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
Peridinin-containing dinoflagellate plastomes are predominantly encoded in nuclear genomes, with less than 20 essential chloroplast proteins carried on "minicircles". Each minicircle generally carries one gene and a short non-coding region (NCR) with a median length of approximately 400-1000 bp. We report here differential nuclease sensitivity and two-dimensional southern blot patterns, suggesting that dsDNA minicircles are in fact the minor forms, with substantial DNA:RNA hybrids (DRHs). Additionally, we observed large molecular weight intermediates, cell-lysate-dependent NCR secondary structures, multiple bidirectional predicted ssDNA structures, and different southern blot patterns when probed with different NCR fragments. In silico analysis suggested the existence of substantial secondary structures with inverted repeats (IR) and palindrome structures within the initial ~650 bp of the NCR sequences, in accordance with conversion event(s) outcomes with PCR. Based on these findings, we propose a new transcription-templating-translation model, which is associated with cross-hopping shift intermediates. Since dinoflagellate chloroplasts are cytosolic and lack nuclear envelope breakdown, the dynamic DRH minicircle transport could have contributed to the spatial-temporal dynamics required for photosystem repair. This represents a paradigm shift from the previous understanding of "minicircle DNAs" to a "working plastome", which will have significant implications for its molecular functionality and evolution.
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Affiliation(s)
- Alvin Chun Man Kwok
- Division of Life Science, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong, China
| | - Siu Kai Leung
- Division of Life Science, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong, China
| | - Joseph Tin Yum Wong
- Division of Life Science, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong, China
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Shi W, Hu S, Song W, Huang Y, Shi C, Wang S. Uncovering the first complete chloroplast genomics, comparative analysis, and phylogenetic relationships of the medicinal plants Rhamnus cathartica and Frangula alnus ( Rhamnaceae). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:855-869. [PMID: 37520808 PMCID: PMC10382440 DOI: 10.1007/s12298-023-01331-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/04/2023] [Accepted: 07/05/2023] [Indexed: 08/01/2023]
Abstract
Rhamnus cathartica and Frangula alnus are economically valuable medicinal plants from the Rhamnaceae family. However, their chloroplast genome structure, phylogenetic position, relationships, and evolution remain poorly understood. Herein, the complete chloroplast genome resources of R. cathartica and F. alnus have been added. The first comparative analysis of the Rhamnus and Frangula species based on complete chloroplast genomes was provided. The chloroplast genomes of R. cathartica and F. alnus exhibited a quadripartite structure, with total lengths of 161,149 bp and 161,255 bp, respectively. The lack of the infA and psbL genes does not negatively impact the normal functioning of Rhamnus and Frangula species. The rpl20 and rpl33 genes are undergoing rapid evolution. Rhamnus and Frangula species prefer amino acids with A/U-terminal codons. There were between 100 and 126 simple sequence repeats and between 38 and 100 long repeats. Several highly divergent intergenic regions (trnK-UUU-trnQ-UUG, atpH-atpI, trnY-GUA-trnE-UUC, trnG-GCC-trnfM-CAU, trnT-UGU-trnF-GAA, rpl20-rps12, and rpl22-rps19) and highly divergent genes (ycf3, ndhA, rpl32, and ycf1) were identified, which could serve as potential phylogenetic markers due to their variability. We reconstructed the phylogenetic relationships among Rhamnus species and F. alnus using complete chloroplast genomes. There is no significant correlation between the medicinal value of the species analyzed and their phylogenetic relationships. These results provide valuable insights for understanding the phylogenetic relationship and evolution of Rhamnus and Frangula species. These findings could serve as a foundation for future studies on the Rhamnaceae. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01331-7.
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Affiliation(s)
- Wenbo Shi
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| | - Siqi Hu
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| | - Weicai Song
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| | - Yahui Huang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| | - Chao Shi
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650204 China
| | - Shuo Wang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
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Mellor SB, Behrendorff JBYH, Ipsen JØ, Crocoll C, Laursen T, Gillam EMJ, Pribil M. Exploiting photosynthesis-driven P450 activity to produce indican in tobacco chloroplasts. FRONTIERS IN PLANT SCIENCE 2023; 13:1049177. [PMID: 36743583 PMCID: PMC9890960 DOI: 10.3389/fpls.2022.1049177] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/14/2022] [Indexed: 05/28/2023]
Abstract
Photosynthetic organelles offer attractive features for engineering small molecule bioproduction by their ability to convert solar energy into chemical energy required for metabolism. The possibility to couple biochemical production directly to photosynthetic assimilation as a source of energy and substrates has intrigued metabolic engineers. Specifically, the chemical diversity found in plants often relies on cytochrome P450-mediated hydroxylations that depend on reductant supply for catalysis and which often lead to metabolic bottlenecks for heterologous production of complex molecules. By directing P450 enzymes to plant chloroplasts one can elegantly deal with such redox prerequisites. In this study, we explore the capacity of the plant photosynthetic machinery to drive P450-dependent formation of the indigo precursor indoxyl-β-D-glucoside (indican) by targeting an engineered indican biosynthetic pathway to tobacco (Nicotiana benthamiana) chloroplasts. We show that both native and engineered variants belonging to the human CYP2 family are catalytically active in chloroplasts when driven by photosynthetic reducing power and optimize construct designs to improve productivity. However, while increasing supply of tryptophan leads to an increase in indole accumulation, it does not improve indican productivity, suggesting that P450 activity limits overall productivity. Co-expression of different redox partners also does not improve productivity, indicating that supply of reducing power is not a bottleneck. Finally, in vitro kinetic measurements showed that the different redox partners were efficiently reduced by photosystem I but plant ferredoxin provided the highest light-dependent P450 activity. This study demonstrates the inherent ability of photosynthesis to support P450-dependent metabolic pathways. Plants and photosynthetic microbes are therefore uniquely suited for engineering P450-dependent metabolic pathways regardless of enzyme origin. Our findings have implications for metabolic engineering in photosynthetic hosts for production of high-value chemicals or drug metabolites for pharmacological studies.
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Affiliation(s)
- Silas B. Mellor
- Section for Plant Biochemistry, Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - James B. Y. H. Behrendorff
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
- Australian Research Council (ARC) Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, Australia
| | - Johan Ø. Ipsen
- Section for Forest, Nature and Biomass, Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg, Denmark
| | - Christoph Crocoll
- DynaMo Center, Section for Molecular Plant Biology, Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - Tomas Laursen
- Section for Plant Biochemistry, Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - Elizabeth M. J. Gillam
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - Mathias Pribil
- Section for Molecular Plant Biology, Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
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Yang S, Deng Y, Li S. Advances in plastid transformation for metabolic engineering in higher plants. ABIOTECH 2022; 3:224-232. [PMID: 36313931 PMCID: PMC9590572 DOI: 10.1007/s42994-022-00083-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/09/2022] [Indexed: 03/12/2023]
Abstract
The plastid (chloroplast) genome of higher plants is an appealing target for metabolic engineering via genetic transformation. Although the bacterial-type plastid genome is small compared with the nuclear genome, it can accommodate large quantities of foreign genes that precisely integrate through homologous recombination. Engineering complex metabolic pathways in plants often requires simultaneous and concerted expression of multiple transgenes, the possibility of stacking several transgenes in synthetic operons makes the transplastomic approach amazing. The potential for extraordinarily high-level transgene expression, absence of epigenetic gene silencing and transgene containment due to the exclusion of plastids from pollen transmission in most angiosperm species further add to the attractiveness of plastid transformation technology. This minireview describes recent advances in expanding the toolboxes for plastid genome engineering, and highlights selected high-value metabolites produced using transplastomic plants, including artemisinin, astaxanthin and paclitaxel.
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Affiliation(s)
- Sheng Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Yi Deng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Shengchun Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 China
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Sørensen M, Andersen-Ranberg J, Hankamer B, Møller BL. Circular biomanufacturing through harvesting solar energy and CO 2. TRENDS IN PLANT SCIENCE 2022; 27:655-673. [PMID: 35396170 DOI: 10.1016/j.tplants.2022.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/16/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
Using synthetic biology, it is now time to expand the biosynthetic repertoire of plants and microalgae by utilizing the chloroplast to augment the production of desired high-value compounds and of oil-, carbohydrate-, or protein-enriched biomass based on direct harvesting of solar energy and the consumption of CO2. Multistream product lines based on separate commercialization of the isolated high-value compounds and of the improved bulk products increase the economic potential of the light-driven production system and accelerate commercial scale up. Here we outline the scientific basis for the establishment of such green circular biomanufacturing systems and highlight recent results that make this a realistic option based on cross-disciplinary basic and applied research to advance long-term solutions.
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Affiliation(s)
- Mette Sørensen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Johan Andersen-Ranberg
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ben Hankamer
- Institute of Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark.
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Song W, Ji C, Chen Z, Cai H, Wu X, Shi C, Wang S. Comparative Analysis the Complete Chloroplast Genomes of Nine Musa Species: Genomic Features, Comparative Analysis, and Phylogenetic Implications. FRONTIERS IN PLANT SCIENCE 2022; 13:832884. [PMID: 35222490 PMCID: PMC8866658 DOI: 10.3389/fpls.2022.832884] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/07/2022] [Indexed: 06/12/2023]
Abstract
Musa (family Musaceae) is monocotyledonous plants in order Zingiberales, which grows in tropical and subtropical regions. It is one of the most important tropical fruit trees in the world. Herein, we used next-generation sequencing technology to assemble and perform in-depth analysis of the chloroplast genome of nine new Musa plants for the first time, including genome structure, GC content, repeat structure, codon usage, nucleotide diversity and etc. The entire length of the Musa chloroplast genome ranged from 167,975 to 172,653 bp, including 113 distinct genes comprising 79 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. In comparative analysis, we found that the contraction and expansion of the inverted repeat (IR) regions resulted in the doubling of the rps19 gene. The several non-coding sites (psbI-atpA, atpH-atpI, rpoB-petN, psbM-psbD, ndhf-rpl32, and ndhG-ndhI) and three genes (ycf1, ycf2, and accD) showed significant variation, indicating that they have the potential of molecular markers. Phylogenetic analysis based on the complete chloroplast genome and coding sequences of 77 protein-coding genes confirmed that Musa can be mainly divided into two groups. These genomic sequences provide molecular foundation for the development and utilization of Musa plants resources. This result may contribute to the understanding of the evolution pattern, phylogenetic relationships as well as classification of Musa plants.
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Affiliation(s)
- Weicai Song
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Chuxuan Ji
- Department of Life Sciences, Imperial College London, Silwood Park, London, United Kingdom
| | - Zimeng Chen
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Haohong Cai
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Xiaomeng Wu
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Chao Shi
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Shuo Wang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
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10
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Son S, Park SR. Challenges Facing CRISPR/Cas9-Based Genome Editing in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:902413. [PMID: 35677236 PMCID: PMC9169250 DOI: 10.3389/fpls.2022.902413] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/29/2022] [Indexed: 05/18/2023]
Abstract
The development of plant varieties with desired traits is imperative to ensure future food security. The revolution of genome editing technologies based on the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9) system has ushered in a new era in plant breeding. Cas9 and the single-guide RNA (sgRNA) form an effective targeting complex on a locus or loci of interest, enabling genome editing in all plants with high accuracy and efficiency. Therefore, CRISPR/Cas9 can save both time and labor relative to what is typically associated with traditional breeding methods. However, despite improvements in gene editing, several challenges remain that limit the application of CRISPR/Cas9-based genome editing in plants. Here, we focus on four issues relevant to plant genome editing: (1) plant organelle genome editing; (2) transgene-free genome editing; (3) virus-induced genome editing; and (4) editing of recalcitrant elite crop inbred lines. This review provides an up-to-date summary on the state of CRISPR/Cas9-mediated genome editing in plants that will push this technique forward.
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Sheng J, She X, Liu X, Wang J, Hu Z. Comparative analysis of codon usage patterns in chloroplast genomes of five Miscanthus species and related species. PeerJ 2021; 9:e12173. [PMID: 34631315 PMCID: PMC8466072 DOI: 10.7717/peerj.12173] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/27/2021] [Indexed: 11/20/2022] Open
Abstract
Miscanthus is not only a perennial fiber biomass crop, but also valuable breeding resource for its low-nutrient requirements, photosynthetic efficiency and strong adaptability to environment. In the present study, the codon usage patterns of five different Miscanthus plants and other two related species were systematically analyzed. The results indicated that the cp genomes of the seven representative species were preference to A/T bases and A/T-ending codons. In addition, 21 common high-frequency codons and 4–11 optimal codons were detected in the seven chloroplast genomes. The results of ENc-plot, PR2-plot and neutrality analysis revealed the codon usage patterns of the seven chloroplast genomes are influenced by multiple factors, in which nature selection is the main influencing factor. Comparative analysis of the codon usage frequencies between the seven representative species and four model organisms suggested that Arabidopsis thaliana, Populus trichocarpa and Saccharomyces cerevisiae could be considered as preferential appropriate exogenous expression receptors. These results might not only provide important reference information for evolutionary analysis, but also shed light on the way to improve the expression efficiency of exogenous gene in transgenic research based on codon optimization.
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Affiliation(s)
- Jiajing Sheng
- Nantong University, School of Life Sciences, Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong, China
| | | | - Xiaoyu Liu
- Nantong University, School of Life Sciences, Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong, China
| | - Jia Wang
- Anhui University of Science and Technology, Huainan, China
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12
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Sørensen M, Møller BL. Metabolic Engineering of Photosynthetic Cells – in Collaboration with Nature. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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13
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Puluhulawa LE, Joni IM, Mohammed AFA, Arima H, Wathoni N. The Use of Megamolecular Polysaccharide Sacran in Food and Biomedical Applications. Molecules 2021; 26:molecules26113362. [PMID: 34199586 PMCID: PMC8199723 DOI: 10.3390/molecules26113362] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 11/16/2022] Open
Abstract
Natural polymer is a frequently used polymer in various food applications and pharmaceutical formulations due to its benefits and its biocompatibility compared to synthetic polymers. One of the natural polymer groups (i.e., polysaccharide) does not only function as an additive in pharmaceutical preparations, but also as an active ingredient with pharmacological effects. In addition, several natural polymers offer potential distinct applications in gene delivery and genetic engineering. However, some of these polymers have drawbacks, such as their lack of water retention and elasticity. Sacran, one of the high-molecular-weight natural polysaccharides (megamolecular polysaccharides) derived from Aphanothece sacrum (A. sacrum), has good water retention and elasticity. Historically, sacran has been used as a dietary food. Moreover, sacran can be applied in biomedical fields as an active material, excipient, and genetic engineering material. This article discusses the characteristics, extraction, isolation procedures, and the use of sacran in food and biomedical applications.
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Affiliation(s)
- Lisa Efriani Puluhulawa
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Universitas Padjajaran, Sumedang 45363, Indonesia;
| | - I Made Joni
- Department of Physics, Faculty of Mathematics and Natural Sciences, Universitas Padjajaran, Sumedang 45363, Indonesia;
- Functional Nano Powder University Center of Excellence (FiNder U CoE) Padjadajaran Universitas Padjajaran, Sumedang 45363, Indonesia
| | | | | | - Nasrul Wathoni
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Universitas Padjajaran, Sumedang 45363, Indonesia;
- Correspondence: ; Tel.: +62-22-842-888888
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14
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Li S, Chang L, Zhang J. Advancing organelle genome transformation and editing for crop improvement. PLANT COMMUNICATIONS 2021; 2:100141. [PMID: 33898977 PMCID: PMC8060728 DOI: 10.1016/j.xplc.2021.100141] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/15/2020] [Accepted: 01/01/2021] [Indexed: 05/05/2023]
Abstract
Plant cells contain three organelles that harbor DNA: the nucleus, plastids, and mitochondria. Plastid transformation has emerged as an attractive platform for the generation of transgenic plants, also referred to as transplastomic plants. Plastid genomes have been genetically engineered to improve crop yield, nutritional quality, and resistance to abiotic and biotic stresses, as well as for recombinant protein production. Despite many promising proof-of-concept applications, transplastomic plants have not been commercialized to date. Sequence-specific nuclease technologies are widely used to precisely modify nuclear genomes, but these tools have not been applied to edit organelle genomes because the efficient homologous recombination system in plastids facilitates plastid genome editing. Unlike plastid transformation, successful genetic transformation of higher plant mitochondrial genome transformation was tested in several research group, but not successful to date. However, stepwise progress has been made in modifying mitochondrial genes and their transcripts, thus enabling the study of their functions. Here, we provide an overview of advances in organelle transformation and genome editing for crop improvement, and we discuss the bottlenecks and future development of these technologies.
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Affiliation(s)
- Shengchun Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Ling Chang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Jiang Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
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15
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Jodlbauer J, Rohr T, Spadiut O, Mihovilovic MD, Rudroff F. Biocatalysis in Green and Blue: Cyanobacteria. Trends Biotechnol 2021; 39:875-889. [PMID: 33468423 DOI: 10.1016/j.tibtech.2020.12.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 12/17/2022]
Abstract
Recently, several studies have proven the potential of cyanobacteria as whole-cell biocatalysts for biotransformation. Compared to heterotrophic hosts, cyanobacteria show unique advantages thanks to their photoautotrophic metabolism. Their ability to use light as energy and CO2 as carbon source promises a truly sustainable production platform. Their photoautotrophic metabolism offers an encouraging source of reducing power, which makes them attractive for redox-based biotechnological purposes. To exploit the full potential of these whole-cell biocatalysts, cyanobacterial cells must be considered in their entirety. With this emphasis, this review summarizes the latest developments in cyanobacteria research with a strong focus on the benefits associated with their unique metabolism. Remaining bottlenecks and recent strategies to overcome them are evaluated for their potential in future applications.
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Affiliation(s)
- Julia Jodlbauer
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9/OC-163, 1060 Vienna, Austria
| | - Thomas Rohr
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9/OC-163, 1060 Vienna, Austria
| | - Oliver Spadiut
- Institute of Chemical Engineering, research area Biochemical Engineering, TU Wien, Gumpendorfer Strasse 1a, 1060 Vienna, Austria
| | - Marko D Mihovilovic
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9/OC-163, 1060 Vienna, Austria
| | - Florian Rudroff
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9/OC-163, 1060 Vienna, Austria.
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Jackson HO, Taunt HN, Mordaka PM, Smith AG, Purton S. The Algal Chloroplast as a Testbed for Synthetic Biology Designs Aimed at Radically Rewiring Plant Metabolism. FRONTIERS IN PLANT SCIENCE 2021; 12:708370. [PMID: 34630459 PMCID: PMC8497815 DOI: 10.3389/fpls.2021.708370] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/10/2021] [Indexed: 05/04/2023]
Abstract
Sustainable and economically viable support for an ever-increasing global population requires a paradigm shift in agricultural productivity, including the application of biotechnology to generate future crop plants. Current genetic engineering approaches aimed at enhancing the photosynthetic efficiency or composition of the harvested tissues involve relatively simple manipulations of endogenous metabolism. However, radical rewiring of central metabolism using new-to-nature pathways, so-called "synthetic metabolism", may be needed to really bring about significant step changes. In many cases, this will require re-programming the metabolism of the chloroplast, or other plastids in non-green tissues, through a combination of chloroplast and nuclear engineering. However, current technologies for sophisticated chloroplast engineering ("transplastomics") of plants are limited to just a handful of species. Moreover, the testing of metabolic rewiring in the chloroplast of plant models is often impractical given their obligate phototrophy, the extended time needed to create stable non-chimeric transplastomic lines, and the technical challenges associated with regeneration of whole plants. In contrast, the unicellular green alga, Chlamydomonas reinhardtii is a facultative heterotroph that allows for extensive modification of chloroplast function, including non-photosynthetic designs. Moreover, chloroplast engineering in C. reinhardtii is facile, with the ability to generate novel lines in a matter of weeks, and a well-defined molecular toolbox allows for rapid iterations of the "Design-Build-Test-Learn" (DBTL) cycle of modern synthetic biology approaches. The recent development of combinatorial DNA assembly pipelines for designing and building transgene clusters, simple methods for marker-free delivery of these clusters into the chloroplast genome, and the pre-existing wealth of knowledge regarding chloroplast gene expression and regulation in C. reinhardtii further adds to the versatility of transplastomics using this organism. Herein, we review the inherent advantages of the algal chloroplast as a simple and tractable testbed for metabolic engineering designs, which could then be implemented in higher plants.
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Affiliation(s)
- Harry O. Jackson
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Henry N. Taunt
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Pawel M. Mordaka
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Alison G. Smith
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Saul Purton
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
- *Correspondence: Saul Purton
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Chen CC, Min J, Zhang L, Yang Y, Yu X, Guo RT. Advanced Understanding of the Electron Transfer Pathway of Cytochrome P450s. Chembiochem 2020; 22:1317-1328. [PMID: 33232569 DOI: 10.1002/cbic.202000705] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/24/2020] [Indexed: 11/08/2022]
Abstract
Cytochrome P450s are heme-thiolate enzymes that participate in carbon source assimilation, natural compound biosynthesis and xenobiotic metabolism in all kingdoms of life. P450s can catalyze various reactions by using a wide range of organic compounds, thus exhibiting great potential in biotechnological applications. The catalytic reactions of P450s are driven by electron equivalents that are sourced from pyridine nucleotides and delivered by cognate or matching redox partners (RPs). The electron transfer (ET) route from RPs to P450s involves one or more redox center-containing domains. As the rate of ET is one of the main determinants of P450 efficacy, an in-depth understanding of the P450 ET pathway should increase our knowledge of these important enzymes and benefit their further applications. Here, the various P450 RP systems along with current understanding of their ET routes will be reviewed. Notably, state-of-the-art structural studies of the two main types of self-sufficient P450 will also be summarized.
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Affiliation(s)
- Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources Hubei Key Laboratory of Industrial Biotechnology School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, P. R. China
| | - Jian Min
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources Hubei Key Laboratory of Industrial Biotechnology School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, P. R. China
| | - Lilan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources Hubei Key Laboratory of Industrial Biotechnology School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, P. R. China
| | - Yu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources Hubei Key Laboratory of Industrial Biotechnology School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, P. R. China
| | - Xuejing Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources Hubei Key Laboratory of Industrial Biotechnology School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, P. R. China
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources Hubei Key Laboratory of Industrial Biotechnology School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, P. R. China
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Diao J, Song X, Zhang L, Cui J, Chen L, Zhang W. Tailoring cyanobacteria as a new platform for highly efficient synthesis of astaxanthin. Metab Eng 2020; 61:275-287. [DOI: 10.1016/j.ymben.2020.07.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 07/07/2020] [Accepted: 07/07/2020] [Indexed: 01/11/2023]
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Newly discovered Synechococcus sp. PCC 11901 is a robust cyanobacterial strain for high biomass production. Commun Biol 2020; 3:215. [PMID: 32382027 PMCID: PMC7205611 DOI: 10.1038/s42003-020-0910-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 03/16/2020] [Indexed: 12/31/2022] Open
Abstract
Cyanobacteria, which use solar energy to convert carbon dioxide into biomass, are potential solar biorefineries for the sustainable production of chemicals and biofuels. However, yields obtained with current strains are still uncompetitive compared to existing heterotrophic production systems. Here we report the discovery and characterization of a new cyanobacterial strain, Synechococcus sp. PCC 11901, with promising features for green biotechnology. It is naturally transformable, has a short doubling time of ≈2 hours, grows at high light intensities and in a wide range of salinities and accumulates up to ≈33 g dry cell weight per litre when cultured in a shake-flask system using a modified growth medium − 1.7 to 3 times more than other strains tested under similar conditions. As a proof of principle, PCC 11901 engineered to produce free fatty acids yielded over 6 mM (1.5 g L−1), an amount comparable to that achieved by similarly engineered heterotrophic organisms. Włodarczyk et al. discover that cyanobacterium Synechococcus sp. PCC 11901 accumulates three times more biomass than other cyanobacterial strains in the same conditions. An engineered version of this strain also produces as much free fatty acid as other commonly used heterotrophic microorganisms, suggesting its utility for the sustainable production of carbon-based molecules.
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20
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Lv X, Cui S, Gu Y, Li J, Du G, Liu L. Enzyme Assembly for Compartmentalized Metabolic Flux Control. Metabolites 2020; 10:E125. [PMID: 32224973 PMCID: PMC7241084 DOI: 10.3390/metabo10040125] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/25/2020] [Accepted: 03/25/2020] [Indexed: 11/16/2022] Open
Abstract
Enzyme assembly by ligand binding or physically sequestrating enzymes, substrates, or metabolites into isolated compartments can bring key molecules closer to enhance the flux of a metabolic pathway. The emergence of enzyme assembly has provided both opportunities and challenges for metabolic engineering. At present, with the development of synthetic biology and systems biology, a variety of enzyme assembly strategies have been proposed, from the initial direct enzyme fusion to scaffold-free assembly, as well as artificial scaffolds, such as nucleic acid/protein scaffolds, and even some more complex physical compartments. These assembly strategies have been explored and applied to the synthesis of various important bio-based products, and have achieved different degrees of success. Despite some achievements, enzyme assembly, especially in vivo, still has many problems that have attracted significant attention from researchers. Here, we focus on some selected examples to review recent research on scaffold-free strategies, synthetic artificial scaffolds, and physical compartments for enzyme assembly or pathway sequestration, and we discuss their notable advances. In addition, the potential applications and challenges in the applications are highlighted.
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Affiliation(s)
- Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Shixiu Cui
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yang Gu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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21
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Yoo BC, Yadav NS, Orozco EM, Sakai H. Cas9/gRNA-mediated genome editing of yeast mitochondria and Chlamydomonas chloroplasts. PeerJ 2020; 8:e8362. [PMID: 31934513 PMCID: PMC6951285 DOI: 10.7717/peerj.8362] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/05/2019] [Indexed: 11/20/2022] Open
Abstract
We present a new approach to edit both mitochondrial and chloroplast genomes. Organelles have been considered off-limits to CRISPR due to their impermeability to most RNA and DNA. This has prevented applications of Cas9/gRNA-mediated genome editing in organelles while the tool has been widely used for engineering of nuclear DNA in a number of organisms in the last several years. To overcome the hurdle, we designed a new approach to enable organelle genome editing. The plasmids, designated "Edit Plasmids," were constructed with two expression cassettes, one for the expression of Cas9, codon-optimized for each organelle, under promoters specific to each organelle, and the other cassette for the expression of guide RNAs under another set of promoters specific to each organelle. In addition, Edit Plasmids were designed to carry the donor DNA for integration between two double-strand break sites induced by Cas9/gRNAs. Each donor DNA was flanked by the regions homologous to both ends of the integration site that were short enough to minimize spontaneous recombination events. Furthermore, the donor DNA was so modified that it did not carry functional gRNA target sites, allowing the stability of the integrated DNA without being excised by further Cas9/gRNAs activity. Edit Plasmids were introduced into organelles through microprojectile transformation. We confirmed donor DNA insertion at the target sites facilitated by homologous recombination only in the presence of Cas9/gRNA activity in yeast mitochondria and Chlamydomonas chloroplasts. We also showed that Edit Plasmids persist and replicate in mitochondria autonomously for several dozens of generations in the presence of the wild-type genomes. Finally, we did not find insertions and/or deletions at one of the Cas9 cleavage sites in Chloroplasts, which are otherwise hallmarks of Cas9/gRNA-mediated non-homologous end joining (NHEJ) repair events in nuclear DNA. This is consistent with previous reports of the lack of NHEJ repair system in most bacteria, which are believed to be ancestors of organelles. This is the first demonstration of CRISPR-mediated genome editing in both mitochondria and chloroplasts in two distantly related organisms. The Edit Plasmid approach is expected to open the door to engineer organelle genomes of a wide range of organisms in a precise fashion.
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22
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Jensen PE, Scharff LB. Engineering of plastids to optimize the production of high-value metabolites and proteins. Curr Opin Biotechnol 2019; 59:8-15. [DOI: 10.1016/j.copbio.2019.01.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 12/08/2018] [Accepted: 01/18/2019] [Indexed: 10/27/2022]
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Gale GAR, Schiavon Osorio AA, Mills LA, Wang B, Lea-Smith DJ, McCormick AJ. Emerging Species and Genome Editing Tools: Future Prospects in Cyanobacterial Synthetic Biology. Microorganisms 2019; 7:E409. [PMID: 31569579 PMCID: PMC6843473 DOI: 10.3390/microorganisms7100409] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 09/22/2019] [Accepted: 09/24/2019] [Indexed: 12/19/2022] Open
Abstract
Recent advances in synthetic biology and an emerging algal biotechnology market have spurred a prolific increase in the availability of molecular tools for cyanobacterial research. Nevertheless, work to date has focused primarily on only a small subset of model species, which arguably limits fundamental discovery and applied research towards wider commercialisation. Here, we review the requirements for uptake of new strains, including several recently characterised fast-growing species and promising non-model species. Furthermore, we discuss the potential applications of new techniques available for transformation, genetic engineering and regulation, including an up-to-date appraisal of current Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein (CRISPR/Cas) and CRISPR interference (CRISPRi) research in cyanobacteria. We also provide an overview of several exciting molecular tools that could be ported to cyanobacteria for more advanced metabolic engineering approaches (e.g., genetic circuit design). Lastly, we introduce a forthcoming mutant library for the model species Synechocystis sp. PCC 6803 that promises to provide a further powerful resource for the cyanobacterial research community.
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Affiliation(s)
- Grant A R Gale
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK.
| | - Alejandra A Schiavon Osorio
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
| | - Lauren A Mills
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
| | - Baojun Wang
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK.
| | - David J Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
| | - Alistair J McCormick
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
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24
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Mellor SB, Vinde MH, Nielsen AZ, Hanke GT, Abdiaziz K, Roessler MM, Burow M, Motawia MS, Møller BL, Jensen PE. Defining optimal electron transfer partners for light-driven cytochrome P450 reactions. Metab Eng 2019; 55:33-43. [PMID: 31091467 DOI: 10.1016/j.ymben.2019.05.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 05/02/2019] [Accepted: 05/04/2019] [Indexed: 12/16/2022]
Abstract
Plants and cyanobacteria are promising heterologous hosts for metabolic engineering, and particularly suited for expression of cytochrome P450 (P450s), enzymes that catalyse key steps in biosynthetic pathways leading to valuable natural products such as alkaloids, terpenoids and phenylpropanoids. P450s are often difficult to express and require a membrane-bound NADPH-dependent reductase, complicating their use in metabolic engineering and bio-production. We previously demonstrated targeting of heterologous P450s to thylakoid membranes both in N. benthamiana chloroplasts and cyanobacteria, and functional substitution of their native reductases with the photosynthetic apparatus via the endogenous soluble electron carrier ferredoxin. However, because ferredoxin acts as a sorting hub for photosynthetic reducing power, there is fierce competition for reducing equivalents, which limits photosynthesis-driven P450 output. This study compares the ability of four electron carriers to increase photosynthesis-driven P450 activity. These carriers, three plant ferredoxins and a flavodoxin-like engineered protein derived from cytochrome P450 reductase, show only modest differences in their electron transfer to our model P450, CYP79A1 in vitro. However, only the flavodoxin-like carrier supplies appreciable reducing power in the presence of competition for reduced ferredoxin, because it possesses a redox potential that renders delivery of reducing equivalents to endogenous processes inefficient. We further investigate the efficacy of these electron carrier proteins in vivo by expressing them transiently in N. benthamiana fused to CYP79A1. All but one of the fusion enzymes show improved sequestration of photosynthetic reducing power. Fusion with the flavodoxin-like carrier offers the greatest improvement in this comparison - nearly 25-fold on a per protein basis. Thus, this study demonstrates that synthetic electron transfer pathways with optimal redox potentials can alleviate the problem of endogenous competition for reduced ferredoxin and sets out a new metabolic engineering strategy useful for producing valuable natural products.
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Affiliation(s)
- Silas Busck Mellor
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Marcos Hamborg Vinde
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Agnieszka Zygadlo Nielsen
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Guy Thomas Hanke
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, United Kingdom
| | - Kaltum Abdiaziz
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, United Kingdom
| | - Maxie M Roessler
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, United Kingdom
| | - Meike Burow
- DyNaMo Center of Excellence, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Mohammed Saddik Motawia
- Villum Research Center for Plant Plasticity, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Birger Lindberg Møller
- Villum Research Center for Plant Plasticity, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Poul Erik Jensen
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
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Russo DA, Zedler JAZ, Wittmann DN, Möllers B, Singh RK, Batth TS, van Oort B, Olsen JV, Bjerrum MJ, Jensen PE. Expression and secretion of a lytic polysaccharide monooxygenase by a fast-growing cyanobacterium. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:74. [PMID: 30976324 PMCID: PMC6442416 DOI: 10.1186/s13068-019-1416-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 03/21/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND Cyanobacteria have the potential to become next-generation cell factories due to their ability to use CO2, light and inorganic nutrients to produce a range of biomolecules of commercial interest. Synechococcus elongatus UTEX 2973, in particular, is a fast-growing, genetically tractable, cyanobacterium that has garnered attention as a potential biotechnological chassis. To establish this unique strain as a host for heterologous protein production, we aimed to demonstrate expression and secretion of the industrially relevant TfAA10A, a lytic polysaccharide monooxygenase from the Gram-positive bacterium Thermobifida fusca. RESULTS Two variations of TfAA10A were successfully expressed in S. elongatus UTEX 2973: One containing the native N-terminal, Sec-targeted, signal peptide and a second with a Tat-targeted signal peptide from the Escherichia coli trimethylamine-N-oxide reductase (TorA). Although the TorA signal peptide correctly targeted the protein to the plasma membrane, the majority of the TorA-TfAA10A was found unprocessed in the plasma membrane with a small fraction of the mature protein ultimately translocated to the periplasm. The native Sec signal peptide allowed for efficient secretion of TfAA10A into the medium with virtually no protein being found in the cytosol, plasma membrane or periplasm. TfAA10A was demonstrated to be correctly cleaved and active on the model substrate phosphoric acid swollen cellulose. Additionally, expression and secretion only had a minor impact on cell growth. The secretion yield was estimated at 779 ± 40 µg L-1 based on densitometric analysis. To our knowledge, this is the highest secretion yield ever registered in cyanobacteria. CONCLUSIONS We have shown for the first time high-titer expression and secretion of an industrially relevant and catalytically active enzyme in S. elongatus UTEX 2973. This proof-of-concept study will be valuable for the development of novel and sustainable applications in the fields of bioremediation and biocatalysis.
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Affiliation(s)
- D. A. Russo
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - J. A. Z. Zedler
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - D. N. Wittmann
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - B. Möllers
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg C, Denmark
| | - R. K. Singh
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - T. S. Batth
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - B. van Oort
- Biophysics of Photosynthesis, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - J. V. Olsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - M. J. Bjerrum
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - P. E. Jensen
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
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Kwon YM, Kim KW, Choi TY, Kim SY, Kim JYH. Manipulation of the microalgal chloroplast by genetic engineering for biotechnological utilization as a green biofactory. World J Microbiol Biotechnol 2018; 34:183. [PMID: 30478596 DOI: 10.1007/s11274-018-2567-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 11/23/2018] [Indexed: 12/16/2022]
Abstract
The chloroplast is an essential organelle in microalgae for conducting photosynthesis, thus enabling the photoautotrophic growth of microalgae. In addition to photosynthesis, the chloroplast is capable of various biochemical processes for the synthesis of proteins, lipids, carbohydrates, and terpenoids. Due to these attractive characteristics, there has been increasing interest in the biotechnological utilization of microalgal chloroplast as a sustainable alternative to the conventional production platforms used in industrial biotechnology. Since the first demonstration of microalgal chloroplast transformation, significant development has occurred over recent decades in the manipulation of microalgal chloroplasts through genetic engineering. In the present review, we describe the advantages of the microalgal chloroplast as a production platform for various bioproducts, including recombinant proteins and high-value metabolites, features of chloroplast genetic systems, and the development of transformation methods, which represent important factors for gene expression in the chloroplast. Furthermore, we address the expression of various recombinant proteins in the microalgal chloroplast through genetic engineering, including reporters, biopharmaceutical proteins, and industrial enzymes. Finally, we present many efforts and achievements in the production of high-value metabolites in the microalgal chloroplast through metabolic engineering. Based on these efforts and advances, the microalgal chloroplast represents an economically viable and sustainable platform for biotechnological applications in the near future.
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Affiliation(s)
- Yong Min Kwon
- Department of Applied Research, National Marine Biodiversity Institute of Korea, Jangsan-ro 101-75, Seocheon, Chungcheongnamdo, 33662, Republic of Korea
| | - Kyung Woo Kim
- Department of Applied Research, National Marine Biodiversity Institute of Korea, Jangsan-ro 101-75, Seocheon, Chungcheongnamdo, 33662, Republic of Korea
| | - Tae-Young Choi
- Department of Genetic Resources Research, National Marine Biodiversity Institute of Korea, Jangsan-ro 101-75, Seocheon, Chungcheongnamdo, 33662, Republic of Korea
| | - Sun Young Kim
- Department of Applied Research, National Marine Biodiversity Institute of Korea, Jangsan-ro 101-75, Seocheon, Chungcheongnamdo, 33662, Republic of Korea
| | - Jaoon Young Hwan Kim
- Department of Applied Research, National Marine Biodiversity Institute of Korea, Jangsan-ro 101-75, Seocheon, Chungcheongnamdo, 33662, Republic of Korea.
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Vavitsas K, Fabris M, Vickers CE. Terpenoid Metabolic Engineering in Photosynthetic Microorganisms. Genes (Basel) 2018; 9:E520. [PMID: 30360565 PMCID: PMC6266707 DOI: 10.3390/genes9110520] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 12/13/2022] Open
Abstract
Terpenoids are a group of natural products that have a variety of roles, both essential and non-essential, in metabolism and in biotic and abiotic interactions, as well as commercial applications such as pharmaceuticals, food additives, and chemical feedstocks. Economic viability for commercial applications is commonly not achievable by using natural source organisms or chemical synthesis. Engineered bio-production in suitable heterologous hosts is often required to achieve commercial viability. However, our poor understanding of regulatory mechanisms and other biochemical processes makes obtaining efficient conversion yields from feedstocks challenging. Moreover, production from carbon dioxide via photosynthesis would significantly increase the environmental and potentially the economic credentials of these processes by disintermediating biomass feedstocks. In this paper, we briefly review terpenoid metabolism, outline some recent advances in terpenoid metabolic engineering, and discuss why photosynthetic unicellular organisms-such as algae and cyanobacteria-might be preferred production platforms for the expression of some of the more challenging terpenoid pathways.
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Affiliation(s)
- Konstantinos Vavitsas
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia.
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia.
| | - Michele Fabris
- Climate Change Cluster, University of Technology Sydney, 15 Broadway, Ultimo, NSW 2007, Australia.
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia.
| | - Claudia E Vickers
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia.
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia.
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Abramson BW, Lensmire J, Lin YT, Jennings E, Ducat DC. Redirecting carbon to bioproduction via a growth arrest switch in a sucrose-secreting cyanobacterium. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.05.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Pinard D, Mizrachi E. Unsung and understudied: plastids involved in secondary growth. CURRENT OPINION IN PLANT BIOLOGY 2018; 42:30-36. [PMID: 29459221 DOI: 10.1016/j.pbi.2018.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/22/2018] [Accepted: 01/31/2018] [Indexed: 05/17/2023]
Abstract
Plastids represent the only subcellular compartment where aromatic amino acid precursors for lignin can be synthesized during secondary growth in vascular plants. Despite this, aside from a general shared understanding that plastid-localized metabolism occurs during secondary growth, virtually no research has been performed on understanding their biology. Of particular importance will be insight into their ontogeny, morphology and ultrastructure, and (given the complex cytonuclear communication required) their nuclear-encoded and organellar-encoded regulation. Updating and integrating this knowledge will contribute to our fundamental understanding of a ubiquitous developmental process in vascular plants, and a major terrestrial carbon sink, as well as carbon-related plant biotechnology. Given available evidence, we propose a new name for a distinct plastid derivative-the 'xyloplast', is required.
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Affiliation(s)
- Desre Pinard
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Eshchar Mizrachi
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria 0028, South Africa.
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30
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Non-photosynthetic plastids as hosts for metabolic engineering. Essays Biochem 2018; 62:41-50. [DOI: 10.1042/ebc20170047] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/13/2018] [Accepted: 01/22/2018] [Indexed: 01/11/2023]
Abstract
Using plants as hosts for production of complex, high-value compounds and therapeutic proteins has gained increasing momentum over the past decade. Recent advances in metabolic engineering techniques using synthetic biology have set the stage for production yields to become economically attractive, but more refined design strategies are required to increase product yields without compromising development and growth of the host system. The ability of plant cells to differentiate into various tissues in combination with a high level of cellular compartmentalization represents so far the most unexploited plant-specific resource. Plant cells contain organelles called plastids that retain their own genome, harbour unique biosynthetic pathways and differentiate into distinct plastid types upon environmental and developmental cues. Chloroplasts, the plastid type hosting the photosynthetic processes in green tissues, have proven to be suitable for high yield protein and bio-compound production. Unfortunately, chloroplast manipulation often affects photosynthetic efficiency and therefore plant fitness. In this respect, plastids of non-photosynthetic tissues, which have focused metabolisms for synthesis and storage of particular classes of compounds, might prove more suitable for engineering the production and storage of non-native metabolites without affecting plant fitness. This review provides the current state of knowledge on the molecular mechanisms involved in plastid differentiation and focuses on non-photosynthetic plastids as alternative biotechnological platforms for metabolic engineering.
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31
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Lima S, Webb CL, Deery E, Robinson C, Zedler JAZ. Human Intrinsic Factor Expression for Bioavailable Vitamin B 12 Enrichment in Microalgae. BIOLOGY 2018; 7:biology7010019. [PMID: 29463047 PMCID: PMC5872045 DOI: 10.3390/biology7010019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/20/2018] [Accepted: 02/13/2018] [Indexed: 11/16/2022]
Abstract
Dietary supplements and functional foods are becoming increasingly popular complements to regular diets. A recurring ingredient is the essential cofactor vitamin B12 (B12). Microalgae are making their way into the dietary supplement and functional food market but do not produce B12, and their B12 content is very variable. In this study, the suitability of using the human B12-binding protein intrinsic factor (IF) to enrich bioavailable B12 using microalgae was tested. The IF protein was successfully expressed from the nuclear genome of the model microalga Chlamydomonasreinhardtii and the addition of an N-terminal ARS2 signal peptide resulted in efficient IF secretion to the medium. Co-abundance of B12 and the secreted IF suggests the algal produced IF protein is functional and B12-binding. Utilizing IF expression could be an efficient tool to generate B12-enriched microalgae in a controlled manner that is suitable for vegetarians and, potentially, more bioavailable for humans.
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Affiliation(s)
- Serena Lima
- Industrial Biotechnology Centre, School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7 NK, UK.
- Dipartimento dell'Innovazione Industriale e Digitale, Università degli Studi di Palermo, Viale delle Scienze Ed. 6, 90128 Palermo, Italy.
| | - Conner L Webb
- Industrial Biotechnology Centre, School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7 NK, UK.
| | - Evelyne Deery
- Industrial Biotechnology Centre, School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7 NK, UK.
| | - Colin Robinson
- Industrial Biotechnology Centre, School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7 NK, UK.
| | - Julie A Z Zedler
- Industrial Biotechnology Centre, School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7 NK, UK.
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark.
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Stensjö K, Vavitsas K, Tyystjärvi T. Harnessing transcription for bioproduction in cyanobacteria. PHYSIOLOGIA PLANTARUM 2018; 162:148-155. [PMID: 28762505 DOI: 10.1111/ppl.12606] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/04/2017] [Accepted: 07/10/2017] [Indexed: 06/07/2023]
Abstract
Sustainable production of biofuels and other valuable compounds is one of our future challenges. One tempting possibility is to use photosynthetic cyanobacteria as production factories. Currently, tools for genetic engineering of cyanobacteria are not good enough to exploit the full potential of cyanobacteria. A wide variety of expression systems will be required to adjust both the expression of heterologous enzyme(s) and metabolic routes to the best possible balance, allowing the optimal production of a particular substance. In bacteria, transcription, especially the initiation of transcription, has a central role in adjusting gene expression and thus also metabolic fluxes of cells according to environmental cues. Here we summarize the recent progress in developing tools for efficient cyanofactories, focusing especially on transcriptional regulation.
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Affiliation(s)
- Karin Stensjö
- Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Konstantinos Vavitsas
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Taina Tyystjärvi
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
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Banerjee A, Hamberger B. P450s controlling metabolic bifurcations in plant terpene specialized metabolism. PHYTOCHEMISTRY REVIEWS : PROCEEDINGS OF THE PHYTOCHEMICAL SOCIETY OF EUROPE 2018; 17:81-111. [PMID: 29563859 PMCID: PMC5842272 DOI: 10.1007/s11101-017-9530-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/20/2017] [Indexed: 05/18/2023]
Abstract
ABSTRACT Catalyzing stereo- and regio-specific oxidation of inert hydrocarbon backbones, and a range of more exotic reactions inherently difficult in formal chemical synthesis, cytochromes P450 (P450s) offer outstanding potential for biotechnological engineering. Plants and their dazzling diversity of specialized metabolites have emerged as rich repository for functional P450s with the advances of deep transcriptomics and genome wide discovery. P450s are of outstanding interest for understanding chemical diversification throughout evolution, for gaining mechanistic insights through the study of their structure-function relationship, and for exploitation in Synthetic Biology. In this review, we highlight recent developments and examples in the discovery of plant P450s involved in the biosynthesis of industrially relevant monoterpenoids, sesquiterpenoids, diterpenoids and triterpenoids, throughout 2016 and early 2017. Examples were selected to illustrate the spectrum of value from commodity chemicals, flavor and fragrance compounds to pharmacologically active terpenoids. We focus on a recently emerging theme, where P450s control metabolic bifurcations and chemical diversity of the final product profile, either within a pathway, or through neo-functionalization in related species. The implications may inform approaches for rational assembly of recombinant pathways, biotechnological production of high value terpenoids and generation of novel chemical entities.
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Affiliation(s)
- Aparajita Banerjee
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824 USA
| | - Björn Hamberger
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824 USA
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Mellor SB, Vavitsas K, Nielsen AZ, Jensen PE. Photosynthetic fuel for heterologous enzymes: the role of electron carrier proteins. PHOTOSYNTHESIS RESEARCH 2017; 134:329-342. [PMID: 28285375 DOI: 10.1007/s11120-017-0364-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 02/27/2017] [Indexed: 05/21/2023]
Abstract
Plants, cyanobacteria, and algae generate a surplus of redox power through photosynthesis, which makes them attractive for biotechnological exploitations. While central metabolism consumes most of the energy, pathways introduced through metabolic engineering can also tap into this source of reducing power. Recent work on the metabolic engineering of photosynthetic organisms has shown that the electron carriers such as ferredoxin and flavodoxin can be used to couple heterologous enzymes to photosynthetic reducing power. Because these proteins have a plethora of interaction partners and rely on electrostatically steered complex formation, they form productive electron transfer complexes with non-native enzymes. A handful of examples demonstrate channeling of photosynthetic electrons to drive the activity of heterologous enzymes, and these focus mainly on hydrogenases and cytochrome P450s. However, competition from native pathways and inefficient electron transfer rates present major obstacles, which limit the productivity of heterologous reactions coupled to photosynthesis. We discuss specific approaches to address these bottlenecks and ensure high productivity of such enzymes in a photosynthetic context.
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Affiliation(s)
- Silas Busck Mellor
- Copenhagen Plant Science Center, Center for Synthetic Biology 'bioSYNergy', Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Konstantinos Vavitsas
- Copenhagen Plant Science Center, Center for Synthetic Biology 'bioSYNergy', Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Agnieszka Zygadlo Nielsen
- Copenhagen Plant Science Center, Center for Synthetic Biology 'bioSYNergy', Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Poul Erik Jensen
- Copenhagen Plant Science Center, Center for Synthetic Biology 'bioSYNergy', Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
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35
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Weiss TL, Young EJ, Ducat DC. A synthetic, light-driven consortium of cyanobacteria and heterotrophic bacteria enables stable polyhydroxybutyrate production. Metab Eng 2017; 44:236-245. [DOI: 10.1016/j.ymben.2017.10.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 09/28/2017] [Accepted: 10/16/2017] [Indexed: 10/18/2022]
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36
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Henriques de Jesus MPR, Zygadlo Nielsen A, Busck Mellor S, Matthes A, Burow M, Robinson C, Erik Jensen P. Tat proteins as novel thylakoid membrane anchors organize a biosynthetic pathway in chloroplasts and increase product yield 5-fold. Metab Eng 2017; 44:108-116. [PMID: 28962875 DOI: 10.1016/j.ymben.2017.09.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 09/05/2017] [Accepted: 09/24/2017] [Indexed: 11/24/2022]
Abstract
Photosynthesis drives the production of ATP and NADPH, and acts as a source of carbon for primary metabolism. NADPH is also used in the production of many natural bioactive compounds. These are usually synthesized in low quantities and are often difficult to produce by chemical synthesis due to their complex structures. Some of the crucial enzymes catalyzing their biosynthesis are the cytochromes P450 (P450s) situated in the endoplasmic reticulum (ER), powered by electron transfers from NADPH. Dhurrin is a cyanogenic glucoside and its biosynthesis involves a dynamic metabolon formed by two P450s, a UDP-glucosyltransferase (UGT) and a P450 oxidoreductase (POR). Its biosynthetic pathway has been relocated to the chloroplast where ferredoxin, reduced through the photosynthetic electron transport chain, serves as an efficient electron donor to the P450s, bypassing the involvement of POR. Nevertheless, translocation of the pathway from the ER to the chloroplast creates other difficulties, such as the loss of metabolon formation and intermediate diversion into other metabolic pathways. We show here that co-localization of these enzymes in the thylakoid membrane leads to a significant increase in product formation, with a concomitant decrease in off-pathway intermediates. This was achieved by exchanging the membrane anchors of the dhurrin pathway enzymes to components of the Twin-arginine translocation pathway, TatB and TatC, which have self-assembly properties. Consequently, we show 5-fold increased titers of dhurrin and a decrease in the amounts of intermediates and side products in Nicotiana benthamiana. Further, results suggest that targeting the UGT to the membrane is a key factor to achieve efficient substrate channeling.
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Affiliation(s)
- Maria Perestrello Ramos Henriques de Jesus
- Copenhagen Plant Science Center, Center for Synthetic Biology "bioSYNergy", Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Agnieszka Zygadlo Nielsen
- Copenhagen Plant Science Center, Center for Synthetic Biology "bioSYNergy", Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Silas Busck Mellor
- Copenhagen Plant Science Center, Center for Synthetic Biology "bioSYNergy", Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Annemarie Matthes
- Copenhagen Plant Science Center, Center for Synthetic Biology "bioSYNergy", Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Meike Burow
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Colin Robinson
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Poul Erik Jensen
- Copenhagen Plant Science Center, Center for Synthetic Biology "bioSYNergy", Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark.
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Hagemann M, Hess WR. Systems and synthetic biology for the biotechnological application of cyanobacteria. Curr Opin Biotechnol 2017; 49:94-99. [PMID: 28843192 DOI: 10.1016/j.copbio.2017.07.008] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 07/13/2017] [Accepted: 07/17/2017] [Indexed: 10/19/2022]
Abstract
Cyanobacteria are the only prokaryotes that perform oxygenic photosynthesis. Their evolutionary relation to plastids in eukaryotic phototrophs and their increasing utilization as green cell factories initiated the use of systems biology approaches early on. For select model strains, extensive 'omics' data sets have been generated, and genome-wide models have been elucidated. Moreover, the results obtained may be used for the optimization of cyanobacterial metabolism, which can direct the biotechnological production of biofuels or chemical feedstock. Synthetic biology approaches permit the rational construction of novel metabolic pathways that are based on the combination of multiple enzymatic activities of different origins. In addition, the manipulation of whole metabolic networks by CRISPR-based and sRNA-based technologies with multiple parallel targets will further stimulate the use of cyanobacteria for diverse applications in basic research and biotechnology.
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Affiliation(s)
- Martin Hagemann
- University of Rostock, Institute of Biological Sciences, Plant Physiology, A.-Einstein-Str. 3, D-18059 Rostock, Germany.
| | - Wolfgang R Hess
- University of Freiburg, Faculty of Biology, Schänzlestr. 1, D-79104 Freiburg, Germany
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38
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Vavitsas K, Rue EØ, Stefánsdóttir LK, Gnanasekaran T, Blennow A, Crocoll C, Gudmundsson S, Jensen PE. Responses of Synechocystis sp. PCC 6803 to heterologous biosynthetic pathways. Microb Cell Fact 2017; 16:140. [PMID: 28806958 PMCID: PMC5556357 DOI: 10.1186/s12934-017-0757-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/09/2017] [Indexed: 11/10/2022] Open
Abstract
Background There are an increasing number of studies regarding genetic manipulation of cyanobacteria to produce commercially interesting compounds. The majority of these works study the expression and optimization of a selected heterologous pathway, largely ignoring the wholeness and complexity of cellular metabolism. Regulation and response mechanisms are largely unknown, and even the metabolic pathways themselves are not fully elucidated. This poses a clear limitation in exploiting the rich biosynthetic potential of cyanobacteria. Results In this work, we focused on the production of two different compounds, the cyanogenic glucoside dhurrin and the diterpenoid 13R-manoyl oxide in Synechocystis PCC 6803. We used genome-scale metabolic modelling to study fluxes in individual reactions and pathways, and we determined the concentrations of key metabolites, such as amino acids, carotenoids, and chlorophylls. This allowed us to identify metabolic crosstalk between the native and the introduced metabolic pathways. Most results and simulations highlight the metabolic robustness of cyanobacteria, suggesting that the host organism tends to keep metabolic fluxes and metabolite concentrations steady, counteracting the effects of the heterologous pathway. However, the amino acid concentrations of the dhurrin-producing strain show an unexpected profile, where the perturbation levels were high in seemingly unrelated metabolites. Conclusions There is a wealth of information that can be derived by combining targeted metabolite identification and computer modelling as a frame of understanding. Here we present an example of how strain engineering approaches can be coupled to ‘traditional’ metabolic engineering with systems biology, resulting in novel and more efficient manipulation strategies. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0757-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Konstantinos Vavitsas
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Emil Østergaard Rue
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | | | - Thiyagarajan Gnanasekaran
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.,ISBP-INSA de Toulouse, Avenue de Rangueil, 31077, Toulouse, France
| | - Andreas Blennow
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Christoph Crocoll
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Steinn Gudmundsson
- Center for Systems Biology, University of Iceland, Sturlugata 8, 101, Reykjavik, Iceland
| | - Poul Erik Jensen
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
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Moses T, Mehrshahi P, Smith AG, Goossens A. Synthetic biology approaches for the production of plant metabolites in unicellular organisms. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4057-4074. [PMID: 28449101 DOI: 10.1093/jxb/erx119] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Synthetic biology is the repurposing of biological systems for novel objectives and applications. Through the co-ordinated and balanced expression of genes, both native and those introduced from other organisms, resources within an industrial chassis can be siphoned for the commercial production of high-value commodities. This developing interdisciplinary field has the potential to revolutionize natural product discovery from higher plants, by providing a diverse array of tools, technologies, and strategies for exploring the large chemically complex space of plant natural products using unicellular organisms. In this review, we emphasize the key features that influence the generation of biorefineries and highlight technologies and strategic solutions that can be used to overcome engineering pitfalls with rational design. Also presented is a succinct guide to assist the selection of unicellular chassis most suited for the engineering and subsequent production of the desired natural product, in order to meet the global demand for plant natural products in a safe and sustainable manner.
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Affiliation(s)
- Tessa Moses
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Payam Mehrshahi
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
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Mellor S, Nielsen AZ, Burow M, Motawia MS, Jakubauskas D, Møller BL, Jensen PE. Fusion of Ferredoxin and Cytochrome P450 Enables Direct Light-Driven Biosynthesis. ACS Chem Biol 2016; 11:1862-9. [PMID: 27119279 PMCID: PMC4949584 DOI: 10.1021/acschembio.6b00190] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 04/27/2016] [Indexed: 01/29/2023]
Abstract
Cytochrome P450s (P450s) are key enzymes in the synthesis of bioactive natural products in plants. Efforts to harness these enzymes for in vitro and whole-cell production of natural products have been hampered by difficulties in expressing them heterologously in their active form, and their requirement for NADPH as a source of reducing power. We recently demonstrated targeting and insertion of plant P450s into the photosynthetic membrane and photosynthesis-driven, NADPH-independent P450 catalytic activity mediated by the electron carrier protein ferredoxin. Here, we report the fusion of ferredoxin with P450 CYP79A1 from the model plant Sorghum bicolor, which catalyzes the initial step in the pathway leading to biosynthesis of the cyanogenic glucoside dhurrin. Fusion with ferredoxin allows CYP79A1 to obtain electrons for catalysis by interacting directly with photosystem I. Furthermore, electrons captured by the fused ferredoxin moiety are directed more effectively toward P450 catalytic activity, making the fusion better able to compete with endogenous electron sinks coupled to metabolic pathways. The P450-ferredoxin fusion enzyme obtains reducing power solely from its fused ferredoxin and outperforms unfused CYP79A1 in vivo. This demonstrates greatly enhanced electron transfer from photosystem I to CYP79A1 as a consequence of the fusion. The fusion strategy reported here therefore forms the basis for enhanced partitioning of photosynthetic reducing power toward P450-dependent biosynthesis of important natural products.
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Affiliation(s)
- Silas
Busck Mellor
- Copenhagen
Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
- Center
for Synthetic Biology “bioSYNergy”, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Agnieszka Zygadlo Nielsen
- Copenhagen
Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
- Center
for Synthetic Biology “bioSYNergy”, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Meike Burow
- Copenhagen
Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
- DynaMo
Center of Excellence, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Mohammed Saddik Motawia
- Copenhagen
Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
- Center
for Synthetic Biology “bioSYNergy”, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Dainius Jakubauskas
- Copenhagen
Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
- Center
for Synthetic Biology “bioSYNergy”, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Birger Lindberg Møller
- Copenhagen
Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
- Center
for Synthetic Biology “bioSYNergy”, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
- Villum
Research Center of Excellence ”Plant Plasticity”, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Poul Erik Jensen
- Copenhagen
Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
- Center
for Synthetic Biology “bioSYNergy”, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
- Villum
Research Center of Excellence ”Plant Plasticity”, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
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41
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Benning C, Sweetlove L. Synthetic biology for basic and applied plant research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:3-4. [PMID: 27483204 DOI: 10.1111/tpj.13245] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- Christoph Benning
- US Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA.
| | - Lee Sweetlove
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
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