Towards synthetic diatoms: The Phaeodactylum tricornutum Pt-syn 1.0 project

Pampuch, Mark; Walker, Emma J.L.; Karas, Bogumil J.

doi:10.1016/j.cogsc.2022.100611

Cited by 8 publications

(11 citation statements)

References 36 publications

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“…muelleri as a new model species for the photosynthetic organism. At present, “the Phaeodactylum tricornutum Pt-syn 1.0 project” for synthetic diatoms has been conceived with increasing interest in synthetic biology C.…”

Section: Introductionmentioning

confidence: 99%

CRISPR/Cas9-Mediated Genome Editing via Homologous Recombination in a Centric Diatom Chaetoceros muelleri

Yin

2023

ACS Synth. Biol.

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Chaetoceros, the most abundant genus of marine planktonic diatoms, can be used in mariculture. An effective genetic transformation system with a short transformation period was established in Chaetoceros muelleri by electroporation in our previous study. In this study, a sequence-specific clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 vector applicable for C. muelleri was constructed, and the expressions of sgRNA, resistance gene, and Cas9 gene were driven by the endogenous promoters U6, acetyl-CoA acetyltransferase, and fucoxanthin chlorophyll a/c binding protein, respectively, in the vector. Nitrate reductase (NR) and urease (URE) genes were edited in C. muelleri, and the NR knockout and NR/URE double-knockout lines displayed the strict auxotrophic phenotype. In addition, the DNA double-strand break was repaired by homologous recombination when a donor DNA was introduced. CRISPR/Cas9 technology was successfully applied to C. muelleri with an editing efficiency of up to 86%, providing a molecular tool for the study of basic biology in C. muelleri and its synthetic biology applications.

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Section: Introductionmentioning

confidence: 99%

CRISPR/Cas9-Mediated Genome Editing via Homologous Recombination in a Centric Diatom Chaetoceros muelleri

Yin

2023

ACS Synth. Biol.

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“…A number of diatom species also find industrial and commercial applications related to their biochemical traits, including aquaculture and the photosynthetic production of high-value bio-products, such as polyunsaturated fatty acids, pigments, and proteins (Butler et al ., 2020; Fabris, Abbriano, et al ., 2020). In particular, the genetically tractable Phaeodactylum tricornutum is a model organism for advanced bioengineering applications, including metabolic engineering and synthetic biology approaches, that could expand the biosynthetic capacity of diatoms beyond their natural traits (Hempel, Bozarth, et al ., 2011; Hempel, Lau, et al ., 2011; D’Adamo et al ., 2018; Fabris, George, et al ., 2020; Pampuch et al ., 2022; Slattery et al ., 2022; Windhagauer et al ., 2022).…”

Section: Introductionmentioning

confidence: 99%

“…The enzyme uridine monophosphate synthase (UMPS) is involved in de novo pyrimidine biosynthesis and its genetic locus is a relevant selectable marker in diatoms (Sakaguchi et al ., 2011; Serif et al ., 2018; Pampuch et al ., 2022). UMPS knock-out mutants are tolerant to 5-fluoroorotic acid (5-FOA) and are uracil auxotrophic.…”

Section: Introductionmentioning

confidence: 99%

Real time mobilization of a novel diatomMutator-Like Element(MULE) transposon to inactivate the uridine monophosphate synthase (UMPS) locus inPhaeodactylum tricornutum

Abbriano

George

Kahlke

et al. 2023

Preprint

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Diatoms are photosynthetic unicellular microalgae that drive global ecological phenomena in the biosphere and are emerging sustainable feedstock for an increasing number of industrial applications. Diatoms exhibit enormous taxonomic and genetic diversity, which often result in peculiar biochemical and biological traits. Transposable elements (TE) represent a substantial portion of diatom genomes and have been hypothesized to exert a relevant role in enriching genetic diversity and centrally contribute to genome evolution. Here, through long-read whole genome sequencing, we identified a novel Mutator-Like Element (MULE) in the model diatomPhaeodactylum tricornutum, and we report the direct observation of its mobilization within the course of one single laboratory experiment. Under selective conditions, this novel TE inactivated the uridine monophosphate synthase (UMPS) gene ofP. tricornutum, one of the two only endogenous genetic loci currently targeted for selectable auxotrophy in functional genetics and genome editing applications. We report the first, real-time observation of the mobilization of a transposon in diatoms that possesses novel peculiar features. These include the combined presence of a MULE transposase domain with Zinc finger, SWIM-type domains, and of a diatom-specific E3 ubiquitin ligase of the zinc finger UBR type, which indicate a novel 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. Ultimately, this raises relevant concerns on the targeting of loci such asUMPSas selectable markers for functional genetics and biotechnological applications in diatoms.

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“…A number of diatom species are also found in industrial and commercial applications related to their biochemical traits, including aquaculture and the photosynthetic production of high‐value bioproducts, such as polyunsaturated fatty acids, pigments and proteins (Butler et al., 2020; Fabris, Abbriano, et al., 2020). In particular, the genetically tractable Phaeodactylum tricornutum is a model organism for advanced bioengineering applications, including metabolic engineering and synthetic biology approaches, that could expand the biosynthetic capacity of diatoms beyond their natural traits (D'Adamo et al., 2018; Fabris, George, et al., 2020; Hempel, Bozarth, et al., 2011; Hempel, Lau, et al., 2011; Pampuch et al., 2022; Slattery et al., 2022; Windhagauer et al., 2022).…”

Section: Introductionmentioning

confidence: 99%

“…The enzyme uridine monophosphate synthase (UMPS) is involved in de novo pyrimidine biosynthesis and its genetic locus is a relevant selectable marker in diatoms (Pampuch et al., 2022; Sakaguchi et al., 2011; Serif et al., 2018). UMPS knockout mutants are tolerant to 5‐fluoroorotic acid (5‐FOA) and are uracil auxotrophic.…”

Section: Introductionmentioning

confidence: 99%

Mobilization of a diatom mutator‐like element (MULE) transposon inactivates the uridine monophosphate synthase (UMPS) locus in Phaeodactylum tricornutum

et al. 2023

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SUMMARYDiatoms 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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Towards synthetic diatoms: The Phaeodactylum tricornutum Pt-syn 1.0 project

Cited by 8 publications

References 36 publications

CRISPR/Cas9-Mediated Genome Editing via Homologous Recombination in a Centric Diatom Chaetoceros muelleri

CRISPR/Cas9-Mediated Genome Editing via Homologous Recombination in a Centric Diatom Chaetoceros muelleri

Real time mobilization of a novel diatomMutator-Like Element(MULE) transposon to inactivate the uridine monophosphate synthase (UMPS) locus inPhaeodactylum tricornutum

Mobilization of a diatom mutator‐like element (MULE) transposon inactivates the uridine monophosphate synthase (UMPS) locus in Phaeodactylum tricornutum

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