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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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2
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Zadabbas Shahabadi H, Akbarzadeh A, Ofoghi H, Kadkhodaei S. Site-specific gene knock-in and bacterial phytase gene expression in Chlamydomonas reinhardtii via Cas9 RNP-mediated HDR. FRONTIERS IN PLANT SCIENCE 2023; 14:1150436. [PMID: 37275253 PMCID: PMC10235511 DOI: 10.3389/fpls.2023.1150436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/28/2023] [Indexed: 06/07/2023]
Abstract
In the present study, we applied the HDR (homology-directed DNA repair) CRISPR-Cas9-mediated knock-in system to accurately insert an optimized foreign bacterial phytase gene at a specific site of the nitrate reductase (NR) gene (exon 2) to achieve homologous recombination with the stability of the transgene and reduce insertion site effects or gene silencing. To this end, we successfully knocked-in the targeted NR gene of Chlamydomonas reinhardtii using the bacterial phytase gene cassette through direct delivery of the CRISPR/Cas9 system as the ribonucleoprotein (RNP) complex consisting of Cas9 protein and the specific single guide RNAs (sgRNAs). The NR insertion site editing was confirmed by PCR and sequencing of the transgene positive clones. Moreover, 24 clones with correct editing were obtained, where the phytase gene cassette was located in exon 2 of the NR gene, and the editing efficiency was determined to be 14.81%. Additionally, site-specific gene expression was analyzed and confirmed using RT-qPCR. Cultivation of the positive knocked-in colonies on the selective media during 10 generations indicated the stability of the correct editing without gene silencing or negative insertion site effects. Our results demonstrated that CRISPR-Cas9-mediated knock-in could be applied for nuclear expression of the heterologous gene of interest, and also confirmed its efficacy as an effective tool for site-specific gene knock-in, avoiding nuclear positional effects and gene silencing in C. reinhardtii. These findings could also provide a new perspective on the advantageous application of RNP-CRISPR/Cas9 gene-editing to accelerate the commercial production of complex recombinant proteins in the food-grade organism "C. reinhardtii".
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Affiliation(s)
- Hassan Zadabbas Shahabadi
- Department of Fisheries, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran
- Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
- Agricultural Biotechnology Research Institute of Iran (ABRII), Isfahan Branch, Agricultural Research, Education and Extension Organization (AREEO), Isfahan, Iran
| | - Arash Akbarzadeh
- Department of Fisheries, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran
| | - Hamideh Ofoghi
- Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
| | - Saeid Kadkhodaei
- Agricultural Biotechnology Research Institute of Iran (ABRII), Isfahan Branch, Agricultural Research, Education and Extension Organization (AREEO), Isfahan, Iran
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3
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Chen H, Yang QL, Xu JX, Deng X, Zhang YJ, Liu T, Rots MG, Xu GL, Huang KY. Efficient methods for multiple types of precise gene-editing in Chlamydomonas. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 37310200 DOI: 10.1111/tpj.16265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/20/2023] [Accepted: 04/26/2023] [Indexed: 06/14/2023]
Abstract
Precise gene-editing using CRISPR/Cas9 technology remains a long-standing challenge, especially for genes with low expression and no selectable phenotypes in Chlamydomonas reinhardtii, a classic model for photosynthesis and cilia research. Here, we developed a multi-type and precise genetic manipulation method in which a DNA break was generated by Cas9 nuclease and the repair was mediated using a homologous DNA template. The efficacy of this method was demonstrated for several types of gene editing, including inactivation of two low-expression genes (CrTET1 and CrKU80), the introduction of a FLAG-HA epitope tag into VIPP1, IFT46, CrTET1 and CrKU80 genes, and placing a YFP tag into VIPP1 and IFT46 for live-cell imaging. We also successfully performed a single amino acid substitution for the FLA3, FLA10 and FTSY genes, and documented the attainment of the anticipated phenotypes. Lastly, we demonstrated that precise fragment deletion from the 3'-UTR of MAA7 and VIPP1 resulted in a stable knock-down effect. Overall, our study has established efficient methods for multiple types of precise gene editing in Chlamydomonas, enabling substitution, insertion and deletion at the base resolution, thus improving the potential of this alga in both basic research and industrial applications.
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Affiliation(s)
- Hui Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Qing-Lin Yang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jia-Xi Xu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuan Deng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yun-Jie Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Ting Liu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Marianne G Rots
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, The Netherlands
| | - Guo-Liang Xu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Shanghai Key Laboratory of Medical Epigenetics, Laboratory of Cancer Epigenetics, Institutes of Biomedical Sciences, Medical College of Fudan University, Chinese Academy of Medical Sciences (RU069), Shanghai, China
| | - Kai-Yao Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
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In Silico Identification of Cassava Genome-Encoded MicroRNAs with Predicted Potential for Targeting the ICMV-Kerala Begomoviral Pathogen of Cassava. Viruses 2023; 15:v15020486. [PMID: 36851701 PMCID: PMC9963618 DOI: 10.3390/v15020486] [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: 12/10/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Cassava mosaic disease (CMD) is caused by several divergent species belonging to the genus Begomovirus (Geminiviridae) transmitted by the whitefly Bemisia tabaci cryptic species group. In India and other parts of Asia, the Indian cassava mosaic virus-Kerala (ICMV-Ker) is an emergent begomovirus of cassava causing damage that results in reduced yield loss and tuber quality. Double-stranded RNA-mediated interference (RNAi) is an evolutionary conserved mechanism in eukaryotes and highly effective, innate defense system to inhibit plant viral replication and/or translation. The objective of this study was to identify and characterize cassava genome-encoded microRNAs (mes-miRNA) that are predicted to target ICMV-Ker ssDNA-encoded mRNAs, based on four in silico algorithms: miRanda, RNA22, Tapirhybrid, and psRNA. The goal is to deploy the predicted miRNAs to trigger RNAi and develop cassava plants with resistance to ICMV-Ker. Experimentally validated mature cassava miRNA sequences (n = 175) were downloaded from the miRBase biological database and aligned with the ICMV-Ker genome. The miRNAs were evaluated for base-pairing with the cassava miRNA seed regions and to complementary binding sites within target viral mRNAs. Among the 175 locus-derived mes-miRNAs evaluated, one cassava miRNA homolog, mes-miR1446a, was identified to have a predicted miRNA target binding site, at position 2053 of the ICMV-Ker genome. To predict whether the cassava miRNA might bind predicted ICMV-Ker mRNA target(s) that could disrupt viral infection of cassava plants, a cassava locus-derived miRNA-mRNA regulatory network was constructed using Circos software. The in silico-predicted cassava locus-derived mes-miRNA-mRNA network corroborated interactions between cassava mature miRNAs and the ICMV-Ker genome that warrant in vivo analysis, which could lead to the development of ICMV-Ker resistant cassava plants.
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Jeena GS, Singh N, Shukla RK. An insight into microRNA biogenesis and its regulatory role in plant secondary metabolism. PLANT CELL REPORTS 2022; 41:1651-1671. [PMID: 35579713 DOI: 10.1007/s00299-022-02877-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
The present review highlights the regulatory roles of microRNAs in plant secondary metabolism and focuses on different bioengineering strategies to modulate secondary metabolite content in plants. MicroRNAs (miRNAs) are the class of small endogenous, essential, non-coding RNAs that riboregulate the gene expression involved in various biological processes in most eukaryotes. MiRNAs has emerged as important regulators in plants that function by silencing target genes through cleavage or translational inhibition. These miRNAs plays an important role in a wide range of plant biological and metabolic processes, including plant development and various environmental response controls. Several important plant secondary metabolites like alkaloids, terpenoids, and phenolics are well studied for their function in plant defense against different types of pests and herbivores. Due to the presence of a wide range of biological and pharmaceutical properties of plant secondary metabolites, it is important to study the regulation of their biosynthetic pathways. The contribution of miRNAs in regulating plant secondary metabolism is not well explored. Recent advancements in molecular techniques have improved our knowledge in understanding the molecular function of genes, proteins, enzymes, and small RNAs involved in different steps of secondary metabolic pathways. In the present review, we have discussed the recent progress made on miRNA biogenesis, its regulation, and highlighted the current research developed in the field of identification, analysis, and characterizations of various miRNAs that regulate plant secondary metabolism. We have also discussed how different bioengineering strategies such as artificial miRNA (amiRNA), endogenous target mimicry, and CRISPR/Cas9 could be utilized to enhance the secondary metabolite production in plants.
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Affiliation(s)
- Gajendra Singh Jeena
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), P.O. CIMAP, Near Kukrail Picnic Spot, Lucknow, 226015, India
| | - Neeti Singh
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), P.O. CIMAP, Near Kukrail Picnic Spot, Lucknow, 226015, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
| | - Rakesh Kumar Shukla
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), P.O. CIMAP, Near Kukrail Picnic Spot, Lucknow, 226015, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India.
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Singh M, Mal N, Mohapatra R, Bagchi T, Parambath SD, Chavali M, Rao KM, Ramanaiah SV, Kadier A, Kumar G, Chandrasekhar K, Kim SH. Recent biotechnological developments in reshaping the microalgal genome: A signal for green recovery in biorefinery practices. CHEMOSPHERE 2022; 293:133513. [PMID: 34990720 DOI: 10.1016/j.chemosphere.2022.133513] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 12/13/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
The use of renewable energy sources as a substitute for nonrenewable fossil fuels is urgently required. Algae biorefinery platform provides an excellent alternate to overcome future energy problems. However, to let this viable biomass be competent with existing feedstocks, it is necessary to exploit genetic manipulation and improvement in upstream and downstream platforms for optimal bio-product recovery. Furthermore, the techno-economic strategies further maximize metabolites production for biofuel, biohydrogen, and other industrial applications. The experimental methodologies in algal photobioreactor promote high biomass production, enriched in lipid and starch content in limited environmental conditions. This review presents an optimization framework combining genetic manipulation methods to simulate microalgal growth dynamics, understand the complexity of algal biorefinery to scale up, and identify green strategies for techno-economic feasibility of algae for biomass conversion. Overall, the algal biorefinery opens up new possibilities for the valorization of algae biomass and the synthesis of various novel products.
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Affiliation(s)
- Meenakshi Singh
- Department of Botany, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, 390002, Gujarat, India
| | - Navonil Mal
- Department of Botany, University of Calcutta, Kolkata, 700019, West Bengal, India
| | - Reecha Mohapatra
- Department of Life Sciences, NIT Rourkela, 769008, Odisha, India
| | - Trisha Bagchi
- Department of Botany, West Bengal State University, Barasat, 700126, West Bengal, India
| | | | - Murthy Chavali
- Office of the Dean (Research) & Division of Chemistry, Department of Science, Faculty of Science & Technology, Alliance University (Central Campus), Chandapura-Anekal Main Road, Bengaluru, 562106, Karnataka, India; NTRC-MCETRC and 109 Nano Composite Technologies Pvt. Ltd., Guntur District, 522201, Andhra Pradesh, India
| | - Kummara Madhusudana Rao
- School of Chemical Engineering, Yeungnam University, 280 Daehak-ro, Joyeong-dong, Gyeongsan-si, Gyeongsangbuk-do, 38541, South Korea; Department of Automotive Lighting Convergence Engineering, Yeungnam University, 280 Daehak-ro, Joyeong-dong, Gyeongsan-si, Gyeongsangbuk-do, 38541, South Korea
| | - S V Ramanaiah
- Food and Biotechnology Research Lab, South Ural State University (National Research University), 454080, Chelyabinsk, Russian Federation
| | - Abudukeremu Kadier
- Laboratory of Environmental Science and Technology, The Xinjiang Technical Institute of Physics and Chemistry, Key Laboratory of Functional Materials and Devices for Special Environments, Chinese Academy of Sciences, Urumqi, 830011, China; Center of Material and Opto-electronic Research, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Gopalakrishnan Kumar
- Institute of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, 4036, Stavanger, Norway
| | - K Chandrasekhar
- School of Civil and Environmental Engineering, Yonsei University, Seoul, 03722, Republic of Korea.
| | - Sang-Hyoun Kim
- School of Civil and Environmental Engineering, Yonsei University, Seoul, 03722, Republic of Korea.
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Insertional mutagenesis in Chlamydomonas reinhardtii: An effective strategy for the identification of new genes involved in the DNA damage response. Eur J Protistol 2021; 82:125855. [PMID: 34954500 DOI: 10.1016/j.ejop.2021.125855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 11/23/2022]
Abstract
The formation of double-strand breaks in DNA represents a serious stress for all types of organisms and requires a precisely regulated and organized DNA damage response (DDR) to maintain genetic information and genome integrity. Chlamydomonas reinhardtii possesses the characteristics of both plants and animals and is therefore suitable for the identification of novel genes connected to a wide spectrum of metabolic pathways, including DDR. One very effective tool for the detection and subsequent characterization of new mutants in C. reinhardtii is insertional mutagenesis. We isolated several insertion mutants sensitive to DNA-damaging agents that had disrupted or completely deleted genes with putative functions in the DDR. In most of the analysed mutants, we identified various changes at both ends and even inside the inserted cassette. Using recent information from databases, we were also able to supplement the characteristics of the previously described mutant with a pleiotropic phenotype. In addition, we confirmed the effectiveness of hairpin-PCR as a strategy for the identification of insertion flanking sites and as a tool for the detection of changes at the site of insertion, thus enabling a better understanding of insertion events.
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8
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Akella S, Ma X, Bacova R, Harmer ZP, Kolackova M, Wen X, Wright DA, Spalding MH, Weeks DP, Cerutti H. Co-targeting strategy for precise, scarless gene editing with CRISPR/Cas9 and donor ssODNs in Chlamydomonas. PLANT PHYSIOLOGY 2021; 187:2637-2655. [PMID: 34618092 PMCID: PMC8644747 DOI: 10.1093/plphys/kiab418] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/30/2021] [Indexed: 05/20/2023]
Abstract
Programmable site-specific nucleases, such as the clustered regularly interspaced short palindromic repeat (CRISPR)/ CRISPR-associated protein 9 (Cas9) ribonucleoproteins (RNPs), have allowed creation of valuable knockout mutations and targeted gene modifications in Chlamydomonas (Chlamydomonas reinhardtii). However, in walled strains, present methods for editing genes lacking a selectable phenotype involve co-transfection of RNPs and exogenous double-stranded DNA (dsDNA) encoding a selectable marker gene. Repair of the dsDNA breaks induced by the RNPs is usually accompanied by genomic insertion of exogenous dsDNA fragments, hindering the recovery of precise, scarless mutations in target genes of interest. Here, we tested whether co-targeting two genes by electroporation of pairs of CRISPR/Cas9 RNPs and single-stranded oligodeoxynucleotides (ssODNs) would facilitate the recovery of precise edits in a gene of interest (lacking a selectable phenotype) by selection for precise editing of another gene (creating a selectable marker)-in a process completely lacking exogenous dsDNA. We used PPX1 (encoding protoporphyrinogen IX oxidase) as the generated selectable marker, conferring resistance to oxyfluorfen, and identified precise edits in the homolog of bacterial ftsY or the WD and TetratriCopeptide repeats protein 1 genes in ∼1% of the oxyfluorfen resistant colonies. Analysis of the target site sequences in edited mutants suggested that ssODNs were used as templates for DNA synthesis during homology directed repair, a process prone to replicative errors. The Chlamydomonas acetolactate synthase gene could also be efficiently edited to serve as an alternative selectable marker. This transgene-free strategy may allow creation of individual strains containing precise mutations in multiple target genes, to study complex cellular processes, pathways, or structures.
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Affiliation(s)
- Soujanya Akella
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska–Lincoln, Lincoln, Nebraska 68588, USA
| | - Xinrong Ma
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska–Lincoln, Lincoln, Nebraska 68588, USA
| | - Romana Bacova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic
| | - Zachary P Harmer
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska–Lincoln, Lincoln, Nebraska 68588, USA
| | - Martina Kolackova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic
| | - Xiaoxue Wen
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska–Lincoln, Lincoln, Nebraska 68588, USA
| | - David A Wright
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Martin H Spalding
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Donald P Weeks
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - Heriberto Cerutti
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska–Lincoln, Lincoln, Nebraska 68588, USA
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Bacova R, Kolackova M, Klejdus B, Adam V, Huska D. Epigenetic mechanisms leading to genetic flexibility during abiotic stress responses in microalgae: A review. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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10
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Effect of biphasic temperature regime on therapeutic recombinant protein production in the green alga Chlamydomonas reinhardtii. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101997] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Fabris M, Abbriano RM, Pernice M, Sutherland DL, Commault AS, Hall CC, Labeeuw L, McCauley JI, Kuzhiuparambil U, Ray P, Kahlke T, Ralph PJ. Emerging Technologies in Algal Biotechnology: Toward the Establishment of a Sustainable, Algae-Based Bioeconomy. FRONTIERS IN PLANT SCIENCE 2020; 11:279. [PMID: 32256509 PMCID: PMC7090149 DOI: 10.3389/fpls.2020.00279] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/24/2020] [Indexed: 05/18/2023]
Abstract
Mankind has recognized the value of land plants as renewable sources of food, medicine, and materials for millennia. Throughout human history, agricultural methods were continuously modified and improved to meet the changing needs of civilization. Today, our rapidly growing population requires further innovation to address the practical limitations and serious environmental concerns associated with current industrial and agricultural practices. Microalgae are a diverse group of unicellular photosynthetic organisms that are emerging as next-generation resources with the potential to address urgent industrial and agricultural demands. The extensive biological diversity of algae can be leveraged to produce a wealth of valuable bioproducts, either naturally or via genetic manipulation. Microalgae additionally possess a set of intrinsic advantages, such as low production costs, no requirement for arable land, and the capacity to grow rapidly in both large-scale outdoor systems and scalable, fully contained photobioreactors. Here, we review technical advancements, novel fields of application, and products in the field of algal biotechnology to illustrate how algae could present high-tech, low-cost, and environmentally friendly solutions to many current and future needs of our society. We discuss how emerging technologies such as synthetic biology, high-throughput phenomics, and the application of internet of things (IoT) automation to algal manufacturing technology can advance the understanding of algal biology and, ultimately, drive the establishment of an algal-based bioeconomy.
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Affiliation(s)
- Michele Fabris
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
- CSIRO Synthetic Biology Future Science Platform, Brisbane, QLD, Australia
| | - Raffaela M. Abbriano
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
| | - Mathieu Pernice
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
| | - Donna L. Sutherland
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
| | - Audrey S. Commault
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
| | - Christopher C. Hall
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
| | - Leen Labeeuw
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
| | - Janice I. McCauley
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
| | | | - Parijat Ray
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
| | - Tim Kahlke
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
| | - Peter J. Ralph
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
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Ashraf F, Ashraf MA, Hu X, Zhang S. A novel computational approach to the silencing of Sugarcane Bacilliform Guadeloupe A Virus determines potential host-derived MicroRNAs in sugarcane ( Saccharum officinarum L.). PeerJ 2020; 8:e8359. [PMID: 31976180 PMCID: PMC6964690 DOI: 10.7717/peerj.8359] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 12/05/2019] [Indexed: 01/24/2023] Open
Abstract
Sugarcane Bacilliform Guadeloupe A Virus (SCBGAV, genus Badnavirus, family Caulimoviridae) is an emerging, deleterious pathogen of sugarcane which presents a substantial barrier to producing high sugarcane earnings. Sugarcane bacilliform viruses (SCBVs) are one of the main species that infect sugarcane. During the last 30 years, significant genetic changes in SCBV strains have been observed with a high risk of disease incidence associated with crop damage. SCBV infection may lead to significant losses in biomass production in susceptible sugarcane cultivars. The circular, double-stranded (ds) DNA genome of SCBGAV (7.4 Kb) is composed of three open reading frames (ORFs) on the positive strand that replicate by a reverse transcriptase. SCBGAV can infect sugarcane in a semipersistent manner via the insect vectors sugarcane mealybug species. In the current study, we used miRNA target prediction algorithms to identify and comprehensively analyze the genome-wide sugarcane (Saccharum officinarum L.)-encoded microRNA (miRNA) targets against the SCBGAV. Mature miRNA target sequences were retrieved from the miRBase (miRNA database) and were further analyzed for hybridization to the SCBGAV genome. Multiple computational approaches—including miRNA-target seed pairing, multiple target positions, minimum free energy, target site accessibility, maximum complementarity, pattern recognition and minimum folding energy for attachments—were considered by all algorithms. Among them, sof-miR396 was identified as the top effective candidate, capable of targeting the vital ORF3 of the SCBGAV genome. miRanda, RNA22 and RNAhybrid algorithms predicted hybridization of sof-miR396 at common locus position 3394. The predicted sugarcane miRNAs against viral mRNA targets possess antiviral activities, leading to translational inhibition by mRNA cleavage. Interaction network of sugarcane-encoded miRNAs with SCBGAV genes, created using Circos, allow analyze new targets. The finding of the present study acts as a first step towards the creation of SCBGAV-resistant sugarcane through the expression of the identified miRNAs.
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Affiliation(s)
- Fakiha Ashraf
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Muhammad Aleem Ashraf
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.,Department of Plant Breeding and Genetics, University College of Agriculture and Environmental Sciences, Islamia University of Bahawalpur, Baghdad-Ul-Jadeed Campus, Bahwalpur, Pakistan
| | - Xiaowen Hu
- Zhanjiang Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guandong, China
| | - Shuzhen Zhang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
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Anwar M, Lou S, Chen L, Li H, Hu Z. Recent advancement and strategy on bio-hydrogen production from photosynthetic microalgae. BIORESOURCE TECHNOLOGY 2019; 292:121972. [PMID: 31444119 DOI: 10.1016/j.biortech.2019.121972] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 08/06/2019] [Accepted: 08/07/2019] [Indexed: 06/10/2023]
Abstract
Recently, ensuring energy security is a key challenge to political and economic strength in the world. Bio-hydrogen production from microalgae is the promising alternative source for potential renewable and self-sustainability energy but still in the initial phase of development. Practically and sustainability of microalgae hydrogen production is still debatable. The genetic engineering and metabolic pathway engineering of hydrogenase and nitrogenase play a key role to enhance hydrogen production. Microalgae have photosynthetic efficiency and synthesize huge carbohydrate biomass, used as 4th generation feedstock to generate bio-hydrogen. Recent genetically modified strains of microalgae are the attractive source for enhancing bio-hydrogen production in the future. The potential of hydrogen production from microRNAs are gaining great interest of researcher. The main objective of this review is attentive discussed recent approaches on new molecular genetics engineering and metabolic pathway developments, modern photo-bioreactors efficiency, economic assessment, limitations and knowledge gap of bio-hydrogen production from microalgae.
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Affiliation(s)
- Muhammad Anwar
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, People's Republic of China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, People's Republic of China
| | - Sulin Lou
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, People's Republic of China
| | - Liu Chen
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, People's Republic of China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, People's Republic of China
| | - Hui Li
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, People's Republic of China; Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen 518060, People's Republic of China
| | - Zhangli Hu
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, People's Republic of China; Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen 518060, People's Republic of China.
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Methyl jasmonate treatment affects the regulation of the 2-C-methyl-D-erythritol 4-phosphate pathway and early steps of the triterpenoid biosynthesis in Chlamydomonas reinhardtii. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101462] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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15
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Navarro FJ, Baulcombe DC. miRNA-Mediated Regulation of Synthetic Gene Circuits in the Green Alga Chlamydomonas reinhardtii. ACS Synth Biol 2019; 8:358-370. [PMID: 30624905 DOI: 10.1021/acssynbio.8b00393] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
MicroRNAs (miRNAs), small RNA molecules of 20-24 nts, have many features that make them useful tools for gene expression regulation-small size, flexible design, target predictability, and action at a late stage of the gene expression pipeline. In addition, their role in fine-tuning gene expression can be harnessed to increase robustness of synthetic gene networks. In this work, we apply a synthetic biology approach to characterize miRNA-mediated gene expression regulation in the unicellular green alga Chlamydomonas reinhardtii. This characterization is then used to build tools based on miRNAs, such as synthetic miRNAs, miRNA-responsive 3'UTRs, miRNA decoys, and self-regulatory loops. These tools will facilitate the engineering of gene expression for new applications and improved traits in this alga.
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Affiliation(s)
- Francisco J. Navarro
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - David C. Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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Bt Md Nasir NAN, Islam AKMA, Anuar N, Yaakob Z. Genetic Improvement and Challenges for Cultivation of Microalgae for Biodiesel: A Review. MINI-REV ORG CHEM 2019. [DOI: 10.2174/1570193x15666180627115502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Microalgae are a viable alternative for biofuel production to replace the world dependency on
fossil fuel. It has a wide range of application for the sustainable production of biomaterials. Microalgae
can convert solar energy into important natural components by utilizing marginal nutrients, wastewater
and exhaust CO2 without sharing expensive crop field. Microalgae also have the potentiality to generate
several promising components such as Polyunsaturated Fatty Acids (PUFAs), organic pigments and
pharmaceutically important hydrocarbons. Cultivation and production of microalgae biomass have multifaceted
challenges due to the requirement of large volume of water for the algae growth, high processing
cost and contamination by pathogens. Genetic improvement and modifications are essential to
construct superior microalgae for manufacturing industries using various methods such as selection of
novel strain, stress tolerance, resistance to pathogens, product development and metabolic pathways and
cellular contents. In addition, technologies related to cultivation, harvesting, extraction and processing
are essential to develop for the growth of novel microalgae strains.
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Affiliation(s)
- Nor-Anis N. Bt Md Nasir
- Department of Plant Science, Kulliyyah of Science, International Islamic University Malaysia, Kuantan Kampus, 25710, Kuantan, Pahang Darul Makmur, Malaysia
| | - A. K. M. Aminul Islam
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Nurina Anuar
- Department of Chemical and Process Engineering, Faculty of Engineering & Built Environment, Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor, 43600, Malaysia
| | - Zahira Yaakob
- Department of Chemical and Process Engineering, Faculty of Engineering & Built Environment, Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor, 43600, Malaysia
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17
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Liang MH, Wang L, Wang Q, Zhu J, Jiang JG. High-value bioproducts from microalgae: Strategies and progress. Crit Rev Food Sci Nutr 2018; 59:2423-2441. [PMID: 29676930 DOI: 10.1080/10408398.2018.1455030] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Microalgae have been considered as alternative sustainable resources for high-value bioproducts such as lipids (especially triacylglycerides [TAGs]), polyunsaturated fatty acids (PUFAs), and carotenoids, due to their relatively high photosynthetic efficiency, no arable land requirement, and ease of scale-up. It is of great significance to exploit microalgae for the production of high-value bioproducts. How to improve the content or productivity of specific bioproducts has become one of the most urgent challenges. In this review, we will describe high-value bioproducts from microalgae and their biosynthetic pathways (mainly for lipids, PUFAs, and carotenoids). Recent progress and strategies for the enhanced production of bioproducts from microalgae are also described in detail, and these strategies take advantages of optimized cultivation conditions with abiotic stress, chemical stress (addition of metabolic precursors, phytohormones, chemical inhibitors, and chemicals inducing oxidative stress response), and molecular approaches such as metabolic engineering, transcriptional engineering, and gene disruption strategies (mainly RNAi, antisense RNA, miRNA-based knockdown, and CRISPR/Cas9).
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Affiliation(s)
- Ming-Hua Liang
- a College of Food Science and Engineering, South China University of Technology , Guangzhou , China
| | - Ling Wang
- b School of Biotechnology, Jiangsu University of Science and Technology , Zhenjiang , China
| | - Qiming Wang
- c College of Bioscience and Biotechnology, Hunan Agricultural University , Changsha , China
| | - Jianhua Zhu
- b School of Biotechnology, Jiangsu University of Science and Technology , Zhenjiang , China.,c College of Bioscience and Biotechnology, Hunan Agricultural University , Changsha , China.,d Department of Plant Science and Landscape Architecture, University of Maryland , College Park , Maryland , USA
| | - Jian-Guo Jiang
- a College of Food Science and Engineering, South China University of Technology , Guangzhou , China
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18
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Lou S, Sun T, Li H, Hu Z. Mechanisms of microRNA-mediated gene regulation in unicellular model alga Chlamydomonas reinhardtii. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:244. [PMID: 30202439 PMCID: PMC6129010 DOI: 10.1186/s13068-018-1249-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/31/2018] [Indexed: 05/30/2023]
Abstract
MicroRNAs are a class of endogenous non-coding RNAs that play a vital role in post-transcriptional gene regulation in eukaryotic cells. In plants and animals, miRNAs are implicated in diverse roles ranging from immunity against viral infections, developmental pathways, molecular pathology of cancer and regulation of protein expression. However, the role of miRNAs in the unicellular model green alga Chlamydomonas reinhardtii remains unclear. The mode of action of miRNA-induced gene silencing in C. reinhardtii is very similar to that of higher eukaryotes, in terms of the activation of the RNA-induced silencing complex and mRNA targeting. Certain studies indicate that destabilization of mRNAs and mRNA turnover could be the major possible functions of miRNAs in eukaryotic algae. Here, we summarize recent findings that have advanced our understanding of miRNA regulatory mechanisms in C. reinhardtii.
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Affiliation(s)
- Sulin Lou
- Guangdong Key Laboratory of Plant Epigenetics, Guangdong Engineering Research Center for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Key Laboratory of Optoeletronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoeletronic Engineering, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Ting Sun
- Guangdong Key Laboratory of Plant Epigenetics, Guangdong Engineering Research Center for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Key Laboratory of Optoeletronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoeletronic Engineering, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Hui Li
- Guangdong Key Laboratory of Plant Epigenetics, Guangdong Engineering Research Center for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Zhangli Hu
- Guangdong Key Laboratory of Plant Epigenetics, Guangdong Engineering Research Center for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
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Petchthai U, Yee CSL, Wong SM. Resistance to CymMV and ORSV in artificial microRNA transgenic Nicotiana benthamiana plants. Sci Rep 2018; 8:9958. [PMID: 29967431 PMCID: PMC6028384 DOI: 10.1038/s41598-018-28388-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/20/2018] [Indexed: 12/23/2022] Open
Abstract
Transgenic plants expressing artificial microRNAs (amiRNAs) have been shown to confer specific resistance to corresponding viruses. Here, we generated Nicotiana benthamiana transgenic lines containing Oryza sativa miR528 as backbone, expressing amiRNAs targeting RNA-dependent RNA polymerase (RdRp) gene of Cymbidium mosaic virus (CymMV) and Odontoglossum ringspot virus (ORSV). The amiRNA transgenic lines could express amiR-CymMV and confer high percentage resistance to CymMV, while lack of detectable level of amiR-ORSV expression in amiR-ORSV transgenic N. benthamiana plants led to weak resistance to ORSV infection. In this project, we provide the first report of CymMV-resistant transgenic N. benthamiana plants based on amiRNA strategy. We believe that this amiRNA approach can be extended to generate CymMV-resistant transgenic orchids.
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Affiliation(s)
- Udomporn Petchthai
- Department of Biological Sciences, National University of Singapore, Singapore, 119543, Singapore
| | - Celestine Shi Le Yee
- Department of Biological Sciences, National University of Singapore, Singapore, 119543, Singapore
| | - Sek-Man Wong
- Department of Biological Sciences, National University of Singapore, Singapore, 119543, Singapore.
- Temasek Life Sciences Laboratory, Singapore, 117604, Singapore.
- National University of Singapore Research Institute in Suzhou, Jiangsu, 215123, P.R. China.
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20
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Chemical Screening for Flagella-Associated Phenotypes in Chlamydomonas reinhardtii. Methods Mol Biol 2018. [PMID: 29846930 DOI: 10.1007/978-1-4939-7874-8_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Flagella of the unicellular green alga Chlamydomonas reinhardtii are nearly identical to cilia of vertebrate cells and provide an excellent model to study ciliogenesis. Cilia and flagella are important organelles used for motility and sensing the extracellular environment. Abnormalities in cilia structure or ciliary dysfunction can have devastating consequences ranging from diabetes and obesity to polycystic kidney disease and mental retardation. Small-molecule inhibitor libraries can be used to screen for flagellum-associated phenotypes in assembly, length, motility, deflagellation, and cellular toxicity. These phenotypes can be assessed from direct microscopic visualization and custom-designed assays. These methods identify fundamental regulators of ciliary biology as well as potential therapeutic interventions for ciliopathies.
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Li H, Liu Y, Wang Y, Chen M, Zhuang X, Wang C, Wang J, Hu Z. Improved photobio-H 2 production regulated by artificial miRNA targeting psbA in green microalga Chlamydomonas reinhardtii. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:36. [PMID: 29449884 PMCID: PMC5808451 DOI: 10.1186/s13068-018-1030-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 01/23/2018] [Indexed: 06/01/2023]
Abstract
BACKGROUND Sulfur-deprived cultivation of Chlamydomonas reinhardtii, referred as "two-stage culture" transferring the cells from regular algal medium to sulfur-deplete one, has been extensively studied to improve photobio-H2 production in this green microalga. During sulfur-deprivation treatment, the synthesis of a key component of photosystem II complex, D1 protein, was inhibited and improved photobio-H2 production could be established in C. reinhardtii. However, separation of algal cells from a regular liquid culture medium to a sulfur-deprived one is not only a discontinuous process, but also a cost- and time-consuming operation. More applicable and economic alternatives for sustained H2 production by C. reinhardtii are still highly required. RESULTS In the present study, a significant improvement in photobio-H2 production was observed in the transgenic green microalga C. reinhardtii, which employed a newly designed strategy based on a heat-inducible artificial miRNA (amiRNA) expression system targeting D1-encoded gene, psbA. A transgenic algal strain referred as "amiRNA-D1" has been successfully obtained by transforming the expression vector containing a heat-inducible promoter. After heat shock conducted in the same algal cultures, the expression of amiRNA-D1 was detected increased 15-fold accompanied with a 73% decrease of target gene psbA. More interestingly, this transgenic alga accumulated about 60% more H2 content than the wild-type strain CC-849 at the end of 7-day cultivation. CONCLUSIONS The photobio-H2 production in the engineered transgenic alga was significantly improved. Without imposing any nutrient-deprived stress, this novel strategy provided a convenient and efficient way for regulation of photobio-H2 production in green microalga by simply "turn on" the expression of a designed amiRNA.
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Affiliation(s)
- Hui Li
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Yanmei Liu
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Yuting Wang
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Meirong Chen
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Xiaoshan Zhuang
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Chaogang Wang
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Jiangxin Wang
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Zhangli Hu
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
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Wang Y, Zhuang X, Chen M, Zeng Z, Cai X, Li H, Hu Z. An endogenous microRNA (miRNA1166.1) can regulate photobio-H 2 production in eukaryotic green alga Chlamydomonas reinhardtii. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:126. [PMID: 29743954 PMCID: PMC5930490 DOI: 10.1186/s13068-018-1126-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/20/2018] [Indexed: 05/12/2023]
Abstract
BACKGROUND Hydrogen photoproduction from green microalgae is regarded as a promising alternative solution for energy problems. However, the simultaneous oxygen evolution from microalgae can prevent continuous hydrogen production due to the hypersensitivity of hydrogenases to oxygen. Sulfur deprivation can extend the duration of algal hydrogen production, but it is uneconomical to alternately culture algal cells in sulfur-sufficient and sulfur-deprived media. RESULTS In this study, we developed a novel way to simulate sulfur-deprivation treatment while constantly maintaining microalgal cells in sulfur-sufficient culture medium by overexpressing an endogenous microRNA (miR1166.1). Based on our previous RNA-seq analysis in the model green alga Chlamydomonas reinhardtii, three endogenous miRNAs responsive to sulfur deprivation (cre-miR1166.1, cre-miR1150.3, and cre-miR1158) were selected. Heat-inducible expression vectors containing the selected miRNAs were constructed and transformed into C. reinhardtii. Comparison of H2 production following heat induction in the three transgenic strains and untransformed control group identified miR1166.1 as the best candidate for H2 production regulation. Moreover, enhanced photobio-H2 production was observed with repeated induction of miR1166.1 expression. CONCLUSIONS This study is the first to identify a physiological function of endogenous miR1166.1 and to show that a natural miRNA can regulate hydrogen photoproduction in the unicellular model organism C. reinhardtii.
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Affiliation(s)
- Yuting Wang
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Xiaoshan Zhuang
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Meirong Chen
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Zhiyong Zeng
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Xiaoqi Cai
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Hui Li
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Zhangli Hu
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
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Voshall A, Kim EJ, Ma X, Yamasaki T, Moriyama EN, Cerutti H. miRNAs in the alga Chlamydomonas reinhardtii are not phylogenetically conserved and play a limited role in responses to nutrient deprivation. Sci Rep 2017; 7:5462. [PMID: 28710366 PMCID: PMC5511227 DOI: 10.1038/s41598-017-05561-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/30/2017] [Indexed: 12/17/2022] Open
Abstract
The unicellular alga Chlamydomonas reinhardtii contains many types of small RNAs (sRNAs) but the biological role(s) of bona fide microRNAs (miRNAs) remains unclear. To address their possible function(s) in responses to nutrient availability, we examined miRNA expression in cells cultured under different trophic conditions (mixotrophic in the presence of acetate or photoautotrophic in the presence or absence of nitrogen). We also reanalyzed miRNA expression data in Chlamydomonas subject to sulfur or phosphate deprivation. Several miRNAs were differentially expressed under the various trophic conditions. However, in transcriptome analyses, the majority of their predicted targets did not show expected changes in transcript abundance, suggesting that they are not subject to miRNA-mediated RNA degradation. Mutant strains, defective in sRNAs or in ARGONAUTE3 (a key component of sRNA-mediated gene silencing), did not display major phenotypic defects when grown under multiple nutritional regimes. Additionally, Chlamydomonas miRNAs were not conserved, even in algae of the closely related Volvocaceae family, and many showed features resembling those of recently evolved, species-specific miRNAs in the genus Arabidopsis. Our results suggest that, in C. reinhardtii, miRNAs might be subject to relatively fast evolution and have only a minor, largely modulatory role in gene regulation under diverse trophic states.
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Affiliation(s)
- Adam Voshall
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Eun-Jeong Kim
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Xinrong Ma
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Tomohito Yamasaki
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki, Aichi Prefecture, Japan
| | - Etsuko N Moriyama
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Heriberto Cerutti
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.
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24
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Girolomoni L, Ferrante P, Berteotti S, Giuliano G, Bassi R, Ballottari M. The function of LHCBM4/6/8 antenna proteins in Chlamydomonas reinhardtii. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:627-641. [PMID: 28007953 PMCID: PMC5441897 DOI: 10.1093/jxb/erw462] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In eukaryotic autotrophs, photosystems are composed of a core moiety, hosting charge separation and electron transport reactions, and an antenna system, enhancing light harvesting and photoprotection. In Chlamydomonas reinhardtii, the major antenna of PSII is a heterogeneous trimeric complex made up of LHCBM1-LHCBM9 subunits. Despite high similarity, specific functions have been reported for several members including LHCBM1, 2, 7, and 9. In this work, we analyzed the function of LHCBM4 and LHCBM6 gene products in vitro by synthesizing recombinant apoproteins from individual sequences and refolding them with pigments. Additionally, we characterized knock-down strains in vivo for LHCBM4/6/8 genes. We show that LHCBM4/6/8 subunits could be found as a component of PSII supercomplexes with different sizes, although the largest pool was free in the membranes and poorly connected to PSII. Impaired accumulation of LHCBM4/6/8 caused a decreased LHCII content per PSII and a reduction in the amplitude of state 1-state 2 transitions. In addition, the reduction of LHCBM4/6/8 subunits caused a significant reduction of the Non-photochemical quenching activity and in the level of photoprotection.
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Affiliation(s)
- Laura Girolomoni
- Dipartimento di Biotecnologie, Università di Verona, Strada le Grazie 15, Verona, Italy
| | - Paola Ferrante
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA), Casaccia Research Center, Rome, Italy
| | - Silvia Berteotti
- Dipartimento di Biotecnologie, Università di Verona, Strada le Grazie 15, Verona, Italy
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA), Casaccia Research Center, Rome, Italy
| | - Roberto Bassi
- Dipartimento di Biotecnologie, Università di Verona, Strada le Grazie 15, Verona, Italy
| | - Matteo Ballottari
- Dipartimento di Biotecnologie, Università di Verona, Strada le Grazie 15, Verona, Italy
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Gao X, Zhang F, Hu J, Cai W, Shan G, Dai D, Huang K, Wang G. MicroRNAs modulate adaption to multiple abiotic stresses in Chlamydomonas reinhardtii. Sci Rep 2016; 6:38228. [PMID: 27910907 PMCID: PMC5133633 DOI: 10.1038/srep38228] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 11/07/2016] [Indexed: 01/08/2023] Open
Abstract
MicroRNAs play an important role in abiotic stress responses in higher plants and animals, but their role in stress adaptation in algae remains unknown. In this study, the expression of identified and putative miRNAs in Chlamydomonas reinhardtii was assessed using quantitative polymerase chain reaction; some of the miRNAs (Cre-miR906-3p) were up-regulated, whereas others (Cre-miR910) were down-regulated when the species was subjected to multiple abiotic stresses. With degradome sequencing data, we also identified ATP4 (the d-subunit of ATP synthase) and NCR2 (NADPH: cytochrome P450 reductase) as one of the several targets of Cre-miR906-3p and Cre-miR910, respectively. Q-PCR data indicated that ATP4, which was expressed inversely in relation to Cre-miR906-3p under stress conditions. Overexpressing of Cre-miR906-3p enhanced resistance to multiple stresses; conversely, overexpressing of ATP4 produced the opposite effect. These data of Q-PCR, degradome sequencing and adaptation of overexpressing lines indicated that Cre-miR906-3p and its target ATP4 were a part of the same pathway for stress adaptation. We found that Cre-miR910 and its target NCR2 were also a part of this pathway. Overexpressing of Cre-miR910 decreased, whereas that of NCR2 increased the adaption to multiple stresses. Our findings suggest that the two classes of miRNAs synergistically mediate stress adaptation in algae.
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Affiliation(s)
- Xiang Gao
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fengge Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinlu Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenkai Cai
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ge Shan
- School of Life Science, Chinese University of Science and Technology, Hefei 230022, China
| | - Dongsheng Dai
- Wuxi Biortus Biosciences Co., Ltd., Jiangyin, Jiangsu 214437, China
| | - Kaiyao Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Gaohong Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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Specht EA, Karunanithi PS, Gimpel JA, Ansari WS, Mayfield SP. Host Organisms: Algae. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Elizabeth A. Specht
- University of California; California Center for Algae Biotechnology; Division of Biological Sciences; 9500 Gilman Drive San Diego, La Jolla CA 92093 USA
| | - Prema S. Karunanithi
- University of California; California Center for Algae Biotechnology; Division of Biological Sciences; 9500 Gilman Drive San Diego, La Jolla CA 92093 USA
| | - Javier A. Gimpel
- Centre for Biotechnology and Bioengineering; Department of Chemical Engineering and Biotechnology, Universidad de Chile; 851 Beaucheff Santiago USA
| | - William S. Ansari
- University of California; California Center for Algae Biotechnology; Division of Biological Sciences; 9500 Gilman Drive San Diego, La Jolla CA 92093 USA
| | - Stephen P. Mayfield
- University of California; California Center for Algae Biotechnology; Division of Biological Sciences; 9500 Gilman Drive San Diego, La Jolla CA 92093 USA
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Oey M, Sawyer AL, Ross IL, Hankamer B. Challenges and opportunities for hydrogen production from microalgae. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1487-99. [PMID: 26801871 PMCID: PMC5066674 DOI: 10.1111/pbi.12516] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 11/12/2015] [Accepted: 11/16/2015] [Indexed: 05/11/2023]
Abstract
The global population is predicted to increase from ~7.3 billion to over 9 billion people by 2050. Together with rising economic growth, this is forecast to result in a 50% increase in fuel demand, which will have to be met while reducing carbon dioxide (CO2 ) emissions by 50-80% to maintain social, political, energy and climate security. This tension between rising fuel demand and the requirement for rapid global decarbonization highlights the need to fast-track the coordinated development and deployment of efficient cost-effective renewable technologies for the production of CO2 neutral energy. Currently, only 20% of global energy is provided as electricity, while 80% is provided as fuel. Hydrogen (H2 ) is the most advanced CO2 -free fuel and provides a 'common' energy currency as it can be produced via a range of renewable technologies, including photovoltaic (PV), wind, wave and biological systems such as microalgae, to power the next generation of H2 fuel cells. Microalgae production systems for carbon-based fuel (oil and ethanol) are now at the demonstration scale. This review focuses on evaluating the potential of microalgal technologies for the commercial production of solar-driven H2 from water. It summarizes key global technology drivers, the potential and theoretical limits of microalgal H2 production systems, emerging strategies to engineer next-generation systems and how these fit into an evolving H2 economy.
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Affiliation(s)
- Melanie Oey
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Qld, Australia
| | | | - Ian Lawrence Ross
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Qld, Australia
| | - Ben Hankamer
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Qld, Australia
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Banerjee C, Dubey KK, Shukla P. Metabolic Engineering of Microalgal Based Biofuel Production: Prospects and Challenges. Front Microbiol 2016; 7:432. [PMID: 27065986 PMCID: PMC4815533 DOI: 10.3389/fmicb.2016.00432] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/17/2016] [Indexed: 12/14/2022] Open
Abstract
The current scenario in renewable energy is focused on development of alternate and sustainable energy sources, amongst which microalgae stands as one of the promising feedstock for biofuel production. It is well known that microalgae generate much larger amounts of biofuels in a shorter time than other sources based on plant seeds. However, the greatest challenge in a transition to algae-based biofuel production is the various other complications involved in microalgal cultivation, its harvesting, concentration, drying and lipid extraction. Several green microalgae accumulate lipids, especially triacylglycerols (TAGs), which are main precursors in the production of lipid. The various aspects on metabolic pathway analysis of an oleaginous microalgae i.e., Chlamydomonas reinhardtii have elucidated some novel metabolically important genes and this enhances the lipid production in this microalgae. Adding to it, various other aspects in metabolic engineering using OptFlux and effectual bioprocess design also gives an interactive snapshot of enhancing lipid production which ultimately improvises the oil yield. This article reviews the current status of microalgal based technologies for biofuel production, bioreactor process design, flux analysis and it also provides various strategies to increase lipids accumulation via metabolic engineering.
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Affiliation(s)
- Chiranjib Banerjee
- Department of Environmental Science and Engineering, Indian School of Mines Dhanbad, India
| | - Kashyap K Dubey
- Department of Biotechnology, University Institute of Engineering and Technology, Maharshi Dayanand University Rohtak, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University Rohtak, India
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Olson AC, Carter CJ. The Involvement of hybrid cluster protein 4, HCP4, in Anaerobic Metabolism in Chlamydomonas reinhardtii. PLoS One 2016; 11:e0149816. [PMID: 26930496 PMCID: PMC4773151 DOI: 10.1371/journal.pone.0149816] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 02/04/2016] [Indexed: 12/28/2022] Open
Abstract
The unicellular green algae Chlamydomonas reinhardtii has long been studied for its unique fermentation pathways and has been evaluated as a candidate organism for biofuel production. Fermentation in C. reinhardtii is facilitated by a network of three predominant pathways producing four major byproducts: formate, ethanol, acetate and hydrogen. Previous microarray studies identified many genes as being highly up-regulated during anaerobiosis. For example, hybrid cluster protein 4 (HCP4) was found to be one of the most highly up-regulated genes under anoxic conditions. Hybrid cluster proteins have long been studied for their unique spectroscopic properties, yet their biological functions remain largely unclear. To probe its role during anaerobiosis, HCP4 was silenced using artificial microRNAs (ami-hcp4) followed by extensive phenotypic analyses of cells grown under anoxic conditions. Both the expression of key fermentative enzymes and their respective metabolites were significantly altered in ami-hcp4, with nitrogen uptake from the media also being significantly different than wild-type cells. The results strongly suggest a role for HCP4 in regulating key fermentative and nitrogen utilization pathways.
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Affiliation(s)
- Adam C. Olson
- Integrated Biosciences Graduate Program, University of Minnesota, Duluth, MN, 55812, United States of America
| | - Clay J. Carter
- Department of Plant Biology, University of Minnesota, Saint Paul, MN, 55108, United States of America
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Dejtisakdi W, Miller SM. Overexpression of Calvin cycle enzyme fructose 1,6-bisphosphatase in Chlamydomonas reinhardtii has a detrimental effect on growth. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.01.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Yamasaki T, Kim EJ, Cerutti H, Ohama T. Argonaute3 is a key player in miRNA-mediated target cleavage and translational repression in Chlamydomonas. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:258-268. [PMID: 26686836 DOI: 10.1111/tpj.13107] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 11/27/2015] [Accepted: 12/07/2015] [Indexed: 06/05/2023]
Abstract
MicroRNAs (miRNAs) play important roles in diverse biological processes in eukaryotes, generally through degradation and/or inhibition of the translation of target mRNAs. MicroRNAs are loaded into Argonaute (AGO) proteins to form the RNA-induced silencing complex (RISC) and used as guides to identify complementary transcripts. The distinct functions and features, such as associated small RNA classes and modes of silencing, of individual AGO paralogs have been well documented in multicellular eukaryotes. However, this aspect of miRNA function remains poorly understood in the unicellular green alga Chlamydomonas reinhardtii, which contains three AGO paralogs. In this study, we isolated AGO2 and AGO3 insertional mutants and confirmed that AGO3 is more abundantly expressed than AGO2. MicroRNA-directed target transcript cleavage and translational repression were impaired in the AGO3 mutant background, indicating that AGO3 can mediate both modes of silencing. In contrast, although the AGO2 mutant is not a null, the involvement of AGO2 in miRNA-directed silencing appears to be more limited. Our results strongly suggest that miRNA-mediated post-transcriptional gene silencing relies primarily on AGO3 in Chlamydomonas.
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Affiliation(s)
- Tomohito Yamasaki
- Department of Environmental Systems Engineering, Kochi University of Technology (KUT), 185 Miyanokuchi, Tosayamada, Kami, Kochi, 782-8502, Japan
| | - Eun-Jeong Kim
- School of Biological Science and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Heriberto Cerutti
- School of Biological Science and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Takeshi Ohama
- Department of Environmental Systems Engineering, Kochi University of Technology (KUT), 185 Miyanokuchi, Tosayamada, Kami, Kochi, 782-8502, Japan
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Doron L, Segal N, Shapira M. Transgene Expression in Microalgae-From Tools to Applications. FRONTIERS IN PLANT SCIENCE 2016; 7:505. [PMID: 27148328 PMCID: PMC4840263 DOI: 10.3389/fpls.2016.00505] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 03/29/2016] [Indexed: 05/17/2023]
Abstract
Microalgae comprise a biodiverse group of photosynthetic organisms that reside in water sources and sediments. The green microalgae Chlamydomonas reinhardtii was adopted as a useful model organism for studying various physiological systems. Its ability to grow under both photosynthetic and heterotrophic conditions allows efficient growth of non-photosynthetic mutants, making Chlamydomonas a useful genetic tool to study photosynthesis. In addition, this green alga can grow as haploid or diploid cells, similar to yeast, providing a powerful genetic system. As a result, easy and efficient transformation systems have been developed for Chlamydomonas, targeting both the chloroplast and nuclear genomes. Since microalgae comprise a rich repertoire of species that offer variable advantages for biotech and biomed industries, gene transfer technologies were further developed for many microalgae to allow for the expression of foreign proteins of interest. Expressing foreign genes in the chloroplast enables the targeting of foreign DNA to specific sites by homologous recombination. Chloroplast transformation also allows for the introduction of genes encoding several enzymes from a complex pathway, possibly as an operon. Expressing foreign proteins in the chloroplast can also be achieved by introducing the target gene into the nuclear genome, with the protein product bearing a targeting signal that directs import of the transgene-product into the chloroplast, like other endogenous chloroplast proteins. Integration of foreign genes into the nuclear genome is mostly random, resulting in large variability between different clones, such that extensive screening is required. The use of different selection modalities is also described, with special emphasis on the use of herbicides and metabolic markers which are considered to be friendly to the environment, as compared to drug-resistance genes that are commonly used. Finally, despite the development of a wide range of transformation tools and approaches, expression of foreign genes in microalgae suffers from low efficiency. Thus, novel tools have appeared in recent years to deal with this problem. Finally, while C. reinhardtii was traditionally used as a model organism for the development of transformation systems and their subsequent improvement, similar technologies can be adapted for other microalgae that may have higher biotechnological value.
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Zalutskaya Z, Kharatyan N, Forchhammer K, Ermilova E. Reduction of PII signaling protein enhances lipid body production in Chlamydomonas reinhardtii. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 240:1-9. [PMID: 26475183 DOI: 10.1016/j.plantsci.2015.08.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/17/2015] [Accepted: 08/25/2015] [Indexed: 06/05/2023]
Abstract
In all examined organisms that have the PII signal transduction machinery, PII coordinates the central C/N anabolic metabolism. In green algae and land plants, PII is localized in the chloroplast and controls the L-arginine biosynthetic pathway pathway. To elucidate additional functions of PII in the model photosynthetic organism Chlamydomonas reinhardtii (CrPII), we generated and analyzed four strains, in which PII was strongly under-expressed by artificial microRNA (GLB1-amiRNA strains). In response to nitrogen deficiency, Chlamydomonas produces triacylglycerols (TAGs) that are accumulated in lipid bodies (LB). Quantification of LBs by confocal microscopy in four GLB1-amiRNA strains showed that reduced PII levels resulted in over-accumulation of LBs compared to their parental strains. Moreover, knock-down of PII caused also an increase in the total TAG level. We propose that the larger yields of TAG-filled LBs in N-starved GLB1-amiRNA cells can be attributed to the strain's depleted PII level and their inability to properly control acetyl-CoA carboxylase activity (ACCase). Together, our results imply that PII in Chlamydomonas negatively controls TAG accumulation in LBs during acclimation to nitrogen starvation of the alga.
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Affiliation(s)
- Zhanneta Zalutskaya
- Laboratory of Adaptation in Microorganisms, Biological Faculty, Saint-Petersburg State University, Universitetskaya em. 7/9, 199034 Saint-Petersburg, Russia
| | - Nina Kharatyan
- Laboratory of Adaptation in Microorganisms, Biological Faculty, Saint-Petersburg State University, Universitetskaya em. 7/9, 199034 Saint-Petersburg, Russia
| | - Karl Forchhammer
- Department of Microbiology/Organismic Interactions, Faculty of Biology, University of Tübingen, Auf der Morgenstelle 28, 72,076 Tübingen, Germany
| | - Elena Ermilova
- Laboratory of Adaptation in Microorganisms, Biological Faculty, Saint-Petersburg State University, Universitetskaya em. 7/9, 199034 Saint-Petersburg, Russia.
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Barahimipour R, Strenkert D, Neupert J, Schroda M, Merchant SS, Bock R. Dissecting the contributions of GC content and codon usage to gene expression in the model alga Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:704-17. [PMID: 26402748 PMCID: PMC4715772 DOI: 10.1111/tpj.13033] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 08/24/2015] [Accepted: 09/14/2015] [Indexed: 05/17/2023]
Abstract
The efficiency of gene expression in all organisms depends on the nucleotide composition of the coding region. GC content and codon usage are the two key sequence features known to influence gene expression, but the underlying molecular mechanisms are not entirely clear. Here we have determined the relative contributions of GC content and codon usage to the efficiency of nuclear gene expression in the unicellular green alga Chlamydomonas reinhardtii. By comparing gene variants that encode an identical amino acid sequence but differ in their GC content and/or codon usage, we show that codon usage is the key factor determining translational efficiency and, surprisingly, also mRNA stability. By contrast, unfavorable GC content affects gene expression at the level of the chromatin structure by triggering heterochromatinization. We further show that mutant algal strains that permit high-level transgene expression are less susceptible to epigenetic transgene suppression and do not establish a repressive chromatin structure at the transgenic locus. Our data disentangle the relationship between GC content and codon usage, and suggest simple strategies to overcome the transgene expression problem in Chlamydomonas.
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Affiliation(s)
- Rouhollah Barahimipour
- Max-Planck-Institut für Molekulare Pflanzenphysiologie (MPI-MP), Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Daniela Strenkert
- University of California Los Angeles, Department of Chemistry and Biochemistry, and Institute for Genomics and Proteomics, 607 Charles E. Young Dr. East, Los Angeles, California 90095, USA
| | - Juliane Neupert
- Max-Planck-Institut für Molekulare Pflanzenphysiologie (MPI-MP), Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Michael Schroda
- Max-Planck-Institut für Molekulare Pflanzenphysiologie (MPI-MP), Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Sabeeha S. Merchant
- University of California Los Angeles, Department of Chemistry and Biochemistry, and Institute for Genomics and Proteomics, 607 Charles E. Young Dr. East, Los Angeles, California 90095, USA
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie (MPI-MP), Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
- For correspondence (Fax: +49-331-567-8701; )
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Hlavova M, Turoczy Z, Bisova K. Improving microalgae for biotechnology — From genetics to synthetic biology. Biotechnol Adv 2015; 33:1194-203. [DOI: 10.1016/j.biotechadv.2015.01.009] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 01/11/2015] [Accepted: 01/17/2015] [Indexed: 01/01/2023]
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Mussgnug JH. Genetic tools and techniques for Chlamydomonas reinhardtii. Appl Microbiol Biotechnol 2015; 99:5407-18. [PMID: 26025017 DOI: 10.1007/s00253-015-6698-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 05/10/2015] [Accepted: 05/15/2015] [Indexed: 11/29/2022]
Abstract
The development of tools has always been a major driving force for the advancement of science. Optical microscopes were the first instruments that allowed discovery and descriptive studies of the subcellular features of microorganisms. Although optical and electron microscopes remained at the forefront of microbiological research tools since their inventions, the advent of molecular genetics brought about questions which had to be addressed with new "genetic tools". The unicellular green microalgal genus Chlamydomonas, especially the most prominent species C. reinhardtii, has become a frequently used model organism for many diverse fields of research and molecular genetic analyses of C. reinhardtii, as well as the available genetic tools and techniques, have become increasingly sophisticated throughout the last decades. The aim of this review is to provide an overview of the molecular key features of C. reinhardtii and summarize the progress related to the development of tools and techniques for genetic engineering of this organism, from pioneering DNA transformation experiments to state-of-the-art techniques for targeted nuclear genome editing and high-throughput screening approaches.
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Affiliation(s)
- Jan H Mussgnug
- Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615, Bielefeld, Germany,
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Jinkerson RE, Jonikas MC. Molecular techniques to interrogate and edit the Chlamydomonas nuclear genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:393-412. [PMID: 25704665 DOI: 10.1111/tpj.12801] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/13/2015] [Accepted: 02/16/2015] [Indexed: 05/23/2023]
Abstract
The success of the green alga Chlamydomonas reinhardtii as a model organism is to a large extent due to the wide range of molecular techniques that are available for its characterization. Here, we review some of the techniques currently used to modify and interrogate the C. reinhardtii nuclear genome and explore several technologies under development. Nuclear mutants can be generated with ultraviolet (UV) light and chemical mutagens, or by insertional mutagenesis. Nuclear transformation methods include biolistic delivery, agitation with glass beads, and electroporation. Transforming DNA integrates into the genome at random sites, and multiple strategies exist for mapping insertion sites. A limited number of studies have demonstrated targeted modification of the nuclear genome by approaches such as zinc-finger nucleases and homologous recombination. RNA interference is widely used to knock down expression levels of nuclear genes. A wide assortment of transgenes has been successfully expressed in the Chlamydomonas nuclear genome, including transformation markers, fluorescent proteins, reporter genes, epitope tagged proteins, and even therapeutic proteins. Optimized expression constructs and strains help transgene expression. Emerging technologies such as the CRISPR/Cas9 system, high-throughput mutant identification, and a whole-genome knockout library are being developed for this organism. We discuss how these advances will propel future investigations.
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Affiliation(s)
- Robert E Jinkerson
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA, 94305, USA
| | - Martin C Jonikas
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA, 94305, USA
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Scranton MA, Ostrand JT, Fields FJ, Mayfield SP. Chlamydomonas as a model for biofuels and bio-products production. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:523-531. [PMID: 25641390 PMCID: PMC5531182 DOI: 10.1111/tpj.12780] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/08/2015] [Accepted: 01/12/2015] [Indexed: 05/18/2023]
Abstract
Developing renewable energy sources is critical to maintaining the economic growth of the planet while protecting the environment. First generation biofuels focused on food crops like corn and sugarcane for ethanol production, and soybean and palm for biodiesel production. Second generation biofuels based on cellulosic ethanol produced from terrestrial plants, has received extensive funding and recently pilot facilities have been commissioned, but to date output of fuels from these sources has fallen well short of what is needed. Recent research and pilot demonstrations have highlighted the potential of algae as one of the most promising sources of sustainable liquid transportation fuels. Algae have also been established as unique biofactories for industrial, therapeutic, and nutraceutical co-products. Chlamydomonas reinhardtii's long established role in the field of basic research in green algae has paved the way for understanding algal metabolism and developing genetic engineering protocols. These tools are now being utilized in C. reinhardtii and in other algal species for the development of strains to maximize biofuels and bio-products yields from the lab to the field.
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40
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Scaife MA, Nguyen GTDT, Rico J, Lambert D, Helliwell KE, Smith AG. Establishing Chlamydomonas reinhardtii as an industrial biotechnology host. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:532-546. [PMID: 25641561 PMCID: PMC4515103 DOI: 10.1111/tpj.12781] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 01/19/2015] [Accepted: 01/20/2015] [Indexed: 05/20/2023]
Abstract
Microalgae constitute a diverse group of eukaryotic unicellular organisms that are of interest for pure and applied research. Owing to their natural synthesis of value-added natural products microalgae are emerging as a source of sustainable chemical compounds, proteins and metabolites, including but not limited to those that could replace compounds currently made from fossil fuels. For the model microalga, Chlamydomonas reinhardtii, this has prompted a period of rapid development so that this organism is poised for exploitation as an industrial biotechnology platform. The question now is how best to achieve this? Highly advanced industrial biotechnology systems using bacteria and yeasts were established in a classical metabolic engineering manner over several decades. However, the advent of advanced molecular tools and the rise of synthetic biology provide an opportunity to expedite the development of C. reinhardtii as an industrial biotechnology platform, avoiding the process of incremental improvement. In this review we describe the current status of genetic manipulation of C. reinhardtii for metabolic engineering. We then introduce several concepts that underpin synthetic biology, and show how generic parts are identified and used in a standard manner to achieve predictable outputs. Based on this we suggest that the development of C. reinhardtii as an industrial biotechnology platform can be achieved more efficiently through adoption of a synthetic biology approach.
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Affiliation(s)
- Mark A Scaife
- Department of Plant Science, University of CambridgeDowning Street, Cambridge, CB2 3EA, UK
- *For correspondence (e-mails or )
| | - Ginnie TDT Nguyen
- Department of Plant Science, University of CambridgeDowning Street, Cambridge, CB2 3EA, UK
| | - Juan Rico
- Department of Plant Science, University of CambridgeDowning Street, Cambridge, CB2 3EA, UK
| | - Devinn Lambert
- Department of Plant Science, University of CambridgeDowning Street, Cambridge, CB2 3EA, UK
| | - Katherine E Helliwell
- Department of Plant Science, University of CambridgeDowning Street, Cambridge, CB2 3EA, UK
| | - Alison G Smith
- Department of Plant Science, University of CambridgeDowning Street, Cambridge, CB2 3EA, UK
- *For correspondence (e-mails or )
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Identification of AGO3-associated miRNAs and computational prediction of their targets in the green alga Chlamydomonas reinhardtii. Genetics 2015; 200:105-21. [PMID: 25769981 DOI: 10.1534/genetics.115.174797] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/11/2015] [Indexed: 11/18/2022] Open
Abstract
The unicellular green alga Chlamydomonas reinhardtii harbors many types of small RNAs (sRNAs) but little is known about their role(s) in the regulation of endogenous genes and cellular processes. To define functional microRNAs (miRNAs) in Chlamydomonas, we characterized sRNAs associated with an argonaute protein, AGO3, by affinity purification and deep sequencing. Using a stringent set of criteria for canonical miRNA annotation, we identified 39 precursor miRNAs, which produce 45 unique, AGO3-associated miRNA sequences including 13 previously reported miRNAs and 32 novel ones. Potential miRNA targets were identified based on the complementarity of miRNAs with candidate binding sites on transcripts and classified, depending on the extent of complementarity, as being likely to be regulated through cleavage or translational repression. The search for cleavage targets identified 74 transcripts. However, only 6 of them showed an increase in messenger RNA (mRNA) levels in a mutant strain almost devoid of sRNAs. The search for translational repression targets, which used complementarity criteria more stringent than those empirically required for a reduction in target protein levels, identified 488 transcripts. However, unlike observations in metazoans, most predicted translation repression targets did not show appreciable changes in transcript abundance in the absence of sRNAs. Additionally, of three candidate targets examined at the protein level, only one showed a moderate variation in polypeptide amount in the mutant strain. Our results emphasize the difficulty in identifying genuine miRNA targets in Chlamydomonas and suggest that miRNAs, under standard laboratory conditions, might have mainly a modulatory role in endogenous gene regulation in this alga.
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Hu G, Ji S, Yu Y, Wang S, Zhou G, Li F. Organisms for biofuel production: natural bioresources and methodologies for improving their biosynthetic potentials. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 147:185-224. [PMID: 24085385 DOI: 10.1007/10_2013_245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
In order to relieve the pressure of energy supply and environment contamination that humans are facing, there are now intensive worldwide efforts to explore natural bioresources for production of energy storage compounds, such as lipids, alcohols, hydrocarbons, and polysaccharides. Around the world, many plants have been evaluated and developed as feedstock for bioenergy production, among which several crops have successfully achieved industrialization. Microalgae are another group of photosynthetic autotroph of interest due to their superior growth rates, relatively high photosynthetic conversion efficiencies, and vast metabolic capabilities. Heterotrophic microorganisms, such as yeast and bacteria, can utilize carbohydrates from lignocellulosic biomass directly or after pretreatment and enzymatic hydrolysis to produce liquid biofuels such as ethanol and butanol. Although finding a suitable organism for biofuel production is not easy, many naturally occurring organisms with good traits have recently been obtained. This review mainly focuses on the new organism resources discovered in the last 5 years for production of transport fuels (biodiesel, gasoline, jet fuel, and alkanes) and hydrogen, and available methods to improve natural organisms as platforms for the production of biofuels.
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Affiliation(s)
- Guangrong Hu
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
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Mathieu-Rivet E, Kiefer-Meyer MC, Vanier G, Ovide C, Burel C, Lerouge P, Bardor M. Protein N-glycosylation in eukaryotic microalgae and its impact on the production of nuclear expressed biopharmaceuticals. FRONTIERS IN PLANT SCIENCE 2014; 5:359. [PMID: 25183966 PMCID: PMC4135232 DOI: 10.3389/fpls.2014.00359] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/04/2014] [Indexed: 05/09/2023]
Abstract
Microalgae are currently used for the production of food compounds. Recently, few microalgae species have been investigated as potential biofactories for the production of biopharmaceuticals. Indeed in this context, microalgae are cheap, classified as Generally Recognized As Safe (GRAS) organisms and can be grown easily. However, problems remain to be solved before any industrial production of microalgae-made biopharmaceuticals. Among them, post-translational modifications of the proteins need to be considered. Especially, N-glycosylation acquired by the secreted recombinant proteins is of major concern since most of the biopharmaceuticals are N-glycosylated and it is well recognized that glycosylation represent one of their critical quality attribute. Therefore, the evaluation of microalgae as alternative cell factory for biopharmaceutical productions thus requires to investigate their N-glycosylation capability in order to determine to what extend it differs from their human counterpart and to determine appropriate strategies for remodeling the microalgae glycosylation into human-compatible oligosaccharides. Here, we review the secreted recombinant proteins which have been successfully produced in microalgae. We also report on recent bioinformatics and biochemical data concerning the structure of glycans N-linked to proteins from various microalgae phyla and comment the consequences on the glycan engineering strategies that may be necessary to render those microalgae-made biopharmaceuticals compatible with human therapy.
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Affiliation(s)
- Elodie Mathieu-Rivet
- Laboratoire Glyco-MEV, Faculté des Sciences et Techniques, UPRES EA 4358, Normandie Université, IRIB, VASIMont-Saint-Aignan, France
| | - Marie-Christine Kiefer-Meyer
- Laboratoire Glyco-MEV, Faculté des Sciences et Techniques, UPRES EA 4358, Normandie Université, IRIB, VASIMont-Saint-Aignan, France
| | - Gaëtan Vanier
- Laboratoire Glyco-MEV, Faculté des Sciences et Techniques, UPRES EA 4358, Normandie Université, IRIB, VASIMont-Saint-Aignan, France
| | - Clément Ovide
- Laboratoire Glyco-MEV, Faculté des Sciences et Techniques, UPRES EA 4358, Normandie Université, IRIB, VASIMont-Saint-Aignan, France
| | - Carole Burel
- Laboratoire Glyco-MEV, Faculté des Sciences et Techniques, UPRES EA 4358, Normandie Université, IRIB, VASIMont-Saint-Aignan, France
| | - Patrice Lerouge
- Laboratoire Glyco-MEV, Faculté des Sciences et Techniques, UPRES EA 4358, Normandie Université, IRIB, VASIMont-Saint-Aignan, France
| | - Muriel Bardor
- Laboratoire Glyco-MEV, Faculté des Sciences et Techniques, UPRES EA 4358, Normandie Université, IRIB, VASIMont-Saint-Aignan, France
- Institut Universitaire de FranceParis, France
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Guo Y, Han Y, Ma J, Wang H, Sang X, Li M. Undesired small RNAs originate from an artificial microRNA precursor in transgenic petunia (Petunia hybrida). PLoS One 2014; 9:e98783. [PMID: 24897430 PMCID: PMC4045805 DOI: 10.1371/journal.pone.0098783] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 05/07/2014] [Indexed: 11/18/2022] Open
Abstract
Although artificial microRNA (amiRNA) technology has been used frequently in gene silencing in plants, little research has been devoted to investigating the accuracy of amiRNA precursor processing. In this work, amiRNAchs1 (amiRchs1), based on the Arabidopsis miR319a precursor, was expressed in order to suppress the expression of CHS genes in petunia. The transgenic plants showed the CHS gene-silencing phenotype. A modified 5′ RACE technique was used to map small-RNA-directed cleavage sites and to detect processing intermediates of the amiRchs1 precursor. The results showed that the target CHS mRNAs were cut at the expected sites and that the amiRchs1 precursor was processed from loop to base. The accumulation of small RNAs in amiRchs1 transgenic petunia petals was analyzed using the deep-sequencing technique. The results showed that, alongside the accumulation of the desired artificial microRNAs, additional small RNAs that originated from other regions of the amiRNA precursor were also accumulated at high frequency. Some of these had previously been found to be accumulated at low frequency in the products of ath-miR319a precursor processing and some of them were accompanied by 3′-tailing variant. Potential targets of the undesired small RNAs were discovered in petunia and other Solanaceae plants. The findings draw attention to the potential occurrence of undesired target silencing induced by such additional small RNAs when amiRNA technology is used. No appreciable production of secondary small RNAs occurred, despite the fact that amiRchs1 was designed to have perfect complementarity to its CHS-J target. This confirmed that perfect pairing between an amiRNA and its targets is not the trigger for secondary small RNA production. In conjunction with the observation that amiRNAs with perfect complementarity to their target genes show high efficiency and specificity in gene silencing, this finding has an important bearing on future applications of amiRNAs in gene silencing in plants.
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Affiliation(s)
- Yulong Guo
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Yao Han
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Jing Ma
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Huiping Wang
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Xianchun Sang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Mingyang Li
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- * E-mail:
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Gu Z, Huang C, Li F, Zhou X. A versatile system for functional analysis of genes and microRNAs in cotton. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:638-49. [PMID: 24521483 DOI: 10.1111/pbi.12169] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 11/26/2013] [Accepted: 01/02/2014] [Indexed: 05/20/2023]
Abstract
Cotton is an important economic crop worldwide. Due to its long growth cycle, large genome size and recalcitrance to stable transformation, traditional methods for the analysis of gene function in this crop are difficult and labour intensive. Here, we report a cotton leaf crumple virus (CLCrV)-based vector and its application in gene function analysis through virus-induced gene silencing (VIGS) and overexpression of microRNAs (miRNAs), small tandem target mimic (STTM) and artificial miRNA (amiRNA) in cotton via an Agrobacterium-mediated infiltration approach. Using this system, we were able to efficiently silence two endogenous genes, magnesium chelatase subunit I (CHLI) and elongation factor-1α (EF-1α), in Gossypium species and the Bacillus thuringiensis cry1A gene in transgenic cotton. Furthermore, our results show that this vector can be used to ectopically express endogenous miR156 in G. hirsutum, causing a reduction in miR156-targeted RNA transcripts resulting in the development of abnormal leaf phenotypes. Ectopic expression of miR165/166 STTM with this vector led to downward curling and crumpled leaves, and a significant increase in the miR165/166 target mRNAs. This versatile system is easy to use and can provide more uniform and persistent gene silencing in cotton, thereby providing a powerful approach for gene discovery in cotton.
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Affiliation(s)
- Zhouhang Gu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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Riesberg G, Bigelow TA, Stessman DJ, Spalding MH, Yao L, Wang T, Xu J. Flow rate and duty cycle effects in lysis of Chlamydomonas reinhardtii using high-energy pulsed focused ultrasound. THE JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA 2014; 135:3632-3638. [PMID: 24916410 DOI: 10.1121/1.4874627] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
To consider microalgae lipid biofuel as a viable energy source, it is a necessity to maximize algal cell lysis, lipid harvest, and thus biofuel production versus the energy used to lyse the cells. Previous techniques have been to use energy consumptive ultrasound waves in the 10-40 kHz range in a stationary exposure environment. This study evaluated the potential of using 1.1 MHz ultrasound pulses in a new flow through type chamber on Chlamydomonas reinhardtii as a model organism for cell breakage. The ultrasound was generated using a spherically focused transducer with a focal length of 6.34 cm and an active diameter of 6.36 cm driven by 20 cycle sine-wave tone bursts at varied pulse repetition frequencies. First, variations in flow rate were examined at a constant duty cycle of 3.6%. After assessing flow rates, the duty cycle was varied to further explore the dependence on the tone burst parameters. Cell lysis was assessed by quantifying protein and chlorophyll release into the supernatant as well as by lipid extractability. Appropriate flow rates with higher duty cycles led to statistically significant increases in cell lysis relative to controls and other exposure conditions.
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Affiliation(s)
- Grant Riesberg
- Department of Electrical and Computer Engineering, Iowa State University, Ames, Iowa 50011
| | - Timothy A Bigelow
- Department of Electrical and Computer Engineering, Iowa State University, Ames, Iowa 50011
| | - Dan J Stessman
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Martin H Spalding
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Linxing Yao
- Department of Food Science and Human Nutrition, Iowa State University, Ames, Iowa 50011
| | - Tong Wang
- Department of Food Science and Human Nutrition, Iowa State University, Ames, Iowa 50011
| | - Jin Xu
- John Brown University, Siloam Springs, Arkansas 72761
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Guo H, Song X, Wang G, Yang K, Wang Y, Niu L, Chen X, Fang R. Plant-generated artificial small RNAs mediated aphid resistance. PLoS One 2014; 9:e97410. [PMID: 24819752 PMCID: PMC4018293 DOI: 10.1371/journal.pone.0097410] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 04/16/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND RNA silencing is an important mechanism for regulation of endogenous gene expression and defense against genomic intruders in plants. This natural defense system was adopted to generate virus-resistant plants even before the mechanism of RNA silencing was unveiled. With the clarification of that mechanism, transgenic antiviral plants were developed that expressed artificial virus-specific hairpin RNAs (hpRNAs) or microRNAs (amiRNAs) in host plants. Previous works also showed that plant-mediated RNA silencing technology could be a practical method for constructing insect-resistant plants by expressing hpRNAs targeting essential genes of insects. METHODOLOGY/PRINCIPAL FINDINGS In this study, we chose aphid Myzus persicae of order Hemiptera as a target insect. To screen for aphid genes vulnerable to attack by plant-mediated RNA silencing to establish plant aphid resistance, we selected nine genes of M. persicae as silencing targets, and constructed their hpRNA-expressing vectors. For the acetylcholinesterase 2 coding gene (MpAChE2), two amiRNA-expressing vectors were also constructed. The vectors were transformed into tobacco plants (Nicotiana tabacum cv. Xanti). Insect challenge assays showed that most of the transgenic plants gained aphid resistance, among which those expressing hpRNAs targeting V-type proton ATPase subunit E-like (V-ATPaseE) or tubulin folding cofactor D (TBCD) genes displayed stronger aphicidal activity. The transgenic plants expressing amiRNAs targeting two different sites in the MpAChE2 gene exhibited better aphid resistance than the plants expressing MpAChE2-specific hpRNA. CONCLUSIONS/SIGNIFICANCE Our results indicated that plant-mediated insect-RNA silencing might be an effective way to develop plants resistant to insects with piercing-sucking mouthparts, and both the selection of vulnerable target genes and the biogenetic type of the small RNAs were crucial for the effectiveness of aphid control. The expression of insect-specific amiRNA is a promising and preferable approach to engineer plants resistant to aphids and, possibly, to other plant-infesting insects.
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Affiliation(s)
- Hongyan Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- National Plant Gene Research Center, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoguang Song
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- National Plant Gene Research Center, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guiling Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Kun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yu Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Libo Niu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoying Chen
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- National Plant Gene Research Center, Beijing, China
| | - Rongxiang Fang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- National Plant Gene Research Center, Beijing, China
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Tenenboim H, Smirnova J, Willmitzer L, Steup M, Brotman Y. VMP1-deficient Chlamydomonas exhibits severely aberrant cell morphology and disrupted cytokinesis. BMC PLANT BIOLOGY 2014; 14:121. [PMID: 24885763 PMCID: PMC4108031 DOI: 10.1186/1471-2229-14-121] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 04/28/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND The versatile Vacuole Membrane Protein 1 (VMP1) has been previously investigated in six species. It has been shown to be essential in macroautophagy, where it takes part in autophagy initiation. In addition, VMP1 has been implicated in organellar biogenesis; endo-, exo- and phagocytosis, and protein secretion; apoptosis; and cell adhesion. These roles underly its proven involvement in pancreatitis, diabetes and cancer in humans. RESULTS In this study we analyzed a VMP1 homologue from the green alga Chlamydomonas reinhardtii. CrVMP1 knockdown lines showed severe phenotypes, mainly affecting cell division as well as the morphology of cells and organelles. We also provide several pieces of evidence for its involvement in macroautophagy. CONCLUSION Our study adds a novel role to VMP1's repertoire, namely the regulation of cytokinesis. Though the directness of the observed effects and the mechanisms underlying them remain to be defined, the protein's involvement in macroautophagy in Chlamydomonas, as found by us, suggests that CrVMP1 shares molecular characteristics with its animal and protist counterparts.
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Affiliation(s)
- Hezi Tenenboim
- Institute of Biochemistry and Biology, Department of Plant Physiology, Universität Potsdam, Potsdam, Germany
- Max Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Julia Smirnova
- Max Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Lothar Willmitzer
- Max Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Martin Steup
- Institute of Biochemistry and Biology, Department of Plant Physiology, Universität Potsdam, Potsdam, Germany
| | - Yariv Brotman
- Max Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
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Bigelow TA, Xu J, Stessman DJ, Yao L, Spalding MH, Wang T. Lysis of Chlamydomonas reinhardtii by high-intensity focused ultrasound as a function of exposure time. ULTRASONICS SONOCHEMISTRY 2014; 21:1258-1264. [PMID: 24355286 DOI: 10.1016/j.ultsonch.2013.11.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 11/25/2013] [Indexed: 06/03/2023]
Abstract
Efficient lysis of microalgae for lipid extraction is an important concern when processing biofuels. Historically, ultrasound frequencies in the range of 10-40 kHz have been utilized for this task. However, greater efficiencies might be achievable if higher frequencies could be used. In our study, we evaluated the potential of using 1.1 MHz ultrasound to lyse microalgae for biofuel production while using Chlamydomonas reinhardtii as a model organism. The ultrasound was generated using a spherically focused transducer with a focal length of 6.34 cm and an active diameter of 6.36 cm driven by 20 cycle sine-wave tone bursts at a pulse repetition frequency of 2 kHz (3.6% duty cycle). The time-average acoustic power output was 26.2 W while the spatial-peak-pulse-average intensity (ISPPA) for each tone burst was 41 kW/cm(2). The peak compressional and rarefactional pressures at the focus were 102 and 17 MPa, respectively. The exposure time was varied for the different cases in the experiments from 5s to 9 min and cell lysis was assessed by quantifying the percentage of protein and chlorophyll release into the supernate as well as the lipid extractability. Free radical generation and lipid oxidation for the different ultrasound exposures were also determined. We found that there was a statistically significant increase in lipid extractability for all of the exposures compared to the control. The longer exposures also completely fragmented the cells releasing almost all of the protein and chlorophyll into the supernate. The cavitation activity did not significantly increase lipid oxidation while there was a minor trend of increased free radical production with increased ultrasound exposure.
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Affiliation(s)
- Timothy A Bigelow
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, USA; Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA.
| | - Jin Xu
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, USA; Department of Engineering, John Brown University, Siloam Springs, AR 72761, USA
| | - Dan J Stessman
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Linxing Yao
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA 50011, USA
| | - Martin H Spalding
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Tong Wang
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA 50011, USA
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