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Russo MT, Rogato A, Jaubert M, Karas BJ, Falciatore A. Phaeodactylum tricornutum: An established model species for diatom molecular research and an emerging chassis for algal synthetic biology. JOURNAL OF PHYCOLOGY 2023; 59:1114-1122. [PMID: 37975560 DOI: 10.1111/jpy.13400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 10/05/2023] [Indexed: 11/19/2023]
Abstract
Diatoms are prominent and highly diverse microalgae in aquatic environments. Compared with other diatom species, Phaeodactylum tricornutum is an "atypical diatom" displaying three different morphotypes and lacking the usual silica shell. Despite being of limited ecological relevance, its ease of growth in the laboratory and well-known physiology, alongside the steady increase in genome-enabled information coupled with effective tools for manipulating gene expression, have meant it has gained increased recognition as a powerful experimental model for molecular research on diatoms. We here present a brief overview of how over the last 25 years P. tricornutum has contributed to the unveiling of fundamental aspects of diatom biology, while also emerging as a new tool for algal process engineering and synthetic biology.
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Affiliation(s)
- Monia T Russo
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Alessandra Rogato
- Institute of Biosciences and Bioresources, National Research Council, IBBR-CNR, Naples, Italy
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Marianne Jaubert
- UMR7141 Laboratoire de Biologie du chloroplaste et perception de la lumière chez les micro-algues, Institut de Biologie Physico-Chimique, Paris, France
| | - Bogumil J Karas
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, Ontario, Canada
| | - Angela Falciatore
- UMR7141 Laboratoire de Biologie du chloroplaste et perception de la lumière chez les micro-algues, Institut de Biologie Physico-Chimique, Paris, France
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Garza EA, Bielinski VA, Espinoza JL, Orlandi K, Alfaro JR, Bolt TM, Beeri K, Weyman PD, Dupont CL. Validating a Promoter Library for Application in Plasmid-Based Diatom Genetic Engineering. ACS Synth Biol 2023; 12:3215-3228. [PMID: 37857380 PMCID: PMC10661051 DOI: 10.1021/acssynbio.3c00163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Indexed: 10/21/2023]
Abstract
While diatoms are promising synthetic biology platforms, there currently exists a limited number of validated genetic regulatory parts available for genetic engineering. The standard method for diatom transformation, nonspecific introduction of DNA into chromosomes via biolistic particle bombardment, is low throughput and suffers from clonal variability and epigenetic effects. Recent developments in diatom engineering have demonstrated that autonomously replicating episomal plasmids serve as stable expression platforms for diverse gene expression technologies. These plasmids are delivered via bacterial conjugation and, when combined with modular DNA assembly technologies, provide a flexibility and speed not possible with biolistic-mediated strain generation. In order to expand the current toolbox for plasmid-based engineering in the diatom Phaeodactylum tricornutum, a conjugation-based forward genetics screen for promoter discovery was developed, and application to a diatom genomic DNA library defined 252 P. tricornutum promoter elements. From this library, 40 promoter/terminator pairs were delivered via conjugation on episomal plasmids, characterized in vivo, and ranked across 4 orders of magnitude difference in reporter gene expression levels.
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Affiliation(s)
- Erin A. Garza
- J. Craig Venter Institute, La Jolla, California 92037, United States
| | | | - Josh L. Espinoza
- J. Craig Venter Institute, La Jolla, California 92037, United States
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Dhokane D, Shaikh A, Yadav A, Giri N, Bandyopadhyay A, Dasgupta S, Bhadra B. CRISPR-based bioengineering in microalgae for production of industrially important biomolecules. Front Bioeng Biotechnol 2023; 11:1267826. [PMID: 37965048 PMCID: PMC10641005 DOI: 10.3389/fbioe.2023.1267826] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/11/2023] [Indexed: 11/16/2023] Open
Abstract
Microalgae, as photosynthetic organisms, have the potential to produce biomolecules for use in food, feed, cosmetics, nutraceuticals, fuel, and other applications. Faster growth rates and higher protein and lipid content make microalgae a popular chassis for many industrial applications. However, challenges such as low productivity and high production costs have limited their commercialization. To overcome these challenges, bioengineering approaches such as genetic engineering, metabolic engineering, and synthetic biology have been employed to improve the productivity and quality of microalgae-based products. Genetic engineering employing genome editing tools like CRISPR/Cas allows precise and targeted genetic modifications. CRISPR/Cas systems are presently used to modify the genetic makeup of microalgae for enhanced production of specific biomolecules. However, these tools are yet to be explored explicitly in microalgae owing to some limitations. Despite the progress made in CRISPR-based bioengineering approaches, there is still a need for further research to optimize the production of microalgae-based products. This includes improving the efficiency of genome editing tools, understanding the regulatory mechanisms of microalgal metabolism, and optimizing growth conditions and cultivation strategies. Additionally, addressing the ethical, social, and environmental concerns associated with genetic modification of microalgae is crucial for the responsible development and commercialization of microalgae-based products. This review summarizes the advancements of CRISPR-based bioengineering for production of industrially important biomolecules and provides key considerations to use CRISPR/Cas systems in microalgae. The review will help researchers to understand the progress and to initiate genome editing experiments in microalgae.
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Affiliation(s)
| | | | | | | | | | | | - Bhaskar Bhadra
- Synthetic Biology Group, Reliance Industries Ltd., Navi Mumbai, India
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Abbriano RM, George J, Kahlke T, Commault AS, Fabris M. Mobilization of a diatom mutator-like element (MULE) transposon inactivates the uridine monophosphate synthase (UMPS) locus in Phaeodactylum tricornutum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:926-936. [PMID: 37147901 DOI: 10.1111/tpj.16271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/18/2023] [Accepted: 04/29/2023] [Indexed: 05/07/2023]
Abstract
Diatoms are photosynthetic unicellular microalgae that drive global ecological phenomena in the biosphere and are emerging as sustainable feedstock for an increasing number of industrial applications. Diatoms exhibit enormous taxonomic and genetic diversity, which often results in peculiar biochemical and biological traits. Transposable elements (TEs) represent a substantial portion of diatom genomes and have been hypothesized to exert a relevant role in enriching genetic diversity and making a core contribution to genome evolution. Here, through long-read whole-genome sequencing, we identified a mutator-like element (MULE) in the model diatom Phaeodactylum tricornutum, and we report the direct observation of its mobilization within the course of a single laboratory experiment. Under selective conditions, this TE inactivated the uridine monophosphate synthase (UMPS) gene of P. tricornutum, one of the few endogenous genetic loci currently targeted for selectable auxotrophy for functional genetics and genome-editing applications. We report the observation of a recently mobilized transposon in diatoms with unique features. These include the combined presence of a MULE transposase with zinc-finger SWIM-type domains and a diatom-specific E3 ubiquitin ligase of the zinc-finger UBR type, which are suggestive of a mobilization mechanism. Our findings provide new elements for the understanding of the role of TEs in diatom genome evolution and in the enrichment of intraspecific genetic variability.
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Affiliation(s)
- Raffaela M Abbriano
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW, 2007, Australia
| | - Jestin George
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW, 2007, Australia
| | - Tim Kahlke
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW, 2007, Australia
| | - Audrey S Commault
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW, 2007, Australia
| | - Michele Fabris
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW, 2007, Australia
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD, 4001, Australia
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Kelly RD, Parmar G, Bayat L, Maitland MER, Lajoie GA, Edgell DR, Schild-Poulter C. Noncanonical functions of Ku may underlie essentiality in human cells. Sci Rep 2023; 13:12162. [PMID: 37500706 PMCID: PMC10374653 DOI: 10.1038/s41598-023-39166-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 07/20/2023] [Indexed: 07/29/2023] Open
Abstract
The Ku70/80 heterodimer is a key player in non-homologous end-joining DNA repair but is involved in other cellular functions like telomere regulation and maintenance, in which Ku's role is not fully characterized. It was previously reported that knockout of Ku80 in a human cell line results in lethality, but the underlying cause of Ku essentiality in human cells has yet to be fully explored. Here, we established conditional Ku70 knockout cells using CRISPR/Cas9 editing to study the essentiality of Ku70 function. While we observed loss of cell viability upon Ku depletion, we did not detect significant changes in telomere length, nor did we record lethal levels of DNA damage upon loss of Ku. Analysis of global proteome changes following Ku70 depletion revealed dysregulations of several cellular pathways including cell cycle/mitosis, RNA related processes, and translation/ribosome biogenesis. Our study suggests that the driving cause of loss of cell viability in Ku70 knockouts is not linked to the functions of Ku in DNA repair or at telomeres. Moreover, our data shows that loss of Ku affects multiple cellular processes and pathways and suggests that Ku plays critical roles in cellular processes beyond DNA repair and telomere maintenance to maintain cell viability.
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Affiliation(s)
- Rachel D Kelly
- Department of Biochemistry, Western University, London, ON, Canada
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Gursimran Parmar
- Department of Biochemistry, Western University, London, ON, Canada
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Laila Bayat
- Department of Biochemistry, Western University, London, ON, Canada
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Matthew E R Maitland
- Department of Biochemistry, Western University, London, ON, Canada
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Gilles A Lajoie
- Department of Biochemistry, Western University, London, ON, Canada
| | - David R Edgell
- Department of Biochemistry, Western University, London, ON, Canada
| | - Caroline Schild-Poulter
- Department of Biochemistry, Western University, London, ON, Canada.
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.
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Koehle AP, Brumwell SL, Seto EP, Lynch AM, Urbaniak C. Microbial applications for sustainable space exploration beyond low Earth orbit. NPJ Microgravity 2023; 9:47. [PMID: 37344487 DOI: 10.1038/s41526-023-00285-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 05/25/2023] [Indexed: 06/23/2023] Open
Abstract
With the construction of the International Space Station, humans have been continuously living and working in space for 22 years. Microbial studies in space and other extreme environments on Earth have shown the ability for bacteria and fungi to adapt and change compared to "normal" conditions. Some of these changes, like biofilm formation, can impact astronaut health and spacecraft integrity in a negative way, while others, such as a propensity for plastic degradation, can promote self-sufficiency and sustainability in space. With the next era of space exploration upon us, which will see crewed missions to the Moon and Mars in the next 10 years, incorporating microbiology research into planning, decision-making, and mission design will be paramount to ensuring success of these long-duration missions. These can include astronaut microbiome studies to protect against infections, immune system dysfunction and bone deterioration, or biological in situ resource utilization (bISRU) studies that incorporate microbes to act as radiation shields, create electricity and establish robust plant habitats for fresh food and recycling of waste. In this review, information will be presented on the beneficial use of microbes in bioregenerative life support systems, their applicability to bISRU, and their capability to be genetically engineered for biotechnological space applications. In addition, we discuss the negative effect microbes and microbial communities may have on long-duration space travel and provide mitigation strategies to reduce their impact. Utilizing the benefits of microbes, while understanding their limitations, will help us explore deeper into space and develop sustainable human habitats on the Moon, Mars and beyond.
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Affiliation(s)
- Allison P Koehle
- Department of Plant Science, Pennsylvania State University, University Park, PA, USA
| | - Stephanie L Brumwell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada
| | | | - Anne M Lynch
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
| | - Camilla Urbaniak
- ZIN Technologies Inc, Middleburg Heights, OH, USA.
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA.
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Diamond A, Diaz-Garza AM, Li J, Slattery SS, Merindol N, Fantino E, Meddeb-Mouelhi F, Karas BJ, Barnabé S, Desgagné-Penix I. Instability of extrachromosomal DNA transformed into the diatom Phaeodactylum tricornutum. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.102998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Vavitsas K, Kugler A, Satta A, Hatzinikolaou DG, Lindblad P, Fewer DP, Lindberg P, Toivari M, Stensjö K. Doing synthetic biology with photosynthetic microorganisms. PHYSIOLOGIA PLANTARUM 2021; 173:624-638. [PMID: 33963557 DOI: 10.1111/ppl.13455] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/22/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
The use of photosynthetic microbes as synthetic biology hosts for the sustainable production of commodity chemicals and even fuels has received increasing attention over the last decade. The number of studies published, tools implemented, and resources made available for microalgae have increased beyond expectations during the last few years. However, the tools available for genetic engineering in these organisms still lag those available for the more commonly used heterotrophic host organisms. In this mini-review, we provide an overview of the photosynthetic microbes most commonly used in synthetic biology studies, namely cyanobacteria, chlorophytes, eustigmatophytes and diatoms. We provide basic information on the techniques and tools available for each model group of organisms, we outline the state-of-the-art, and we list the synthetic biology tools that have been successfully used. We specifically focus on the latest CRISPR developments, as we believe that precision editing and advanced genetic engineering tools will be pivotal to the advancement of the field. Finally, we discuss the relative strengths and weaknesses of each group of organisms and examine the challenges that need to be overcome to achieve their synthetic biology potential.
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Affiliation(s)
- Konstantinos Vavitsas
- Enzyme and Microbial Biotechnology Unit, Department of Biology, National and Kapodistrian University of Athens, Zografou Campus, Athens, Greece
| | - Amit Kugler
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Alessandro Satta
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
- CSIRO Synthetic Biology Future Science Platform, Brisbane, Australia
| | - Dimitris G Hatzinikolaou
- Enzyme and Microbial Biotechnology Unit, Department of Biology, National and Kapodistrian University of Athens, Zografou Campus, Athens, Greece
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - David P Fewer
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Pia Lindberg
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Mervi Toivari
- VTT, Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Karin Stensjö
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
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Defrel G, Marsaud N, Rifa E, Martins F, Daboussi F. Identification of Loci Enabling Stable and High-Level Heterologous Gene Expression. Front Bioeng Biotechnol 2021; 9:734902. [PMID: 34660556 PMCID: PMC8517075 DOI: 10.3389/fbioe.2021.734902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/08/2021] [Indexed: 11/17/2022] Open
Abstract
Efficient and reliable genome engineering technologies have yet to be developed for diatoms. The delivery of DNA in diatoms results in the random integration of multiple copies, quite often leading to heterogeneous gene activity, as well as host instability. Transgenic diatoms are generally selected on the basis of transgene expression or high enzyme activity, without consideration of the copy number or the integration locus. Here, we propose an integrated pipeline for the diatom, Phaeodactylum tricornutum, that accurately quantifies transgene activity using a β-glucuronidase assay and the number of transgene copies integrated into the genome through Droplet Digital PCR (ddPCR). An exhaustive and systematic analysis performed on 93 strains indicated that 42% of them exhibited high β-glucuronidase activity. Though most were attributed to high transgene copy numbers, we succeeded in isolating single-copy clones, as well as sequencing the integration loci. In addition to demonstrating the impact of the genomic integration site on gene activity, this study identifies integration sites for stable transgene expression in Phaeodactylum tricornutum.
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Affiliation(s)
- Gilles Defrel
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Nathalie Marsaud
- Toulouse Biotechnology Institute (TBI), Plateforme Genome et Transcriptome (GeT-Biopuces) Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Etienne Rifa
- Toulouse Biotechnology Institute (TBI), Plateforme Genome et Transcriptome (GeT-Biopuces) Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Frédéric Martins
- Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), UMR1297, INSERM, UPS, Toulouse, France
- Plateforme Genome et Transcriptome (GeT), Genopole Toulouse, Toulouse, France
| | - Fayza Daboussi
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- Toulouse White Biotechnology (TWB), INSA, Toulouse, France
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