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Efficient synthetic biology methods to genetically engineer microalgae

Scientists from the J. Craig Venter Institute (JCVI), Scripps Institution of Oceanography at UC San Diego, and their colleagues have published a paper outlining new synthetic biology methods to manipulate a type of microalgae called diatoms.

The researchers, including PhD students Rachel Diner and Jeff McQuiad and their advisor Andrew Allen from Scripps, conclude that these new and efficient methods will enable better understanding and manipulation of diatom genetics and thus facilitate advances in engineering these microoganisms to produce important products such as biofuels and chemicals. The paper, titled “Designer diatom episomes delivered by conjugation,” was published April 21st in Nature Communications.

Microalgae are some of the most abundant and important organisms in aquatic ecosystems. They use light energy to fuel photosynthesis and produce lipids for growth and other cellular functions. While they do this efficiently enough for their own growth and survival, they do not do this naturally at a scale that enables lipid biofuel and chemical production that is cost competitive with current fossil fuel prices.

While many researchers are working on ways to enhance diatoms and increase lipid production, there has not been development of efficient tools for large-scale DNA delivery that can enable effective genetic engineering methodology in diatoms like  that which exist for two main synthetic biology model organisms, Escherichia coli (E. coli) and Saccharomyces cerevisiae (yeast).

The JCVI-led team, which includes experts in diatom biology and others with expertise in synthetic biology, set out to discover and develop efficient genetic modification tools using episomes or plasmids. They were initially looking for diatom DNA sequences that allowed for plasmid replication but instead identified a yeast plasmid that replicates in diatoms and functions like an artificial chromosome.

“It is really exciting to see the power of synthetic biology applied to diatom research. For years transformative breakthroughs in diatom biology have been hindered by inefficiencies in DNA delivery methods,” said Allen, a joint associate professor at Scripps and JCVI. “This exciting new method for DNA delivery in diatoms, which is the direct result of collaboration between diatom biologists and ecologists with synthetic biologists, will enable studies of genome biology and evolution and biotechnological applications that were not possible previously.” 

The researchers then demonstrated that E. coli employs a mating process called conjugation that can be used to transfer the plasmid to the diatom. This is a very rapid and efficient genetic transfer process. The team then observed that E. coli can transfer plasmids into two genetically different diatom species, P. tricornutum and T. pseudonana, and that the plasmids replicate stably in both species.

“This new, very accessible method of genetic transformation will enable exciting new discoveries and progress in the study of marine microbes,” said Diner, a Scripps PhD student. “It is also amazing that bacteria can directly transfer genetic material into marine algae, an observation that raises exciting possibilities about horizontal gene transfer and the nature of eukaryotic microbial genomes.”

In addition to the implications of their work in biotechnology applications, the team also concluded that the research likely sheds light into the evolution of diatoms and adds more evidence to the notion that conjugation is an important influence on microbial ecology in oceans.

“This technology is so easy to use and does not require any expensive reagents or equipment. It really lowers the barriers to genetic manipulation of algae so that any laboratory studying diatoms can do this,” said senior author Philip Weyman.

Researchers from the National Center for Microscopy and Imaging Research at UC San Diego also contributed to the work in this paper.

This research is funded in part by the Gordon and Betty Moore Foundation through Grant GBMF3828 to Scripps, A.E. Allen, Synthetic Genomics Inc. and the United States Department of Energy Genomics Science Program  grant  DE-SC0008593 for biodesign to JCVI, A.E. Allen.

 

Story source: Scripps Institution of Oceanography at UC San Diego news release, 24 Apr 2015

Journal reference: Bogumil J. Karas et al. Designer diatom episomes delivered by bacterial conjugation. Nature Communications 6, Article number: 6925. Published 21 April 2015. doi:10.1038/ncomms7925. 

 

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