Genome editing in diatoms: achievements and goals

  title={Genome editing in diatoms: achievements and goals},
  author={Peter G. Kroth and Atle Magnar Bones and Fayza Daboussi and Maria Immacolata Ferrante and Marianne Jaubert and Mikhail Kolot and Marianne Nymark and Carolina R{\'i}o B{\'a}rtulos and Andr{\'e}s Ritter and Monia Teresa Russo and Manuel Serif and Per Winge and Angela Falciatore},
  journal={Plant Cell Reports},
Diatoms are major components of phytoplankton and play a key role in the ecology of aquatic ecosystems. These algae are of great scientific importance for a wide variety of research areas, ranging from marine ecology and oceanography to biotechnology. During the last 20 years, the availability of genomic information on selected diatom species and a substantial progress in genetic manipulation, strongly contributed to establishing diatoms as molecular model organisms for marine biology research… 

Diatom Molecular Research Comes of Age: Model Species for Studying Phytoplankton Biology and Diversity[OPEN]

How functional genomics and reverse genetics have contributed to the understanding of this important class of microalgae in the context of evolution, cell biology, and metabolic adaptations is described.

A Critical Review of Genome Editing and Synthetic Biology Applications in Metabolic Engineering of Microalgae and Cyanobacteria.

The model microalgae and cyanobacteria presented as chassis hosts in synthetic biology, recent advances of their genome editing techniques by CRISPR technology, and potential applications of their metabolic engineering and regulation approaches are examined in this review.

Integrative omics identification, evolutionary and structural analysis of low affinity nitrate transporters in diatoms, diNPFs

A comprehensive characterization of the Nitrate Transporter 1/Peptide Transporter Family (NPF) in diatoms, diNPFs is reported, suggesting that diNPF diversification led to genetic adaptations that might contribute to di atoms ability to flourish in diverse environmental conditions.

An optimised method for intact nuclei isolation from diatoms.

This protocol has proved to be a flexible and versatile method to obtain intact nuclei preparations from different diatom species and it has the potential to speed up applications such as epigenetic explorations as well as single cell ("single nuclei") genomics, transcriptomics and proteomics in different diatoms.

Biochemical and Molecular Aspects of Phosphorus Limitation in Diatoms and Their Relationship with Biomolecule Accumulation

All current knowledge regarding the biochemical and molecular mechanisms of diatoms related to managing P deficiency are gathered in order to provide a wider insight into and understanding of their responses, as well as the metabolic pathways affected by the limitation of this nutrient.

Regulation of Carbon Metabolism by Environmental Conditions: A Perspective From Diatoms and Other Chromalveolates

Diatoms and other chromalveolates are understudied compared to the Viridiplantae, but it is believed that the ever-growing number of sequenced genomes combined with proteomics, metabolomics, enzyme measurements, and the application of novel techniques will provide a better understanding of how this important group of algae maintain their productivity under changing conditions.

Marine and Freshwater Plants: Challenges and Expectations

Six grand challenges, requiring multidisciplinary approaches, are introduced below and functional genomics and ecophysiology occupy a pivotal position linking molecular and cellular analyses and ecosystem-level studies.

Carbon Orientation in the Diatom Phaeodactylum tricornutum: The Effects of Carbon Limitation and Photon Flux Density

The results presented here demonstrate that under carbon limitation, diatom cells still reorient carbon metabolism toward either phosphoenolpyruvate or pyruvates, which serves as a hub for the production of more complex molecules.

Identification of Loci Enabling Stable and High-Level Heterologous Gene Expression

This study proposes an integrated pipeline for the diatom, Phaeodactylum tricornutum, that accurately quantifies transgene activity using a β-glucuronidase assay and the number of transgenes integrated into the genome through Droplet Digital PCR (ddPCR).



Genetic and metabolic engineering in diatoms

This review provides an overview of recent advances in genetic engineering methods for diatoms, from the development of gene expression cassettes and gene delivery methods, to cutting-edge genome-editing technologies.

CRISPR/Cas9 Gene Editing in the Marine Diatom Phaeodactylum tricornutum.

A detailed protocol of how to perform CRISPR/Cas9 gene editing of the marine diatom Phaeodactylum tricornutum is presented, including insertion of guide RNA target site in the diatom optimized CRISpr/Cas 9 vector (pKS diaCas9-sgRNA).

Gene silencing in the marine diatom Phaeodactylum tricornutum

Initial molecular analyses reveal that targeted downregulation likely occurs through transcriptional and post-transcriptional gene silencing mechanisms, and molecular players involved in RNA silencing in other eukaryotes are only poorly conserved in diatoms.

A new molecular tool for transgenic diatoms

It is demonstrated that the Pnr/Tnr cassette enables inducible gene expression and control of both the level and timing of mRNA and protein expression in transgenic diatoms.

Genome engineering empowers the diatom Phaeodactylum tricornutum for biotechnology.

The generation of an enhanced lipid-producing strain through the disruption of the UDP-glucose pyrophosphorylase gene exemplifies the power of genome engineering to harness diatoms for biofuel production.

Molecular toolbox for studying diatom biology in Phaeodactylum tricornutum.

Editing of the urease gene by CRISPR-Cas in the diatom Thalassiosira pseudonana

This work presents a methodology to edit the genome of Thalassiosira pseudonana, a model centric diatom with both ecological significance and high biotechnological potential, using CRISPR-Cas, a recent and powerful addition to the molecular toolbox which allows programmable genome editing.

Designer diatom episomes delivered by bacterial conjugation

A yeast-derived sequence is identified that enables stable episome replication in these diatoms even in the absence of antibiotic selection and it is shown that episomes are maintained as closed circles at copy number equivalent to native chromosomes.

Genetic Manipulation of Competition for Nitrate between Heterotrophic Bacteria and Diatoms

A genetically tractable model system using the pennate diatom Phaeodactylum tricornutum and the widespread heterotrophic bacteria Alteromonas macleodii to examine carbon-nitrogen dynamics is developed and lays the foundation for developing a mechanistic understanding of these interactions using co-culturing and genetic manipulation.

A new molecular tool for transgenic diatoms: control of mRNA and protein biosynthesis by an inducible promoter-terminator cassette.

It is demonstrated that the Pnr/Tnr cassette enables inducible gene expression and control of both the level and timing of mRNA and protein expression in transgenic diatoms.