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Windhagauer M, Doblin MA, Signal B, Kuzhiumparambil U, Fabris M, Abbriano RM. Metabolic response to a heterologous poly-3-hydroxybutyrate (PHB) pathway in Phaeodactylum tricornutum. Appl Microbiol Biotechnol 2024; 108:104. [PMID: 38212969 DOI: 10.1007/s00253-023-12823-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 01/13/2024]
Abstract
The marine diatom Phaeodactylum tricornutum is an emerging host for metabolic engineering, but little is known about how introduced pathways are integrated into the existing metabolic framework of the host or influence transgene expression. In this study, we expressed the heterologous poly-3-hydroxybutyrate (PHB) pathway using episomal expression, which draws on the precursor acetyl coenzyme-A (AcCoA). By experimentally perturbing cultivation conditions, we gained insight into the regulation of the endogenous metabolism in transgenic lines under various environmental scenarios, as well as on alterations in AcCoA flux within the host cell. Biosynthesis of PHB led to distinct shifts in the metabolome of the host, and further analysis revealed a condition-dependent relationship between endogenous and transgenic metabolic pathways. Under N limitation, which induced a significant increase in neutral lipid content, both metabolic and transcriptomic data suggest that AcCoA was preferably shunted into the endogenous pathway for lipid biosynthesis over the transgenic PHB pathway. In contrast, supply of organic carbon in the form of glycerol supported both fatty acid and PHB biosynthesis, suggesting cross-talk between cytosolic and plastidial AcCoA precursors. This is the first study to investigate the transcriptomic and metabolomic response of diatom cell lines expressing a heterologous multi-gene pathway under different environmental conditions, providing useful insights for future engineering attempts for pathways based on the precursor AcCoA. KEY POINTS: • PHB expression had minimal effects on transcription of adjacent pathways. • N limitation favoured native lipid rather than transgenic PHB synthesis. • Glycerol addition allowed simultaneous lipid and PHB accumulation.
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Affiliation(s)
- Matthias Windhagauer
- Climate Change Cluster, University of Technology Sydney, 15 Broadway, Ultimo, NSW, 2007, Australia.
| | - Martina A Doblin
- Climate Change Cluster, University of Technology Sydney, 15 Broadway, Ultimo, NSW, 2007, Australia
| | - Brandon Signal
- School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia
| | | | - Michele Fabris
- SDU Biotechnology, Faculty of Engineering, University of Southern Denmark, 5230, Odense M, Denmark
| | - Raffaela M Abbriano
- Climate Change Cluster, University of Technology Sydney, 15 Broadway, Ultimo, NSW, 2007, Australia
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2
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Macdonald Miller S, Abbriano RM, Herdean A, Banati R, Ralph PJ, Pernice M. Random mutagenesis of Phaeodactylum tricornutum using ultraviolet, chemical, and X-radiation demonstrates the need for temporal analysis of phenotype stability. Sci Rep 2023; 13:22385. [PMID: 38104215 PMCID: PMC10725415 DOI: 10.1038/s41598-023-45899-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 10/25/2023] [Indexed: 12/19/2023] Open
Abstract
We investigated two non-ionising mutagens in the form of ultraviolet radiation (UV) and ethyl methanosulfonate (EMS) and an ionising mutagen (X-ray) as methods to increase fucoxanthin content in the model diatom Phaeodactylum tricornutum. We implemented an ultra-high throughput method using fluorescence-activated cell sorting (FACS) and live culture spectral deconvolution for isolation and screening of potential pigment mutants, and assessed phenotype stability by measuring pigment content over 6 months using high-performance liquid chromatography (HPLC) to investigate the viability of long-term mutants. Both UV and EMS resulted in significantly higher fucoxanthin within the 6 month period after treatment, likely as a result of phenotype instability. A maximum fucoxanthin content of 135 ± 10% wild-type found in the EMS strain, a 35% increase. We found mutants generated using all methods underwent reversion to the wild-type phenotype within a 6 month time period. X-ray treatments produced a consistently unstable phenotype even at the maximum treatment of 1000 Grays, while a UV mutant and an EMS mutant reverted to wild-type after 4 months and 6 months, respectively, despite showing previously higher fucoxanthin than wild-type. This work provides new insights into key areas of microalgal biotechnology, by (i) demonstrating the use of an ionising mutagen (X-ray) on a biotechnologically relevant microalga, and by (ii) introducing temporal analysis of mutants which has substantial implications for strain creation and utility for industrial applications.
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Affiliation(s)
- Sean Macdonald Miller
- Faculty of Science, Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW, 2007, Australia.
| | - Raffaela M Abbriano
- Faculty of Science, Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Andrei Herdean
- Faculty of Science, Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Richard Banati
- Australian Nuclear Science and Technology Organisation (ANSTO), Kirrawee DC, NSW, 2232, Australia
- Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Peter J Ralph
- Faculty of Science, Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Mathieu Pernice
- Faculty of Science, Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW, 2007, Australia
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3
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Walsh SK, Wolkis D, Abbriano RM, Barton KE. Variability in seed salinity tolerance in an island coastal community. Ann Bot 2023; 132:485-498. [PMID: 37665955 PMCID: PMC10666991 DOI: 10.1093/aob/mcad129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/31/2023] [Indexed: 09/06/2023]
Abstract
BACKGROUND AND AIMS Islands, with their long coastlines and increased vulnerability to sea level rise, offer compelling opportunities to investigate the salinity tolerance of coastal plants. Seeds are generally more vulnerable than other plant stages to increased stressors. The aim of this study was to characterize salinity tolerance during germination across a diverse pool of 21 species from 14 plant families found in coastal communities throughout the Hawaiian Islands in order to increase our general understanding of coastal plant ecology for conservation and restoration. METHODS Seeds of each species were exposed to unfiltered/untreated seawater (35 ppt total salinity) and two salinity treatments (10 and 20 ppt) in which the seawater was diluted with distilled water, and germination percent and timing were compared to seeds in a distilled water control. Non-germinated seeds were then tested for recovery germination. We quantified and compared germination percent, time and recovery among species and across salinity levels and tested for heterogeneity related to seed size, dormancy class, habit and threatened status. KEY RESULTS Although salinity tolerance varied considerably among species, salinity exposure generally reduced and delayed germination. The greatest effects were detected at higher salinity levels. Recovery germination overall was higher for seeds that had been exposed to higher salinity. None of the factors we explored emerged as predictors of salinity tolerance except seed mass, which tended to enhance germination at higher salinity. CONCLUSIONS Species responses to salinity exposure indicate high vulnerability of coastal systems to increased salinity stress, and variability among species could lead to shifts in community assembly and composition under sea level rise. These results can help guide coastal ecosystem conservation and restoration management decisions in the face of climate change.
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Affiliation(s)
- Seana K Walsh
- Department of Science and Conservation, National Tropical Botanical Garden, Kalāheo, Hawaiʻi, USA
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Dustin Wolkis
- Department of Science and Conservation, National Tropical Botanical Garden, Kalāheo, Hawaiʻi, USA
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Raffaela M Abbriano
- Department of Science and Conservation, National Tropical Botanical Garden, Kalāheo, Hawaiʻi, USA
| | - Kasey E Barton
- School of Life Sciences, University of Hawaiʻi at Mānoa, Honolulu, Hawaiʻi, USA
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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. Plant J 2023; 115:926-936. [PMID: 37147901 DOI: 10.1111/tpj.16271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Yee DP, Samo TJ, Abbriano RM, Shimasaki B, Vernet M, Mayali X, Weber PK, Mitchell BG, Hildebrand M, Decelle J, Tresguerres M. The V-type ATPase enhances photosynthesis in marine phytoplankton and further links phagocytosis to symbiogenesis. Curr Biol 2023; 33:2541-2547.e5. [PMID: 37263270 PMCID: PMC10326425 DOI: 10.1016/j.cub.2023.05.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/20/2023] [Accepted: 05/09/2023] [Indexed: 06/03/2023]
Abstract
Diatoms, dinoflagellates, and coccolithophores are dominant groups of marine eukaryotic phytoplankton that are collectively responsible for the majority of primary production in the ocean.1 These phytoplankton contain additional intracellular membranes around their chloroplasts, which are derived from ancestral engulfment of red microalgae by unicellular heterotrophic eukaryotes that led to secondary and tertiary endosymbiosis.2 However, the selectable evolutionary advantage of these membranes and the physiological significance for extant phytoplankton remain poorly understood. Since intracellular digestive vacuoles are ubiquitously acidified by V-type H+-ATPase (VHA),3 proton pumps were proposed to acidify the microenvironment around secondary chloroplasts to promote the dehydration of dissolved inorganic carbon (DIC) into CO2, thus enhancing photosynthesis.4,5 We report that VHA is localized around the chloroplasts of centric diatoms and that VHA significantly contributes to their photosynthesis across a wide range of oceanic irradiances. Similar results in a pennate diatom, dinoflagellate, and coccolithophore, but not green or red microalgae, imply the co-option of phagocytic VHA activity into a carbon-concentrating mechanism (CCM) is common to secondary endosymbiotic phytoplankton. Furthermore, analogous mechanisms in extant photosymbiotic marine invertebrates6,7,8 provide functional evidence for an adaptive advantage throughout the transition from endosymbiosis to symbiogenesis. Based on the contribution of diatoms to ocean biogeochemical cycles, VHA-mediated enhancement of photosynthesis contributes at least 3.5 Gtons of fixed carbon per year (or 7% of primary production in the ocean), providing an example of a symbiosis-derived evolutionary innovation with global environmental implications.
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Affiliation(s)
- Daniel P Yee
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Cell and Plant Physiology Laboratory, University of Grenoble Alpes, CNRS, CEA, INRAE, and IRIG, 17 Avenue des Martyrs, Grenoble 38054, Auvergne-Rhone-Alpes, France.
| | - Ty J Samo
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Raffaela M Abbriano
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Bethany Shimasaki
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Maria Vernet
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - B Greg Mitchell
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Mark Hildebrand
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Johan Decelle
- Cell and Plant Physiology Laboratory, University of Grenoble Alpes, CNRS, CEA, INRAE, and IRIG, 17 Avenue des Martyrs, Grenoble 38054, Auvergne-Rhone-Alpes, France
| | - Martin Tresguerres
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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Barolo L, Commault AS, Abbriano RM, Padula MP, Kim M, Kuzhiumparambil U, Ralph PJ, Pernice M. Unassembled cell wall proteins form aggregates in the extracellular space of Chlamydomonas reinhardtii strain UVM4. Appl Microbiol Biotechnol 2022; 106:4145-4156. [PMID: 35599258 PMCID: PMC9200674 DOI: 10.1007/s00253-022-11960-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/28/2022] [Accepted: 05/02/2022] [Indexed: 11/25/2022]
Abstract
Abstract
The green microalga Chlamydomonas reinhardtii is emerging as a promising cell biofactory for secreted recombinant protein (RP) production. In recent years, the generation of the broadly used cell wall–deficient mutant strain UVM4 has allowed for a drastic increase in secreted RP yields. However, purification of secreted RPs from the extracellular space of C. reinhardtii strain UVM4 is challenging. Previous studies suggest that secreted RPs are trapped in a matrix of cell wall protein aggregates populating the secretome of strain UVM4, making it difficult to isolate and purify the RPs. To better understand the nature and behaviour of these extracellular protein aggregates, we analysed and compared the extracellular proteome of the strain UVM4 to its cell-walled ancestor, C. reinhardtii strain 137c. When grown under the same conditions, strain UVM4 produced a unique extracellular proteomic profile, including a higher abundance of secreted cell wall glycoproteins. Further characterization of high molecular weight extracellular protein aggregates in strain UVM4 revealed that they are largely comprised of pherophorins, a specific class of cell wall glycoproteins. Our results offer important new insights into the extracellular space of strain UVM4, including strain-specific secreted cell wall proteins and the composition of the aggregates possibly related to impaired RP purification. The discovery of pherophorins as a major component of extracellular protein aggregates will inform future strategies to remove or prevent aggregate formation, enhance purification of secreted RPs, and improve yields of recombinant biopharmaceuticals in this emerging cell biofactory. Key points • Extracellular protein aggregates hinder purification of recombinant proteins in C. reinhardtii • Unassembled cell wall pherophorins are major components of extracellular protein aggregates • Known aggregate composition informs future strategies for recombinant protein purification Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-11960-9.
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Affiliation(s)
- Lorenzo Barolo
- Climate Change Cluster, University of Technology Sydney, 15 Broadway, Ultimo, Sydney, NSW, 2007, Australia.
| | - Audrey S Commault
- Climate Change Cluster, University of Technology Sydney, 15 Broadway, Ultimo, Sydney, NSW, 2007, Australia
| | - Raffaela M Abbriano
- Climate Change Cluster, University of Technology Sydney, 15 Broadway, Ultimo, Sydney, NSW, 2007, Australia
| | - Matthew P Padula
- School of Life Sciences and Proteomics Core Facility, Faculty of Science, University of Technology Sydney, 15 Broadway, Ultimo, Sydney, NSW, 2007, Australia
| | - Mikael Kim
- Climate Change Cluster, University of Technology Sydney, 15 Broadway, Ultimo, Sydney, NSW, 2007, Australia
| | | | - Peter J Ralph
- Climate Change Cluster, University of Technology Sydney, 15 Broadway, Ultimo, Sydney, NSW, 2007, Australia
| | - Mathieu Pernice
- Climate Change Cluster, University of Technology Sydney, 15 Broadway, Ultimo, Sydney, NSW, 2007, Australia
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Commault AS, Kuzhiumparambil U, Herdean A, Fabris M, Jaramillo-Madrid AC, Abbriano RM, Ralph PJ, Pernice M. Methyl Jasmonate and Methyl-β-Cyclodextrin Individually Boost Triterpenoid Biosynthesis in Chlamydomonas Reinhardtii UVM4. Pharmaceuticals (Basel) 2021; 14:125. [PMID: 33562714 PMCID: PMC7915139 DOI: 10.3390/ph14020125] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/01/2021] [Accepted: 02/01/2021] [Indexed: 01/01/2023] Open
Abstract
The commercialisation of valuable plant triterpenoids faces major challenges, including low abundance in natural hosts and costly downstream purification procedures. Endeavours to produce these compounds at industrial scale using microbial systems are gaining attention. Here, we report on a strategy to enrich the biomass of the biotechnologically-relevant Chlamydomonas reinhardtii strain UVM4 with valuable triterpenes, such as squalene and (S)-2,3-epoxysqualene. C. reinhardtii UVM4 was subjected to the elicitor compounds methyl jasmonate (MeJA) and methyl-β-cyclodextrine (MβCD) to increase triterpene yields. MeJA treatment triggered oxidative stress, arrested growth, and altered the photosynthetic activity of the cells, while increasing squalene, (S)-2,3-epoxysqualene, and cycloartenol contents. Applying MβCD to cultures of C. reinhardtii lead to the sequestration of the two main sterols (ergosterol and 7-dehydroporiferasterol) into the growth medium and the intracellular accumulation of the intermediate cycloartenol, without compromising cell growth. When MβCD was applied in combination with MeJA, it counteracted the negative effects of MeJA on cell growth and physiology, but no synergistic effect on triterpene yield was observed. Together, our findings provide strategies for the triterpene enrichment of microalgal biomass and medium.
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Affiliation(s)
- Audrey S. Commault
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia; (U.K.); (A.H.); (M.F.); (A.C.J.-M.); (R.M.A.); (P.J.R.); (M.P.)
| | - Unnikrishnan Kuzhiumparambil
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia; (U.K.); (A.H.); (M.F.); (A.C.J.-M.); (R.M.A.); (P.J.R.); (M.P.)
| | - Andrei Herdean
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia; (U.K.); (A.H.); (M.F.); (A.C.J.-M.); (R.M.A.); (P.J.R.); (M.P.)
| | - Michele Fabris
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia; (U.K.); (A.H.); (M.F.); (A.C.J.-M.); (R.M.A.); (P.J.R.); (M.P.)
- Synthetic Biology Future Science Platform, CSIRO, Brisbane, QLD 4001, Australia
| | - Ana Cristina Jaramillo-Madrid
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia; (U.K.); (A.H.); (M.F.); (A.C.J.-M.); (R.M.A.); (P.J.R.); (M.P.)
| | - Raffaela M. Abbriano
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia; (U.K.); (A.H.); (M.F.); (A.C.J.-M.); (R.M.A.); (P.J.R.); (M.P.)
| | - Peter J. Ralph
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia; (U.K.); (A.H.); (M.F.); (A.C.J.-M.); (R.M.A.); (P.J.R.); (M.P.)
| | - Mathieu Pernice
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia; (U.K.); (A.H.); (M.F.); (A.C.J.-M.); (R.M.A.); (P.J.R.); (M.P.)
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George J, Kahlke T, Abbriano RM, Kuzhiumparambil U, Ralph PJ, Fabris M. Metabolic Engineering Strategies in Diatoms Reveal Unique Phenotypes and Genetic Configurations With Implications for Algal Genetics and Synthetic Biology. Front Bioeng Biotechnol 2020; 8:513. [PMID: 32582656 PMCID: PMC7290003 DOI: 10.3389/fbioe.2020.00513] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/30/2020] [Indexed: 12/23/2022] Open
Abstract
Diatoms are photosynthetic microeukaryotes that dominate phytoplankton populations and have increasing applicability in biotechnology. Uncovering their complex biology and elevating strains to commercial standards depends heavily on robust genetic engineering tools. However, engineering microalgal genomes predominantly relies on random integration of transgenes into nuclear DNA, often resulting in detrimental “position-effects” such as transgene silencing, integration into transcriptionally-inactive regions, and endogenous sequence disruption. With the recent development of extrachromosomal transgene expression via independent episomes, it is timely to investigate both strategies at the phenotypic and genomic level. Here, we engineered the model diatom Phaeodactylum tricornutum to produce the high-value heterologous monoterpenoid geraniol, which, besides applications as fragrance and insect repellent, is a key intermediate of high-value pharmaceuticals. Using high-throughput phenotyping we confirmed the suitability of episomes for synthetic biology applications and identified superior geraniol-yielding strains following random integration. We used third generation long-read sequencing technology to generate a complete analysis of all transgene integration events including their genomic locations and arrangements associated with high-performing strains at a genome-wide scale with subchromosomal detail, never before reported in any microalga. This revealed very large, highly concatenated insertion islands, offering profound implications on diatom functional genetics and next generation genome editing technologies, and is key for developing more precise genome engineering approaches in diatoms, including possible genomic safe harbour locations to support high transgene expression for targeted integration approaches. Furthermore, we have demonstrated that exogenous DNA is not integrated inadvertently into the nuclear genome of extrachromosomal-expression clones, an important characterisation of this novel engineering approach that paves the road to synthetic biology applications.
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Affiliation(s)
- Jestin George
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia
| | - Tim Kahlke
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia
| | - Raffaela M Abbriano
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia
| | | | - Peter J Ralph
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia
| | - Michele Fabris
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia.,CSIRO Synthetic Biology Future Science Platform, Brisbane, QLD, Australia
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Fabris M, George J, Kuzhiumparambil U, Lawson CA, Jaramillo-Madrid AC, Abbriano RM, Vickers CE, Ralph P. Extrachromosomal Genetic Engineering of the Marine Diatom Phaeodactylum tricornutum Enables the Heterologous Production of Monoterpenoids. ACS Synth Biol 2020; 9:598-612. [PMID: 32032487 DOI: 10.1021/acssynbio.9b00455] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Geraniol is a commercially relevant plant-derived monoterpenoid that is a main component of rose essential oil and used as insect repellent. Geraniol is also a key intermediate compound in the biosynthesis of the monoterpenoid indole alkaloids (MIAs), a group of over 2000 compounds that include high-value pharmaceuticals. As plants naturally produce extremely small amounts of these molecules and their chemical synthesis is complex, industrially sourcing these compounds is costly and inefficient. Hence, microbial hosts suitable to produce MIA precursors through synthetic biology and metabolic engineering are currently being sought. Here, we evaluated the suitability of a eukaryotic microalga, the marine diatom Phaeodactylum tricornutum, for the heterologous production of monoterpenoids. Profiling of endogenous metabolism revealed that P. tricornutum, unlike other microbes employed for industrial production of terpenoids, accumulates free pools of the precursor geranyl diphosphate. To evaluate the potential for larger synthetic biology applications, we engineered P. tricornutum through extrachromosomal, episome-based expression, for the heterologous biosynthesis of the MIA intermediate geraniol. By profiling the production of geraniol resulting from various genetic and cultivation arrangements, P. tricornutum reached the maximum geraniol titer of 0.309 mg/L in phototrophic conditions. This work provides (i) a detailed analysis of P. tricornutum endogenous terpenoid metabolism, (ii) a successful demonstration of extrachromosomal expression for metabolic pathway engineering with potential gene-stacking applications, and (iii) a convincing proof-of-concept of the suitability of P. tricornutum as a novel production platform for heterologous monoterpenoids, with potential for complex pathway engineering aimed at the heterologous production of MIAs.
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Affiliation(s)
- 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
| | - Jestin George
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW 2007, Australia
| | | | - Caitlin A. Lawson
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW 2007, Australia
| | | | - Raffaela M. Abbriano
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW 2007, Australia
| | - Claudia E. Vickers
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Peter Ralph
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW 2007, Australia
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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. Front Plant Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Barolo L, Abbriano RM, Commault AS, George J, Kahlke T, Fabris M, Padula MP, Lopez A, Ralph PJ, Pernice M. Perspectives for Glyco-Engineering of Recombinant Biopharmaceuticals from Microalgae. Cells 2020; 9:E633. [PMID: 32151094 PMCID: PMC7140410 DOI: 10.3390/cells9030633] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 02/28/2020] [Accepted: 02/28/2020] [Indexed: 12/15/2022] Open
Abstract
Microalgae exhibit great potential for recombinant therapeutic protein production, due to lower production costs, immunity to human pathogens, and advanced genetic toolkits. However, a fundamental aspect to consider for recombinant biopharmaceutical production is the presence of correct post-translational modifications. Multiple recent studies focusing on glycosylation in microalgae have revealed unique species-specific patterns absent in humans. Glycosylation is particularly important for protein function and is directly responsible for recombinant biopharmaceutical immunogenicity. Therefore, it is necessary to fully characterise this key feature in microalgae before these organisms can be established as industrially relevant microbial biofactories. Here, we review the work done to date on production of recombinant biopharmaceuticals in microalgae, experimental and computational evidence for N- and O-glycosylation in diverse microalgal groups, established approaches for glyco-engineering, and perspectives for their application in microalgal systems. The insights from this review may be applied to future glyco-engineering attempts to humanize recombinant therapeutic proteins and to potentially obtain cheaper, fully functional biopharmaceuticals from microalgae.
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Affiliation(s)
- Lorenzo Barolo
- Climate Change Cluster, University of Technology Sydney, Broadway Campus, Ultimo NSW 2007, Sydney, Australia; (R.M.A.); (A.S.C.); (J.G.); (T.K.); (M.F.); (P.J.R.)
| | - Raffaela M. Abbriano
- Climate Change Cluster, University of Technology Sydney, Broadway Campus, Ultimo NSW 2007, Sydney, Australia; (R.M.A.); (A.S.C.); (J.G.); (T.K.); (M.F.); (P.J.R.)
| | - Audrey S. Commault
- Climate Change Cluster, University of Technology Sydney, Broadway Campus, Ultimo NSW 2007, Sydney, Australia; (R.M.A.); (A.S.C.); (J.G.); (T.K.); (M.F.); (P.J.R.)
| | - Jestin George
- Climate Change Cluster, University of Technology Sydney, Broadway Campus, Ultimo NSW 2007, Sydney, Australia; (R.M.A.); (A.S.C.); (J.G.); (T.K.); (M.F.); (P.J.R.)
| | - Tim Kahlke
- Climate Change Cluster, University of Technology Sydney, Broadway Campus, Ultimo NSW 2007, Sydney, Australia; (R.M.A.); (A.S.C.); (J.G.); (T.K.); (M.F.); (P.J.R.)
| | - Michele Fabris
- Climate Change Cluster, University of Technology Sydney, Broadway Campus, Ultimo NSW 2007, Sydney, Australia; (R.M.A.); (A.S.C.); (J.G.); (T.K.); (M.F.); (P.J.R.)
- CSIRO Synthetic Biology Future Science Platform, Brisbane, QLD 4001, Australia
| | - Matthew P. Padula
- School of Life Sciences and Proteomics Core Facility, Faculty of Science, University of Technology Sydney, Ultimo NSW 2007, Sydney, Australia;
| | - Angelo Lopez
- Department of Chemistry, University of York, York, YO10 5DD, UK;
| | - Peter J. Ralph
- Climate Change Cluster, University of Technology Sydney, Broadway Campus, Ultimo NSW 2007, Sydney, Australia; (R.M.A.); (A.S.C.); (J.G.); (T.K.); (M.F.); (P.J.R.)
| | - Mathieu Pernice
- Climate Change Cluster, University of Technology Sydney, Broadway Campus, Ultimo NSW 2007, Sydney, Australia; (R.M.A.); (A.S.C.); (J.G.); (T.K.); (M.F.); (P.J.R.)
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Smith SR, Glé C, Abbriano RM, Traller JC, Davis A, Trentacoste E, Vernet M, Allen AE, Hildebrand M. Transcript level coordination of carbon pathways during silicon starvation-induced lipid accumulation in the diatom Thalassiosira pseudonana. New Phytol 2016; 210:890-904. [PMID: 26844818 PMCID: PMC5067629 DOI: 10.1111/nph.13843] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 12/03/2015] [Indexed: 05/06/2023]
Abstract
Diatoms are one of the most productive and successful photosynthetic taxa on Earth and possess attributes such as rapid growth rates and production of lipids, making them candidate sources of renewable fuels. Despite their significance, few details of the mechanisms used to regulate growth and carbon metabolism are currently known, hindering metabolic engineering approaches to enhance productivity. To characterize the transcript level component of metabolic regulation, genome-wide changes in transcript abundance were documented in the model diatom Thalassiosira pseudonana on a time-course of silicon starvation. Growth, cell cycle progression, chloroplast replication, fatty acid composition, pigmentation, and photosynthetic parameters were characterized alongside lipid accumulation. Extensive coordination of large suites of genes was observed, highlighting the existence of clusters of coregulated genes as a key feature of global gene regulation in T. pseudonana. The identity of key enzymes for carbon metabolic pathway inputs (photosynthesis) and outputs (growth and storage) reveals these clusters are organized to synchronize these processes. Coordinated transcript level responses to silicon starvation are probably driven by signals linked to cell cycle progression and shifts in photophysiology. A mechanistic understanding of how this is accomplished will aid efforts to engineer metabolism for development of algal-derived biofuels.
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Affiliation(s)
- Sarah R. Smith
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
- J. Craig Venter Institute4120 Capricorn LaneLa JollaCA92037USA
| | - Corine Glé
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
| | - Raffaela M. Abbriano
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
| | - Jesse C. Traller
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
| | - Aubrey Davis
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
| | - Emily Trentacoste
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
| | - Maria Vernet
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
| | - Andrew E. Allen
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
- J. Craig Venter Institute4120 Capricorn LaneLa JollaCA92037USA
| | - Mark Hildebrand
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
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Hildebrand M, Abbriano RM, Polle JEW, Traller JC, Trentacoste EM, Smith SR, Davis AK. Metabolic and cellular organization in evolutionarily diverse microalgae as related to biofuels production. Curr Opin Chem Biol 2013; 17:506-14. [PMID: 23538202 DOI: 10.1016/j.cbpa.2013.02.027] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 02/18/2013] [Accepted: 02/26/2013] [Indexed: 12/18/2022]
Abstract
Microalgae are among the most diverse organisms on the planet, and as a result of symbioses and evolutionary selection, the configuration of core metabolic networks is highly varied across distinct algal classes. The differences in photosynthesis, carbon fixation and processing, carbon storage, and the compartmentation of cellular and metabolic processes are substantial and likely to transcend into the efficiency of various steps involved in biofuel molecule production. By highlighting these differences, we hope to provide a framework for comparative analyses to determine the efficiency of the different arrangements or processes. This sets the stage for optimization on the based on information derived from evolutionary selection to diverse algal classes and to synthetic systems.
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Affiliation(s)
- Mark Hildebrand
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202, USA.
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