1
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Torres-Tiji Y, Sethuram H, Gupta A, McCauley J, Dutra-Molino JV, Pathania R, Saxton L, Kang K, Hillson NJ, Mayfield SP. Bioinformatic Prediction and High Throughput In Vivo Screening to Identify Cis-Regulatory Elements for the Development of Algal Synthetic Promoters. ACS Synth Biol 2024; 13:2150-2165. [PMID: 38986010 PMCID: PMC11264317 DOI: 10.1021/acssynbio.4c00199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/12/2024]
Abstract
Algae biotechnology holds immense promise for revolutionizing the bioeconomy through the sustainable and scalable production of various bioproducts. However, their development has been hindered by the lack of advanced genetic tools. This study introduces a synthetic biology approach to develop such tools, focusing on the construction and testing of synthetic promoters. By analyzing conserved DNA motifs within the promoter regions of highly expressed genes across six different algal species, we identified cis-regulatory elements (CREs) associated with high transcriptional activity. Combining the algorithms POWRS, STREME, and PhyloGibbs, we predicted 1511 CREs and inserted them into a minimal synthetic promoter sequence in 1, 2, or 3 copies, resulting in 4533 distinct synthetic promoters. These promoters were evaluated in vivo for their capacity to drive the expression of a transgene in a high-throughput manner through next-generation sequencing post antibiotic selection and fluorescence-activated cell sorting. To validate our approach, we sequenced hundreds of transgenic lines showing high levels of GFP expression. Further, we individually tested 14 identified promoters, revealing substantial increases in GFP expression─up to nine times higher than the baseline synthetic promoter, with five matching or even surpassing the performance of the native AR1 promoter. As a result of this study, we identified a catalog of CREs that can now be used to build superior synthetic algal promoters. More importantly, here we present a validated pipeline to generate building blocks for innovative synthetic genetic tools applicable to any algal species with a sequenced genome and transcriptome data set.
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Affiliation(s)
- Y. Torres-Tiji
- Division
of Biological Sciences, University of California
San Diego, La Jolla, California 92093, United States
| | - H. Sethuram
- Division
of Biological Sciences, University of California
San Diego, La Jolla, California 92093, United States
| | - A. Gupta
- Division
of Biological Sciences, University of California
San Diego, La Jolla, California 92093, United States
| | - J. McCauley
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE
Agile BioFoundry, Emeryville, California 94608, United States
| | - J.-V. Dutra-Molino
- Division
of Biological Sciences, University of California
San Diego, La Jolla, California 92093, United States
| | - R. Pathania
- Division
of Biological Sciences, University of California
San Diego, La Jolla, California 92093, United States
| | - L. Saxton
- Division
of Biological Sciences, University of California
San Diego, La Jolla, California 92093, United States
| | - K. Kang
- Division
of Biological Sciences, University of California
San Diego, La Jolla, California 92093, United States
| | - N. J. Hillson
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE
Agile BioFoundry, Emeryville, California 94608, United States
| | - S. P. Mayfield
- Division
of Biological Sciences, University of California
San Diego, La Jolla, California 92093, United States
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2
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Cagney MH, O'Neill EC. Strategies for producing high value small molecules in microalgae. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108942. [PMID: 39024780 DOI: 10.1016/j.plaphy.2024.108942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 06/11/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024]
Abstract
Eukaryotic microalgae are a diverse group of organisms that can be used for the sustainable production of a wide range of high value compounds, including lipids, flavours and dyes, bioplastics, and cosmetics. Optimising total biomass production often does not lead to optimal product yield and more sophisticated biphasic growth strategies are needed, introducing specific stresses to induce product synthesis. Genetic tools have been used to increase yields of natural products or to introduce new pathways to algae, and wider deployment of these tools offers promising routes for commercial production of high value compounds utilising minimal inputs.
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Affiliation(s)
- Michael H Cagney
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK; Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Ellis C O'Neill
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK; Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
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3
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Leprovost S, Plasson C, Balieu J, Walet-Balieu ML, Lerouge P, Bardor M, Mathieu-Rivet E. Fine-tuning the N-glycosylation of recombinant human erythropoietin using Chlamydomonas reinhardtii mutants. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38968612 DOI: 10.1111/pbi.14424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 06/06/2024] [Accepted: 06/18/2024] [Indexed: 07/07/2024]
Abstract
Microalgae are considered as attractive expression systems for the production of biologics. As photosynthetic unicellular organisms, they do not require costly and complex media for growing and are able to secrete proteins and perform protein glycosylation. Some biologics have been successfully produced in the green microalgae Chlamydomonas reinhardtii. However, post-translational modifications like glycosylation of these Chlamydomonas-made biologics have poorly been investigated so far. Therefore, in this study, we report on the first structural investigation of glycans linked to human erythropoietin (hEPO) expressed in a wild-type C. reinhardtii strain and mutants impaired in key Golgi glycosyltransferases. The glycoproteomic analysis of recombinant hEPO (rhEPO) expressed in the wild-type strain demonstrated that the three N-glycosylation sites are 100% glycosylated with mature N-glycans containing four to five mannose residues and carrying core xylose, core fucose and O-methyl groups. Moreover, expression in C. reinhardtii insertional mutants defective in xylosyltransferases A and B and fucosyltransferase resulted in drastic decreases of core xylosylation and core fucosylation of glycans N-linked to the rhEPOs, thus demonstrating that this strategy offers perspectives for humanizing the N-glycosylation of the Chlamydomonas-made biologics.
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Affiliation(s)
- S Leprovost
- Université de Rouen Normandie, Normandie Univ, GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, IRIB, GDR CNRS Chemobiologie, Rouen, France
- Institute for Plant Biology and Biotechnology (IBBP), University of Münster, Münster, Germany
| | - C Plasson
- Université de Rouen Normandie, Normandie Univ, GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, IRIB, GDR CNRS Chemobiologie, Rouen, France
| | - J Balieu
- Université de Rouen Normandie, Normandie Univ, GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, IRIB, GDR CNRS Chemobiologie, Rouen, France
| | - M-L Walet-Balieu
- Infrastructure de Recherche HeRacLeS, Plate-forme protéomique PISSARO, Université de Rouen Normandie, Rouen, France
| | - P Lerouge
- Université de Rouen Normandie, Normandie Univ, GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, IRIB, GDR CNRS Chemobiologie, Rouen, France
| | - M Bardor
- Université de Rouen Normandie, Normandie Univ, GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, IRIB, GDR CNRS Chemobiologie, Rouen, France
| | - E Mathieu-Rivet
- Université de Rouen Normandie, Normandie Univ, GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, IRIB, GDR CNRS Chemobiologie, Rouen, France
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4
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Lihanova Y, Nagel R, Jakob T, Sasso S. Characterization of activating cis-regulatory elements from the histone genes of Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:525-539. [PMID: 38693717 DOI: 10.1111/tpj.16781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 05/03/2024]
Abstract
Regulation of gene expression in eukaryotes is controlled by cis-regulatory modules (CRMs). A major class of CRMs are enhancers which are composed of activating cis-regulatory elements (CREs) responsible for upregulating transcription. To date, most enhancers and activating CREs have been studied in angiosperms; in contrast, our knowledge about these key regulators of gene expression in green algae is limited. In this study, we aimed at characterizing putative activating CREs/CRMs from the histone genes of the unicellular model alga Chlamydomonas reinhardtii. To test the activity of four candidates, reporter constructs consisting of a tetramerized CRE, an established promoter, and a gene for the mCerulean3 fluorescent protein were incorporated into the nuclear genome of C. reinhardtii, and their activity was quantified by flow cytometry. Two tested candidates, Eupstr and Ehist cons, significantly upregulated gene expression and were characterized in detail. Eupstr, which originates from highly expressed genes of C. reinhardtii, is an orientation-independent CRE capable of activating both the RBCS2 and β2-tubulin promoters. Ehist cons, which is a CRM from histone genes of angiosperms, upregulates the β2-tubulin promoter in C. reinhardtii over a distance of at least 1.5 kb. The octamer motif present in Ehist cons was identified in C. reinhardtii and the related green algae Chlamydomonas incerta, Chlamydomonas schloesseri, and Edaphochlamys debaryana, demonstrating its high evolutionary conservation. The results of this investigation expand our knowledge about the regulation of gene expression in green algae. Furthermore, the characterized activating CREs/CRMs can be applied as valuable genetic tools.
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Affiliation(s)
- Yuliia Lihanova
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Raimund Nagel
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Torsten Jakob
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Severin Sasso
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
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5
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Li DX, Guo Q, Yang YX, Jiang SJ, Ji XJ, Ye C, Wang YT, Shi TQ. Recent Advances and Multiple Strategies of Monoterpenoid Overproduction in Saccharomyces cerevisiae and Yarrowia lipolytica. ACS Synth Biol 2024; 13:1647-1662. [PMID: 38860708 DOI: 10.1021/acssynbio.4c00297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Monoterpenoids are an important subclass of terpenoids that play important roles in the energy, cosmetics, pharmaceuticals, and fragrances fields. With the development of biotechnology, microbial synthesis of monoterpenoids has received great attention. Yeasts such Saccharomyces cerevisiae and Yarrowia lipolytica are emerging as potential hosts for monoterpenoids production because of unique advantages including rapid growth cycles, mature gene editing tools, and clear genetic background. Recently, advancements in metabolic engineering and fermentation engineering have significantly enhanced the accumulation of monoterpenoids in cell factories. First, this review introduces the biosynthetic pathway of monoterpenoids and comprehensively summarizes the latest production strategies, which encompass enhancing precursor flux, modulating the expression of rate-limited enzymes, suppressing competitive pathway flux, mitigating cytotoxicity, optimizing substrate utilization, and refining the fermentation process. Subsequently, this review introduces four representative monoterpenoids. Finally, we outline the future prospects for efficient construction cell factories tailored for the production of monoterpenoids and other terpenoids.
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Affiliation(s)
- Dong-Xun Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Qi Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Yu-Xin Yang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Shun-Jie Jiang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Xiao-Jun Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Yue-Tong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
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6
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Einhaus A, Baier T, Kruse O. Molecular design of microalgae as sustainable cell factories. Trends Biotechnol 2024; 42:728-738. [PMID: 38092627 DOI: 10.1016/j.tibtech.2023.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 06/09/2024]
Abstract
Microalgae are regarded as sustainable and potent chassis for biotechnology. Their capacity for efficient photosynthesis fuels dynamic growth independent from organic carbon sources and converts atmospheric CO2 directly into various valuable hydrocarbon-based metabolites. However, approaches to gene expression and metabolic regulation have been inferior to those in more established heterotrophs (e.g., prokaryotes or yeast) since the genetic tools and insights in expression regulation have been distinctly less advanced. In recent years, however, these tools and their efficiency have dramatically improved. Various examples have demonstrated new trends in microalgal biotechnology and the potential of microalgae for the transition towards a sustainable bioeconomy.
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Affiliation(s)
- Alexander Einhaus
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Thomas Baier
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Olaf Kruse
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
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7
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Jacobebbinghaus N, Lauersen KJ, Kruse O, Baier T. Bicistronic expression of nuclear transgenes in Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1400-1412. [PMID: 38415961 DOI: 10.1111/tpj.16677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 01/19/2024] [Accepted: 01/29/2024] [Indexed: 02/29/2024]
Abstract
In eukaryotic organisms, proteins are typically translated from monocistronic messenger RNAs containing a single coding sequence (CDS). However, recent long transcript sequencing identified 87 nuclear polycistronic mRNAs in Chlamydomonas reinhardtii natively carrying multiple co-expressed CDSs. In this study, we investigated the dynamics of 22 short intergenic sequences derived from these native polycistronic loci by their application in genetic constructs for synthetic transgene expression. A promising candidate sequence was identified based on the quantification of transformation efficiency and expression strength of a fluorescence reporter protein. Subsequently, the expression of independent proteins from one mRNA was verified by cDNA amplification and protein molecular mass characterization. We demonstrated engineered bicistronic expression in vivo to drive successful co-expression of several terpene synthases with the selection marker aphVIII. Bicistronic transgene design resulted in significantly increased (E)-α-bisabolene production of 7.95 mg L-1 from a single open reading frame, 18.1× fold higher than previous reports. Use of this strategy simplifies screening procedures for identification of high-level expressing transformants, does not require the application of additional fluorescence reporters, and reduces the nucleotide footprint compared to classical monocistronic expression cassettes. Although clear advantages for bicistronic transgene expression were observed, this strategy was found to be limited to the aphVIII marker, and further studies are necessary to gain insights into the underlying mechanism that uniquely permits this co-expression from the algal nuclear genome.
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Affiliation(s)
- Nick Jacobebbinghaus
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Kyle J Lauersen
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Olaf Kruse
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Thomas Baier
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
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8
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Kneip JS, Kniepkamp N, Jang J, Mortaro MG, Jin E, Kruse O, Baier T. CRISPR/Cas9-Mediated Knockout of the Lycopene ε-Cyclase for Efficient Astaxanthin Production in the Green Microalga Chlamydomonas reinhardtii. PLANTS (BASEL, SWITZERLAND) 2024; 13:1393. [PMID: 38794462 PMCID: PMC11125023 DOI: 10.3390/plants13101393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/09/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024]
Abstract
Carotenoids are valuable pigments naturally occurring in all photosynthetic plants and microalgae as well as in selected fungi, bacteria, and archaea. Green microalgae developed a complex carotenoid profile suitable for efficient light harvesting and light protection and harbor great capacity for carotenoid production through the substantial power of the endogenous 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway. Previous works established successful genome editing and induced significant changes in the cellular carotenoid content in Chlamydomonas reinhardtii. This study employs a tailored carotenoid pathway for engineered bioproduction of the valuable ketocarotenoid astaxanthin. Functional knockout of lycopene ε-cyclase (LCYE) and non-homologous end joining (NHEJ)-based integration of donor DNA at the target site inhibit the accumulation of α-carotene and consequently lutein and loroxanthin, abundant carotenoids in C. reinhardtii without changes in cellular fitness. PCR-based screening indicated that 4 of 96 regenerated candidate lines carried (partial) integrations of donor DNA and increased ß-carotene as well as derived carotenoid contents. Iterative overexpression of CrBKT, PacrtB, and CrCHYB resulted in a 2.3-fold increase in astaxanthin accumulation in mutant ΔLCYE#3 (1.8 mg/L) compared to the parental strain UVM4, which demonstrates the potential of genome editing for the design of a green cell factory for astaxanthin bioproduction.
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Affiliation(s)
- Jacob Sebastian Kneip
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Niklas Kniepkamp
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Junhwan Jang
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Maria Grazia Mortaro
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - EonSeon Jin
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Olaf Kruse
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Thomas Baier
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
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9
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Sun H, Wang J, Li Y, Yang S, Chen DD, Tu Y, Liu J, Sun Z. Synthetic biology in microalgae towards fucoxanthin production for pharmacy and nutraceuticals. Biochem Pharmacol 2024; 220:115958. [PMID: 38052271 DOI: 10.1016/j.bcp.2023.115958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/16/2023] [Accepted: 11/29/2023] [Indexed: 12/07/2023]
Abstract
Synthetic biology has emerged as a powerful tool for engineering biological systems to produce valuable compounds, including pharmaceuticals and nutraceuticals. Microalgae, in particular, offer a promising platform for the production of bioactive compounds due to their high productivity, low land and water requirements, and ability to perform photosynthesis. Fucoxanthin, a carotenoid pigment found predominantly in brown seaweeds and certain microalgae, has gained significant attention in recent years due to its numerous health benefits, such as antioxidation, antitumor effect and precaution osteoporosis. This review provides an overview of the principles and applications of synthetic biology in the microbial engineering of microalgae for enhanced fucoxanthin production. Firstly, the fucoxanthin bioavailability and metabolism in vivo was introduced for the beneficial roles, followed by the biological functions of anti-oxidant activity, anti-inflammatory activity, antiapoptotic role antidiabetic and antilipemic effects. Secondly, the cultivation condition and strategy were summarized for fucoxanthin improvement with low production costs. Thirdly, the genetic engineering of microalgae, including gene overexpression, knockdown and knockout strategies were discussed for further improving the fucoxanthin production. Then, synthetic biology tools of CRISPR-Cas9 genome editing, transcription activator-like effector nucleases as well as modular assembly and chassis engineering were proposed to precise modification of microalgal genomes to improve fucoxanthin production. Finally, challenges and future perspectives were discussed to realize the industrial production and development of functional foods of fucoxanthin from microalgae.
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Affiliation(s)
- Han Sun
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education; International Research Center for Marine Biosciences, Ministry of Science and Technology; Shanghai Ocean University, Shanghai 201306, China; Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Jia Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Yuelian Li
- China National Chemical Information Center, Beijing 100020, China
| | - Shufang Yang
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | | | - Yidong Tu
- Technology Center, Shanghai Inoherb Co. Ltd, 121 Chengyin Road, Shanghai 200083, China
| | - Jin Liu
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Algae Innovation Center for Engineering Research, School of Resources and Environment, Nanchang University, Nanchang 330031, China
| | - Zheng Sun
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education; International Research Center for Marine Biosciences, Ministry of Science and Technology; Shanghai Ocean University, Shanghai 201306, China; Marine Biomedical Science and Technology Innovation Platform of Lin-gang Special Area, Shanghai 201306, China.
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10
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Pang AP, Wang Y, Zhang T, Gao F, Shen JD, Huang L, Zhou J, Zhang B, Liu ZQ, Zheng YG. Highly efficient production of rhamnolipid in P. putida using a novel sacB-based system and mixed carbon source. BIORESOURCE TECHNOLOGY 2024; 394:130220. [PMID: 38109979 DOI: 10.1016/j.biortech.2023.130220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 12/20/2023]
Abstract
Pseudomonas putida KT2440, a GRAS strain, has been used for synthesizing bulk and fine chemicals. However, the gene editing tool to metabolically engineer KT2440 showed low efficiency. In this study, a novel sacB-based system pK51mobsacB was established to improve the efficiency for marker-free gene disruption. Then the rhamnolipid synthetic pathway was introduced in KT2440 and genes of the competitive pathways were deleted to lower the metabolic burden based on pK51mobsacB. A series of endogenous and synthetic promoters were used for fine tuning rhlAB expression. The limited supply of dTDP-L-rhamnose was enhanced by heterologous rmlBDAC expression. Cell growth and rhamnolipid production were well balanced by using glucose/glycerol as mixed carbon sources. The final strain produced 3.64 g/L at shake-flask and 19.77 g/L rhamnolipid in a 5 L fermenter, the highest obtained among metabolically engineered KT2440, which implied the potential of KT2440 as a promising microbial cell factory for industrial rhamnolipid production.
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Affiliation(s)
- Ai-Ping Pang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Yun Wang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Teng Zhang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Feng Gao
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Ji-Dong Shen
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Lianggang Huang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Junping Zhou
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Bo Zhang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Zhi-Qiang Liu
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China.
| | - Yu-Guo Zheng
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
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11
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Gupta A, Kang K, Pathania R, Saxton L, Saucedo B, Malik A, Torres-Tiji Y, Diaz CJ, Dutra Molino JV, Mayfield SP. Harnessing genetic engineering to drive economic bioproduct production in algae. Front Bioeng Biotechnol 2024; 12:1350722. [PMID: 38347913 PMCID: PMC10859422 DOI: 10.3389/fbioe.2024.1350722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/16/2024] [Indexed: 02/15/2024] Open
Abstract
Our reliance on agriculture for sustenance, healthcare, and resources has been essential since the dawn of civilization. However, traditional agricultural practices are no longer adequate to meet the demands of a burgeoning population amidst climate-driven agricultural challenges. Microalgae emerge as a beacon of hope, offering a sustainable and renewable source of food, animal feed, and energy. Their rapid growth rates, adaptability to non-arable land and non-potable water, and diverse bioproduct range, encompassing biofuels and nutraceuticals, position them as a cornerstone of future resource management. Furthermore, microalgae's ability to capture carbon aligns with environmental conservation goals. While microalgae offers significant benefits, obstacles in cost-effective biomass production persist, which curtails broader application. This review examines microalgae compared to other host platforms, highlighting current innovative approaches aimed at overcoming existing barriers. These approaches include a range of techniques, from gene editing, synthetic promoters, and mutagenesis to selective breeding and metabolic engineering through transcription factors.
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Affiliation(s)
- Abhishek Gupta
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Kalisa Kang
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Ruchi Pathania
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Lisa Saxton
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Barbara Saucedo
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Ashleyn Malik
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Yasin Torres-Tiji
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Crisandra J. Diaz
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - João Vitor Dutra Molino
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Stephen P. Mayfield
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
- California Center for Algae Biotechnology, University of California San Diego, San Diego, CA, United States
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12
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Yan Q, Han L, Liu Z, Zhou S, Zhou Z. Stepwise genetic modification for efficient expression of heterologous proteins in Aspergillus nidulans. Appl Microbiol Biotechnol 2023; 107:6923-6935. [PMID: 37698610 DOI: 10.1007/s00253-023-12755-2] [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: 04/06/2023] [Revised: 08/09/2023] [Accepted: 08/26/2023] [Indexed: 09/13/2023]
Abstract
Filamentous fungi are widely used in food fermentation and therapeutic protein production due to their prominent protein secretion and post-translational modification system. Aspergillus nidulans is an important model strain of filamentous fungi, but not a fully developed cell factory for heterologous protein expression. One of the limitations is its relatively low capacity of protein secretion. To alleviate this limitation, in this study, the protein secretory pathway and mycelium morphology were stepwise modified. With eGFP as a reporter protein, protein secretion was significantly enhanced through reducing the degradation of heterologous proteins by endoplasmic reticulum-associated protein degradation (ERAD) and vacuoles in the secretory pathway. Elimination of mycelial aggregation resulted in a 1.5-fold and 1.3-fold increase in secretory expression of eGFP in typical constitutive and inducible expression systems, respectively. Combined with these modifications, high secretory expression of human interleukin-6 (HuIL-6) was achieved. Consequently, a higher yield of secretory HuIL-6 was realized by further disruption of extracellular proteases. Overall, a superior chassis cell of A. nidulans suitable for efficient secretory expression of heterologous proteins was successfully obtained, providing a promising platform for biosynthesis using filamentous fungi as hosts. KEY POINTS: • Elimination of mycelial aggregation and decreasing the degradation of heterologous protein are effective strategies for improving the heterologous protein expression. • The work provides a high-performance chassis host △agsB-derA for heterologous protein secretory expression. • Human interleukin-6 (HuIL-6) was expressed efficiently in the high-performance chassis host △agsB-derA.
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Affiliation(s)
- Qin Yan
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Laichuang Han
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Zhongmei Liu
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Shengmin Zhou
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai, China.
| | - Zhemin Zhou
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, 214122, China.
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13
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Shitanaka T, Higa L, Bryson AE, Bertucci C, Vande Pol N, Lucker B, Khanal SK, Bonito G, Du ZY. Flocculation of oleaginous green algae with Mortierella alpina fungi. BIORESOURCE TECHNOLOGY 2023; 385:129391. [PMID: 37364649 DOI: 10.1016/j.biortech.2023.129391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
Microalgae are promising sources of valuable bioproducts such as biofuels, food, and nutraceuticals. However, harvesting microalgae is challenging due to their small size and low biomass concentrations. To address this challenge, bio-flocculation of starchless mutants of Chlamydomonas reinhardtii (sta6/sta7) was investigated with Mortierella alpina, an oleaginous fungus with high concentrations of arachidonic acid (ARA). Triacylglycerides (TAG) reached 85 % of total lipids in sta6 and sta7 through a nitrogen regime. Scanning electron microscopy determined cell-wall attachment and extra polymeric substances (EPS) to be responsible for flocculation. An algal-fungal biomass ratio around 1:1 (three membranes) was optimal for bio-flocculation (80-85 % flocculation efficiency in 24 h). Nitrogen-deprived sta6/sta7 were flocculated with strains of M. alpina (NVP17b, NVP47, and NVP153) with aggregates exhibiting fatty acid profiles similar to C. reinhardtii, with ARA (3-10 % of total fatty acids). This study showcases M. alpina as a strong bio-flocculation candidate for microalgae and advances a mechanistic understanding of algal-fungal interaction.
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Affiliation(s)
- Ty Shitanaka
- Department of Molecular Biosciences & Bioengineering, University of Hawai'i at Mānoa, Honolulu, HI 96822, United States
| | - Lauren Higa
- Department of Molecular Biosciences & Bioengineering, University of Hawai'i at Mānoa, Honolulu, HI 96822, United States
| | - Abigail E Bryson
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States
| | - Conor Bertucci
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States
| | - Natalie Vande Pol
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States
| | - Ben Lucker
- Trait Biosciences, Los Alamos, NM 87544, United States
| | - Samir Kumar Khanal
- Department of Molecular Biosciences & Bioengineering, University of Hawai'i at Mānoa, Honolulu, HI 96822, United States; Department of Civil and Environmental Engineering, University of Hawai'i at Mānoa, Honolulu, HI 96822, United States
| | - Gregory Bonito
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States.
| | - Zhi-Yan Du
- Department of Molecular Biosciences & Bioengineering, University of Hawai'i at Mānoa, Honolulu, HI 96822, United States.
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14
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Milito A, Aschern M, McQuillan JL, Yang JS. Challenges and advances towards the rational design of microalgal synthetic promoters in Chlamydomonas reinhardtii. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3833-3850. [PMID: 37025006 DOI: 10.1093/jxb/erad100] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
Microalgae hold enormous potential to provide a safe and sustainable source of high-value compounds, acting as carbon-fixing biofactories that could help to mitigate rapidly progressing climate change. Bioengineering microalgal strains will be key to optimizing and modifying their metabolic outputs, and to render them competitive with established industrial biotechnology hosts, such as bacteria or yeast. To achieve this, precise and tuneable control over transgene expression will be essential, which would require the development and rational design of synthetic promoters as a key strategy. Among green microalgae, Chlamydomonas reinhardtii represents the reference species for bioengineering and synthetic biology; however, the repertoire of functional synthetic promoters for this species, and for microalgae generally, is limited in comparison to other commercial chassis, emphasizing the need to expand the current microalgal gene expression toolbox. Here, we discuss state-of-the-art promoter analyses, and highlight areas of research required to advance synthetic promoter development in C. reinhardtii. In particular, we exemplify high-throughput studies performed in other model systems that could be applicable to microalgae, and propose novel approaches to interrogating algal promoters. We lastly outline the major limitations hindering microalgal promoter development, while providing novel suggestions and perspectives for how to overcome them.
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Affiliation(s)
- Alfonsina Milito
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Moritz Aschern
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Josie L McQuillan
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - Jae-Seong Yang
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
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15
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Perozeni F, Baier T. Current Nuclear Engineering Strategies in the Green Microalga Chlamydomonas reinhardtii. Life (Basel) 2023; 13:1566. [PMID: 37511941 PMCID: PMC10381326 DOI: 10.3390/life13071566] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/07/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
The green model microalga Chlamydomonas reinhardtii recently emerged as a sustainable production chassis for the efficient biosynthesis of recombinant proteins and high-value metabolites. Its capacity for scalable, rapid and light-driven growth in minimal salt solutions, its simplicity for genetic manipulation and its "Generally Recognized As Safe" (GRAS) status are key features for its application in industrial biotechnology. Although nuclear transformation has typically resulted in limited transgene expression levels, recent developments now allow the design of powerful and innovative bioproduction concepts. In this review, we summarize the main obstacles to genetic engineering in C. reinhardtii and describe all essential aspects in sequence adaption and vector design to enable sufficient transgene expression from the nuclear genome. Several biotechnological examples of successful engineering serve as blueprints for the future establishment of C. reinhardtii as a green cell factory.
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Affiliation(s)
- Federico Perozeni
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Thomas Baier
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
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16
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Niemeyer J, Fischer L, Aylward FO, Schroda M. Analysis of Viral Promoters for Transgene Expression and of the Effect of 5'-UTRs on Alternative Translational Start Sites in Chlamydomonas. Genes (Basel) 2023; 14:genes14040948. [PMID: 37107706 PMCID: PMC10138193 DOI: 10.3390/genes14040948] [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: 03/14/2023] [Revised: 04/15/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
Microalgae biotechnology has the potential to produce high quality bioproducts in a sustainable manner. Here, Chlamydomonas reinhardtii has shown great potential as a host for biotechnological exploitation. However, low expression of nuclear transgenes is still a problem and needs to be optimized. In many model organisms, viral promoters are used to drive transgene expression at high levels. However, no viruses are known to infect Chlamydomonas, and known viral promoters are not functional. Recently, two different lineages of giant viruses were identified in the genomes of Chlamydomonas reinhardtii field isolates. In this work, we tested six potentially strong promoters from these viral genomes for their ability to drive transgene expression in Chlamydomonas. We used ble, NanoLUC, and mCherry as reporter genes, and three native benchmark promoters as controls. None of the viral promoters drove expression of any reporter gene beyond background. During our study, we found that mCherry variants are produced by alternative in-frame translational start sites in Chlamydomonas. We show that this problem can be overcome by mutating the responsible methionine codons to codons for leucine and by using the 5'-UTR of βTUB2 instead of the 5'-UTRs of PSAD or RBCS2. Apparently, the βTUB2 5'-UTR promotes the use of the first start codon. This could be mediated by the formation of a stem-loop between sequences of the βTUB2 5'-UTR and sequences downstream of the first AUG in the mCherry reporter, potentially increasing the dwell time of the scanning 40S subunit on the first AUG and thus decreasing the probability of leaky scanning.
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Affiliation(s)
- Justus Niemeyer
- Molecular Biotechnology & Systems Biology, RPTU Kaiserslautern-Landau, Paul-Ehrlich-Straße 23, 67663 Kaiserslautern, Germany
| | - Laura Fischer
- Molecular Biotechnology & Systems Biology, RPTU Kaiserslautern-Landau, Paul-Ehrlich-Straße 23, 67663 Kaiserslautern, Germany
| | | | - Michael Schroda
- Molecular Biotechnology & Systems Biology, RPTU Kaiserslautern-Landau, Paul-Ehrlich-Straße 23, 67663 Kaiserslautern, Germany
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17
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Barone GD, Cernava T, Ullmann J, Liu J, Lio E, Germann AT, Nakielski A, Russo DA, Chavkin T, Knufmann K, Tripodi F, Coccetti P, Secundo F, Fu P, Pfleger B, Axmann IM, Lindblad P. Recent developments in the production and utilization of photosynthetic microorganisms for food applications. Heliyon 2023; 9:e14708. [PMID: 37151658 PMCID: PMC10161259 DOI: 10.1016/j.heliyon.2023.e14708] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 05/09/2023] Open
Abstract
The growing use of photosynthetic microorganisms for food and food-related applications is driving related biotechnology research forward. Increasing consumer acceptance, high sustainability, demand of eco-friendly sources for food, and considerable global economic concern are among the main factors to enhance the focus on the novel foods. In the cases of not toxic strains, photosynthetic microorganisms not only provide a source of sustainable nutrients but are also potentially healthy. Several published studies showed that microalgae are sources of accessible protein and fatty acids. More than 400 manuscripts were published per year in the last 4 years. Furthermore, industrial approaches utilizing these microorganisms are resulting in new jobs and services. This is in line with the global strategy for bioeconomy that aims to support sustainable development of bio-based sectors. Despite the recognized potential of the microalgal biomass value chain, significant knowledge gaps still exist especially regarding their optimized production and utilization. This review highlights the potential of microalgae and cyanobacteria for food and food-related applications as well as their market size. The chosen topics also include advanced production as mixed microbial communities, production of high-value biomolecules, photoproduction of terpenoid flavoring compounds, their utilization for sustainable agriculture, application as source of nutrients in space, and a comparison with heterotrophic microorganisms like yeast to better evaluate their advantages over existing nutrient sources. This comprehensive assessment should stimulate further interest in this highly relevant research topic.
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Affiliation(s)
- Giovanni D. Barone
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
- Corresponding author.
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010, Graz, Austria
| | - Jörg Ullmann
- Roquette Klötze GmbH & Co. KG, Lockstedter Chaussee 1, D-38486, Klötze, Germany
| | - Jing Liu
- State Key Laboratory of Marine Resource Utilization in South China Sea Hainan University, 58 Renmin Avenue, Meilan District, Haikou, Hainan Province, 570228, PR China
| | - Elia Lio
- Institute of Chemical Sciences and Technologies (SCITEC) “Giulio Natta” Italian National Research Council (CNR), via Mario Bianco 9, 20131, Milan, Italy
| | - Anna T. Germann
- Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Andreas Nakielski
- Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - David A. Russo
- Friedrich Schiller University Jena, Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Lessingstr. 8, D-07743, Jena, Germany
| | - Ted Chavkin
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Farida Tripodi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milano, Italy
| | - Paola Coccetti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milano, Italy
| | - Francesco Secundo
- Institute of Chemical Sciences and Technologies (SCITEC) “Giulio Natta” Italian National Research Council (CNR), via Mario Bianco 9, 20131, Milan, Italy
| | - Pengcheng Fu
- State Key Laboratory of Marine Resource Utilization in South China Sea Hainan University, 58 Renmin Avenue, Meilan District, Haikou, Hainan Province, 570228, PR China
| | - Brian Pfleger
- Knufmann GmbH, Bergstraße 23, D-38486, Klötze, Germany
| | - Ilka M. Axmann
- Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, D-40001, Düsseldorf, Germany
- Corresponding author. Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany.
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry–Ångström, Uppsala University, Box 523, SE-75120, Uppsala, Sweden
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18
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Amendola S, Kneip JS, Meyer F, Perozeni F, Cazzaniga S, Lauersen KJ, Ballottari M, Baier T. Metabolic Engineering for Efficient Ketocarotenoid Accumulation in the Green Microalga Chlamydomonas reinhardtii. ACS Synth Biol 2023; 12:820-831. [PMID: 36821819 DOI: 10.1021/acssynbio.2c00616] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Astaxanthin is a valuable ketocarotenoid with various pharmaceutical and nutraceutical applications. Green microalgae harbor natural capacities for pigment accumulation due to their 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway. Recently, a redesigned ß-carotene ketolase (BKT) was found to enable ketocarotenoid accumulation in the model microalga Chlamydomonas reinhardtii, and transformants exhibited reduced photoinhibition under high-light. Here, a systematic screening by synthetic transgene design of carotenoid pathway enzymes and overexpression from the nuclear genome identified phytoene synthase (PSY/crtB) as a bottleneck for carotenoid accumulation in C. reinhardtii. Increased ß-carotene hydroxylase (CHYB) activity was found to be essential for engineered astaxanthin accumulation. A combined BKT, crtB, and CHYB expression strategy resulted in a volumetric astaxanthin production of 9.5 ± 0.3 mg L-1 (4.5 ± 0.1 mg g-1 CDW) in mixotrophic and 23.5 mg L-1 (1.09 mg L-1 h-1) in high cell density conditions, a 4-fold increase compared to previous reports in C. reinhardtii. This work presents a systematic investigation of bottlenecks in astaxanthin accumulation in C. reinhardtii and the phototrophic green cell factory design for competitive use in industrial biotechnology.
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Affiliation(s)
- Sofia Amendola
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Jacob S Kneip
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Florian Meyer
- Genetics of Prokaryotes, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Federico Perozeni
- Department of Biotechnology, University of Verona, 37129 Verona, Italy
| | - Stefano Cazzaniga
- Department of Biotechnology, University of Verona, 37129 Verona, Italy
| | - Kyle J Lauersen
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Kingdom of Saudi Arabia
| | - Matteo Ballottari
- Department of Biotechnology, University of Verona, 37129 Verona, Italy
| | - Thomas Baier
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
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19
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Li X, Lan C, Li X, Hu Z, Jia B. A review on design-build-test-learn cycle to potentiate progress in isoprenoid engineering of photosynthetic microalgae. BIORESOURCE TECHNOLOGY 2022; 363:127981. [PMID: 36130687 DOI: 10.1016/j.biortech.2022.127981] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/10/2022] [Accepted: 09/12/2022] [Indexed: 06/15/2023]
Abstract
Currently, the generation of isoprenoid factories in microalgae relies on two strategies: 1) enhanced production of endogenous isoprenoids; or 2) production of heterologous terpenes by metabolic engineering. Nevertheless, low titers and productivity are still a feature of isoprenoid biotechnology and need to be addressed. In this context, the mechanisms underlying isoprenoid biosynthesis in microalgae and its relationship with central carbon metabolism are reviewed. Developments in microalgal biotechnology are discussed, and a new approach of integrated "design-build-test-learn" cycle is advocated to the trends, challenges and prospects involved in isoprenoid engineering. The emerging and promising strategies and tools are discussed for microalgal engineering in the future. This review encourages a systematic engineering perspective aimed at potentiating progress in isoprenoid engineering of photosynthetic microalgae.
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Affiliation(s)
- Xiangyu Li
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Chengxiang Lan
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Xinyi Li
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Zhangli Hu
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Bin Jia
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
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20
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Dehghani J, Movafeghi A, Mathieu-Rivet E, Mati-Baouche N, Calbo S, Lerouge P, Bardor M. Microalgae as an Efficient Vehicle for the Production and Targeted Delivery of Therapeutic Glycoproteins against SARS-CoV-2 Variants. Mar Drugs 2022; 20:md20110657. [PMID: 36354980 PMCID: PMC9698596 DOI: 10.3390/md20110657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/27/2022] Open
Abstract
Severe acute respiratory syndrome–Coronavirus 2 (SARS-CoV-2) can infect various human organs, including the respiratory, circulatory, nervous, and gastrointestinal ones. The virus is internalized into human cells by binding to the human angiotensin-converting enzyme 2 (ACE2) receptor through its spike protein (S-glycoprotein). As S-glycoprotein is required for the attachment and entry into the human target cells, it is the primary mediator of SARS-CoV-2 infectivity. Currently, this glycoprotein has received considerable attention as a key component for the development of antiviral vaccines or biologics against SARS-CoV-2. Moreover, since the ACE2 receptor constitutes the main entry route for the SARS-CoV-2 virus, its soluble form could be considered as a promising approach for the treatment of coronavirus disease 2019 infection (COVID-19). Both S-glycoprotein and ACE2 are highly glycosylated molecules containing 22 and 7 consensus N-glycosylation sites, respectively. The N-glycan structures attached to these specific sites are required for the folding, conformation, recycling, and biological activity of both glycoproteins. Thus far, recombinant S-glycoprotein and ACE2 have been produced primarily in mammalian cells, which is an expensive process. Therefore, benefiting from a cheaper cell-based biofactory would be a good value added to the development of cost-effective recombinant vaccines and biopharmaceuticals directed against COVID-19. To this end, efficient protein synthesis machinery and the ability to properly impose post-translational modifications make microalgae an eco-friendly platform for the production of pharmaceutical glycoproteins. Notably, several microalgae (e.g., Chlamydomonas reinhardtii, Dunaliella bardawil, and Chlorella species) are already approved by the U.S. Food and Drug Administration (FDA) as safe human food. Because microalgal cells contain a rigid cell wall that could act as a natural encapsulation to protect the recombinant proteins from the aggressive environment of the stomach, this feature could be used for the rapid production and edible targeted delivery of S-glycoprotein and soluble ACE2 for the treatment/inhibition of SARS-CoV-2. Herein, we have reviewed the pathogenesis mechanism of SARS-CoV-2 and then highlighted the potential of microalgae for the treatment/inhibition of COVID-19 infection.
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Affiliation(s)
- Jaber Dehghani
- Université de Rouen Normandie, Laboratoire GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, F-76000 Rouen, France
| | - Ali Movafeghi
- Department of Plant, Cell and Molecular Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz 5166616471, Iran
| | - Elodie Mathieu-Rivet
- Université de Rouen Normandie, Laboratoire GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, F-76000 Rouen, France
| | - Narimane Mati-Baouche
- Université de Rouen Normandie, Laboratoire GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, F-76000 Rouen, France
| | - Sébastien Calbo
- Université de Rouen Normandie, Inserm U1234, F-76000 Rouen, France
| | - Patrice Lerouge
- Université de Rouen Normandie, Laboratoire GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, F-76000 Rouen, France
| | - Muriel Bardor
- Université de Rouen Normandie, Laboratoire GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, F-76000 Rouen, France
- Correspondence: ; Tel.: +33-2-35-14-67-51
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21
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Freudenberg RA, Wittemeier L, Einhaus A, Baier T, Kruse O. Advanced pathway engineering for phototrophic putrescine production. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1968-1982. [PMID: 35748533 PMCID: PMC9491463 DOI: 10.1111/pbi.13879] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/13/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
The polyamine putrescine (1,4-diaminobutane) contributes to cellular fitness in most organisms, where it is derived from the amino acids ornithine or arginine. In the chemical industry, putrescine serves as a versatile building block for polyamide synthesis. The green microalga Chlamydomonas reinhardtii accumulates relatively high putrescine amounts, which, together with recent advances in genetic engineering, enables the generation of a powerful green cell factory to promote sustainable biotechnology for base chemical production. Here, we report a systematic investigation of the native putrescine metabolism in C. reinhardtii, leading to the first CO2 -based bio-production of putrescine, by employing modern synthetic biology and metabolic engineering strategies. A CRISPR/Cas9-based knockout of key enzymes of the polyamine biosynthesis pathway identified ornithine decarboxylase 1 (ODC1) as a gatekeeper for putrescine accumulation and demonstrated that the arginine decarboxylase (ADC) route is likely inactive and that amine oxidase 2 (AMX2) is mainly responsible for putrescine degradation in C. reinhardtii. A 4.5-fold increase in cellular putrescine levels was achieved by engineered overexpression of potent candidate ornithine decarboxylases (ODCs). We identified unexpected substrate promiscuity in two bacterial ODCs, which exhibited co-production of cadaverine and 4-aminobutanol. Final pathway engineering included overexpression of recombinant arginases for improved substrate availability as well as functional knockout of putrescine degradation, which resulted in a 10-fold increase in cellular putrescine titres and yielded 200 mg/L in phototrophic high cell density cultivations after 10 days.
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Affiliation(s)
- Robert A. Freudenberg
- Faculty of Biology, Center for Biotechnology (CeBiTec)Bielefeld UniversityBielefeldGermany
| | - Luisa Wittemeier
- Faculty of Biology, Center for Biotechnology (CeBiTec)Bielefeld UniversityBielefeldGermany
| | - Alexander Einhaus
- Faculty of Biology, Center for Biotechnology (CeBiTec)Bielefeld UniversityBielefeldGermany
| | - Thomas Baier
- Faculty of Biology, Center for Biotechnology (CeBiTec)Bielefeld UniversityBielefeldGermany
| | - Olaf Kruse
- Faculty of Biology, Center for Biotechnology (CeBiTec)Bielefeld UniversityBielefeldGermany
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22
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Gutiérrez S, Wellman GB, Lauersen KJ. Teaching an old ‘doc’ new tricks for algal biotechnology: Strategic filter use enables multi-scale fluorescent protein signal detection. Front Bioeng Biotechnol 2022; 10:979607. [PMID: 36213064 PMCID: PMC9540369 DOI: 10.3389/fbioe.2022.979607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
Fluorescent proteins (FPs) are powerful reporters with a broad range of applications in gene expression and subcellular localization. High-throughput screening is often required to identify individual transformed cell lines in organisms that favor non-homologous-end-joining integration of transgenes into genomes, like in the model green microalga Chlamydomonas reinhardtii. Strategic transgene design, including genetic fusion of transgenes to FPs, and strain domestication have aided engineering efforts in this host but have not removed the need for screening large numbers of transformants to identify those with robust transgene expression levels. FPs facilitate transformant screening by providing a visual signal indicating transgene expression. However, limited combinations of FPs have been described in alga and inherent background fluorescence from cell pigments can hinder FP detection efforts depending on available infrastructure. Here, an updated set of algal nuclear genome-domesticated plasmid parts for seven FPs and six epitope tags were generated and tested in C. reinhardtii. Strategic filter selection was found to enable detection of up to five independent FPs signals from cyan to far-red separately from inherent chlorophyll fluorescence in live algae at the agar plate-level and also in protein electrophoresis gels. This work presents technical advances for algal engineering that can assist reporter detection efforts in other photosynthetic host cells or organisms with inherent background fluorescence.
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Metabolic Engineering of the Isopentenol Utilization Pathway Enhanced the Production of Terpenoids in Chlamydomonas reinhardtii. Mar Drugs 2022; 20:md20090577. [PMID: 36135766 PMCID: PMC9505001 DOI: 10.3390/md20090577] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/24/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022] Open
Abstract
Eukaryotic green microalgae show considerable promise for the sustainable light-driven biosynthesis of high-value fine chemicals, especially terpenoids because of their fast and inexpensive phototrophic growth. Here, the novel isopentenol utilization pathway (IUP) was introduced into Chlamydomonas reinhardtii to enhance the hemiterpene (isopentenyl pyrophosphate, IPP) titers. Then, diphosphate isomerase (IDI) and limonene synthase (MsLS) were further inserted for limonene production. Transgenic algae showed 8.6-fold increase in IPP compared with the wild type, and 23-fold increase in limonene production compared with a single MsLS expressing strain. Following the culture optimization, the highest limonene production reached 117 µg/L, when the strain was cultured in a opt2 medium supplemented with 10 mM isoprenol under a light: dark regimen. This demonstrates that transgenic algae expressing the IUP represent an ideal chassis for the high-value terpenoid production. The IUP will facilitate further the metabolic and enzyme engineering to enhance the terpenoid titers by significantly reducing the number of enzyme steps required for an optimal biosynthesis.
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24
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Wichmann J, Eggert A, Elbourne LDH, Paulsen IT, Lauersen KJ, Kruse O. Farnesyl pyrophosphate compartmentalization in the green microalga Chlamydomonas reinhardtii during heterologous (E)-α-bisabolene production. Microb Cell Fact 2022; 21:190. [PMID: 36104783 PMCID: PMC9472337 DOI: 10.1186/s12934-022-01910-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/26/2022] [Indexed: 11/10/2022] Open
Abstract
Background Eukaryotic algae have recently emerged as hosts for metabolic engineering efforts to generate heterologous isoprenoids. Isoprenoid metabolic architectures, flux, subcellular localization, and transport dynamics have not yet been fully elucidated in algal hosts. Results In this study, we investigated the accessibility of different isoprenoid precursor pools for C15 sesquiterpenoid generation in the cytoplasm and chloroplast of Chlamydomonas reinhardtii using the Abies grandis bisabolene synthase (AgBS) as a reporter. The abundance of the C15 sesquiterpene precursor farnesyl pyrophosphate (FPP) was not increased in the cytosol by co-expression and fusion of AgBS with different FPP synthases (FPPSs), indicating limited C5 precursor availability in the cytoplasm. However, FPP was shown to be available in the plastid stroma, where bisabolene titers could be improved several-fold by FPPSs. Sesquiterpene production was greatest when AgBS-FPPS fusions were directed to the plastid and could further be improved by increasing the gene dosage. During scale-up cultivation with different carbon sources and light regimes, specific sesquiterpene productivities from the plastid were highest with CO2 as the only carbon source and light:dark illumination cycles. Potential prenyl unit transporters are proposed based on bioinformatic analyses, which may be in part responsible for our observations. Conclusions Our findings indicate that the algal chloroplast can be harnessed in addition to the cytosol to exploit the full potential of algae as green cell factories for non-native sesquiterpenoid generation. Identification of a prenyl transporter may be leveraged for further extending this capacity. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01910-5.
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25
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Einhaus A, Steube J, Freudenberg RA, Barczyk J, Baier T, Kruse O. Engineering a powerful green cell factory for robust photoautotrophic diterpenoid production. Metab Eng 2022; 73:82-90. [PMID: 35717002 DOI: 10.1016/j.ymben.2022.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/10/2022] [Accepted: 06/12/2022] [Indexed: 01/05/2023]
Abstract
Diterpenoids display a large and structurally diverse class of natural compounds mainly found as specialized plant metabolites. Due to their diverse biological functions they represent an essential source for various industrially relevant applications as biopharmaceuticals, nutraceuticals, and fragrances. However, commercial production utilizing their native hosts is inhibited by low abundances, limited cultivability, and challenging extraction, while the precise stereochemistry displays a particular challenge for chemical synthesis. Due to a high carbon flux through their native 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway towards photosynthetically active pigments, green microalgae hold great potential as efficient and sustainable heterologous chassis for sustainable biosynthesis of plant-derived diterpenoids. In this study, innovative synthetic biology and efficient metabolic engineering strategies were systematically combined to re-direct the metabolic flux through the MEP pathway for efficient heterologous diterpenoid synthesis in C. reinhardtii. Engineering of the 1-Deoxy-D-xylulose 5-phosphate synthase (DXS) as the main rate-limiting enzyme of the MEP pathway and overexpression of diterpene synthase fusion proteins increased the production of high-value diterpenoids. Applying fully photoautotrophic high cell density cultivations demonstrate potent and sustainable production of the high-value diterpenoid sclareol up to 656 mg L-1 with a maximal productivity of 78 mg L-1 day-1 in a 2.5 L scale photobioreactor, which is comparable to sclareol titers reached by highly engineered yeast. Consequently, this work represents a breakthrough in establishing a powerful phototrophic green cell factory for the competetive use in industrial biotechnology.
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Affiliation(s)
- Alexander Einhaus
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Jasmin Steube
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Robert Ansgar Freudenberg
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Jonas Barczyk
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Thomas Baier
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Olaf Kruse
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615, Bielefeld, Germany.
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26
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Abdallah MN, Wellman GB, Overmans S, Lauersen KJ. Combinatorial Engineering Enables Photoautotrophic Growth in High Cell Density Phosphite-Buffered Media to Support Engineered Chlamydomonas reinhardtii Bio-Production Concepts. Front Microbiol 2022; 13:885840. [PMID: 35633717 PMCID: PMC9141048 DOI: 10.3389/fmicb.2022.885840] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 03/28/2022] [Indexed: 12/15/2022] Open
Abstract
Chlamydomonas reinhardtii has emerged as a powerful green cell factory for metabolic engineering of sustainable products created from the photosynthetic lifestyle of this microalga. Advances in nuclear genome modification and transgene expression are allowing robust engineering strategies to be demonstrated in this host. However, commonly used lab strains are not equipped with features to enable their broader implementation in non-sterile conditions and high-cell density concepts. Here, we used combinatorial chloroplast and nuclear genome engineering to augment the metabolism of the C. reinhardtii strain UVM4 with publicly available genetic tools to enable the use of inorganic phosphite and nitrate as sole sources of phosphorous and nitrogen, respectively. We present recipes to create phosphite-buffered media solutions that enable high cell density algal cultivation. We then combined previously reported engineering strategies to produce the heterologous sesquiterpenoid patchoulol to high titers from our engineered green cell factories and show these products are possible to produce in non-sterile conditions. Our work presents a straightforward means to generate C. reinhardtii strains for broader application in bio-processes for the sustainable generation of products from green microalgae.
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Affiliation(s)
| | | | | | - Kyle J. Lauersen
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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27
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Abdallah MN, Wellman GB, Overmans S, Lauersen KJ. Combinatorial Engineering Enables Photoautotrophic Growth in High Cell Density Phosphite-Buffered Media to Support Engineered Chlamydomonas reinhardtii Bio-Production Concepts. Front Microbiol 2022; 13:885840. [PMID: 35633717 DOI: 10.1101/2022.02.28.482248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 03/28/2022] [Indexed: 05/28/2023] Open
Abstract
Chlamydomonas reinhardtii has emerged as a powerful green cell factory for metabolic engineering of sustainable products created from the photosynthetic lifestyle of this microalga. Advances in nuclear genome modification and transgene expression are allowing robust engineering strategies to be demonstrated in this host. However, commonly used lab strains are not equipped with features to enable their broader implementation in non-sterile conditions and high-cell density concepts. Here, we used combinatorial chloroplast and nuclear genome engineering to augment the metabolism of the C. reinhardtii strain UVM4 with publicly available genetic tools to enable the use of inorganic phosphite and nitrate as sole sources of phosphorous and nitrogen, respectively. We present recipes to create phosphite-buffered media solutions that enable high cell density algal cultivation. We then combined previously reported engineering strategies to produce the heterologous sesquiterpenoid patchoulol to high titers from our engineered green cell factories and show these products are possible to produce in non-sterile conditions. Our work presents a straightforward means to generate C. reinhardtii strains for broader application in bio-processes for the sustainable generation of products from green microalgae.
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Affiliation(s)
- Malak N Abdallah
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Gordon B Wellman
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sebastian Overmans
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Kyle J Lauersen
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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28
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New destination vectors facilitate Modular Cloning for Chlamydomonas. Curr Genet 2022; 68:531-536. [PMID: 35429260 PMCID: PMC9279246 DOI: 10.1007/s00294-022-01239-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/04/2022] [Accepted: 03/24/2022] [Indexed: 11/30/2022]
Abstract
Synthetic Biology is revolutionizing biological research by introducing principles of mechanical engineering, including the standardization of genetic parts and standardized part assembly routes. Both are realized in the Modular Cloning (MoClo) strategy. MoClo allows for the rapid and robust assembly of individual genes and multigene clusters, enabling iterative cycles of gene design, construction, testing, and learning in short time. This is particularly true if generation times of target organisms are short, as is the case for the unicellular green alga Chlamydomonas reinhardtii. Testing a gene of interest in Chlamydomonas with MoClo requires two assembly steps, one for the gene of interest itself and another to combine it with a selection marker. To reduce this to a single assembly step, we constructed five new destination vectors. They contain genes conferring resistance to commonly used antibiotics in Chlamydomonas and a site for the direct assembly of basic genetic parts. The vectors employ red/white color selection and, therefore, do not require costly compounds like X-gal and IPTG. mCherry expression is used to demonstrate the functionality of these vectors.
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29
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The Spermidine Synthase Gene SPD1: A Novel Auxotrophic Marker for Chlamydomonas reinhardtii Designed by Enhanced CRISPR/Cas9 Gene Editing. Cells 2022; 11:cells11050837. [PMID: 35269459 PMCID: PMC8909627 DOI: 10.3390/cells11050837] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/15/2022] [Accepted: 02/24/2022] [Indexed: 01/09/2023] Open
Abstract
Biotechnological application of the green microalga Chlamydomonas reinhardtii hinges on the availability of selectable markers for effective expression of multiple transgenes. However, biological safety concerns limit the establishment of new antibiotic resistance genes and until today, only a few auxotrophic markers exist for C. reinhardtii. The recent improvements in gene editing via CRISPR/Cas allow directed exploration of new endogenous selectable markers. Since editing frequencies remain comparably low, a Cas9-sgRNA ribonucleoprotein (RNP) delivery protocol was strategically optimized by applying nitrogen starvation to the pre-culture, which improved successful gene edits from 10% to 66% after pre-selection. Probing the essential polyamine biosynthesis pathway, the spermidine synthase gene (SPD1) is shown to be a potent selectable marker with versatile biotechnological applicability. Very low levels of spermidine (0.75 mg/L) were required to maintain normal mixotrophic and phototrophic growth in newly designed spermidine auxotrophic strains. Complementation of these strains with a synthetic SPD1 gene was achieved when the mature protein was expressed in the cytosol or targeted to the chloroplast. This work highlights the potential of new selectable markers for biotechnology as well as basic research and proposes an effective pipeline for the identification of new auxotrophies in C. reinhardtii.
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30
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Schroda M, Remacle C. Molecular Advancements Establishing Chlamydomonas as a Host for Biotechnological Exploitation. FRONTIERS IN PLANT SCIENCE 2022; 13:911483. [PMID: 35845675 PMCID: PMC9277225 DOI: 10.3389/fpls.2022.911483] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 06/07/2022] [Indexed: 05/13/2023]
Abstract
Chlamydomonas reinhardtii is emerging as a production platform for biotechnological purposes thanks to recent achievements, which we briefly summarize in this review. Firstly, robust nuclear transgene expression is now possible because several impressive improvements have been made in recent years. Strains allowing efficient and stable nuclear transgene expression are available and were recently made more amenable to rational biotechnological approaches by enabling genetic crosses and identifying their causative mutation. The MoClo synthetic biology strategy, based on Golden Gate cloning, was developed for Chlamydomonas and includes a growing toolkit of more than 100 genetic parts that can be robustly and rapidly assembled in a predefined order. This allows for rapid iterative cycles of transgene design, building, testing, and learning. Another major advancement came from various findings improving transgene design and expression such as the systematic addition of introns into codon-optimized coding sequences. Lastly, the CRISPR/Cas9 technology for genome editing has undergone several improvements since its first successful report in 2016, which opens the possibility of optimizing biosynthetic pathways by switching off competing ones. We provide a few examples demonstrating that all these recent developments firmly establish Chlamydomonas as a chassis for synthetic biology and allow the rewiring of its metabolism to new capabilities.
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Affiliation(s)
- Michael Schroda
- Molecular Biotechnology and Systems Biology, TU Kaiserslautern, Kaiserslautern, Germany
| | - Claire Remacle
- Genetics and Physiology of Microalgae, InBios/Phytosystems Research Unit, University of Liege, Liege, Belgium
- *Correspondence: Claire Remacle,
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31
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The Papain-like Cysteine Protease HpXBCP3 from Haematococcus pluvialis Involved in the Regulation of Growth, Salt Stress Tolerance and Chlorophyll Synthesis in Microalgae. Int J Mol Sci 2021; 22:ijms222111539. [PMID: 34768970 PMCID: PMC8583958 DOI: 10.3390/ijms222111539] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/21/2021] [Accepted: 10/25/2021] [Indexed: 12/16/2022] Open
Abstract
The papain-like cysteine proteases (PLCPs), the most important group of cysteine proteases, have been reported to participate in the regulation of growth, senescence, and abiotic stresses in plants. However, the functions of PLCPs and their roles in stress response in microalgae was rarely reported. The responses to different abiotic stresses in Haematococcus pluvialis were often observed, including growth regulation and astaxanthin accumulation. In this study, the cDNA of HpXBCP3 containing 1515 bp open reading frame (ORF) was firstly cloned from H. pluvialis by RT-PCR. The analysis of protein domains and molecular evolution showed that HpXBCP3 was closely related to AtXBCP3 from Arabidopsis. The expression pattern analysis revealed that it significantly responds to NaCl stress in H. pluvialis. Subsequently, transformants expressing HpXBCP3 in Chlamydomonas reinhardtii were obtained and subjected to transcriptomic analysis. Results showed that HpXBCP3 might affect the cell cycle regulation and DNA replication in transgenic Chlamydomonas, resulting in abnormal growth of transformants. Moreover, the expression of HpXBCP3 might increase the sensitivity to NaCl stress by regulating ubiquitin and the expression of WD40 proteins in microalgae. Furthermore, the expression of HpXBCP3 might improve chlorophyll content by up-regulating the expression of NADH-dependent glutamate synthases in C. reinhardtii. This study indicated for the first time that HpXBCP3 was involved in the regulation of cell growth, salt stress response, and chlorophyll synthesis in microalgae. Results in this study might enrich the understanding of PLCPs in microalgae and provide a novel perspective for studying the mechanism of environmental stress responses in H. pluvialis.
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32
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Vavitsas K, Kugler A, Satta A, Hatzinikolaou DG, Lindblad P, Fewer DP, Lindberg P, Toivari M, Stensjö K. Doing synthetic biology with photosynthetic microorganisms. PHYSIOLOGIA PLANTARUM 2021; 173:624-638. [PMID: 33963557 DOI: 10.1111/ppl.13455] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/22/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
The use of photosynthetic microbes as synthetic biology hosts for the sustainable production of commodity chemicals and even fuels has received increasing attention over the last decade. The number of studies published, tools implemented, and resources made available for microalgae have increased beyond expectations during the last few years. However, the tools available for genetic engineering in these organisms still lag those available for the more commonly used heterotrophic host organisms. In this mini-review, we provide an overview of the photosynthetic microbes most commonly used in synthetic biology studies, namely cyanobacteria, chlorophytes, eustigmatophytes and diatoms. We provide basic information on the techniques and tools available for each model group of organisms, we outline the state-of-the-art, and we list the synthetic biology tools that have been successfully used. We specifically focus on the latest CRISPR developments, as we believe that precision editing and advanced genetic engineering tools will be pivotal to the advancement of the field. Finally, we discuss the relative strengths and weaknesses of each group of organisms and examine the challenges that need to be overcome to achieve their synthetic biology potential.
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Affiliation(s)
- Konstantinos Vavitsas
- Enzyme and Microbial Biotechnology Unit, Department of Biology, National and Kapodistrian University of Athens, Zografou Campus, Athens, Greece
| | - Amit Kugler
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Alessandro Satta
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
- CSIRO Synthetic Biology Future Science Platform, Brisbane, Australia
| | - Dimitris G Hatzinikolaou
- Enzyme and Microbial Biotechnology Unit, Department of Biology, National and Kapodistrian University of Athens, Zografou Campus, Athens, Greece
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - David P Fewer
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Pia Lindberg
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Mervi Toivari
- VTT, Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Karin Stensjö
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
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