Today's KNOWLEDGE Share: The first synthetic Eukaryotic Genome.

Today's KNOWLEDGE Share

First Synthetic Eukaryotic Genome Completed

Scientists at the Macquarie University in Australia worked with an international team of scientists to achieve a major milestone in synthetic biology by completing the creation of the final chromosome in the world’s first synthetic yeast genome. This achievement represents the completion of the global Sc2.0 project to create the world’s first synthetic eukaryotic genome from Saccharomyces cerevisiae (baker’s yeast) and a new-to-nature tRNA neochromosome.

Using genome-editing techniques, including the CRISPR D-BUGS protocol, the team identified and corrected genetic errors that impacted yeast growth. These changes restored the strain’s ability to grow on glycerol, a key carbon source, under elevated temperatures.

The study “Construction and iterative redesign of synXVI a 903 kb synthetic Saccharomyces cerevisiae chromosome,” published in Nature Communications, demonstrates how engineered chromosomes can be designed, built and debugged to create more resilient organisms that could help secure supply chains for food and medicine production in the face of climate change and future pandemics, according to the researchers.

Landmark moment

“This is a landmark moment in synthetic biology,” says Sakkie Pretorius, PhD, co-chief investigator and deputy vice chancellor (research) of Macquarie University. “It is the final piece of a puzzle that has occupied synthetic biology researchers for many years now.”

“By successfully constructing and debugging the final synthetic chromosome, we’ve helped complete a powerful platform for engineering biology that could revolutionize how we produce medicines, sustainable materials, and other vital resources,” adds Distinguished Professor Ian Paulsen, PhD, director of the ARC Centre of Excellence in Synthetic Biology and co-director of the project.

The research team used specialized gene editing tools to identify and fix problems in the synthetic chromosome affecting how well the yeast could reproduce and grow under challenging conditions. They discovered that the placement of genetic markers near uncertain gene regions accidentally interfered with how essential genes were turned on and off, particularly affecting crucial processes like copper metabolism and how cells divide their genetic material.“The Sc2.0 global consortium to design and construct a synthetic genome based on the Saccharomyces cerevisiae genome commenced in 2006, comprising 16 synthetic chromosomes and a new-to-nature tRNA neochromosome,” write the investigators.

“In this paper we describe assembly and debugging of the 902,994-bp synthetic Saccharomyces cerevisiae chromosome synXVI of the Sc2.0 project. Application of the CRISPR D-BUGS protocol identified defective loci, which were modified to improve sporulation and recover wild-type like growth when grown on glycerol as a sole carbon source when grown at 37˚C. LoxPsym sites inserted downstream of dubious open reading frames impacted the 5’ UTR of genes required for optimal growth and were identified as a systematic cause of defective growth.

“Based on lessons learned from analysis of Sc2.0 defects and synXVI, an in-silico redesign of the synXVI chromosome was performed, which can be used as a blueprint for future synthetic yeast genome designs. The in-silico redesign of synXVI includes reduced PCR tag frequency, modified chunk and megachunk termini, and adjustments to allocation of loxPsym sites and TAA stop codons to dubious ORFs.

“This redesign provides a roadmap into applications of Sc2.0 strategies in non-yeast organisms.”

One of our key findings was how the positioning of genetic markers could disrupt the expression of essential genes, noted co-lead author Hugh Goold, PhD, research scientist at The NSW department of primary industries and Honorary Postdoctoral Research Fellow from Macquarie University’s School of Natural Sciences. “This discovery has important implications for future genome engineering projects, helping establish design principles that can be applied to other organisms.”

New possibilities in metabolic engineering and strain optimization

The completion of the chromosome known as synXVI allows scientists to explore new possibilities in metabolic engineering and strain optimization. The synthetic chromosome includes features that enable researchers to generate genetic diversity on demand, accelerating the development of yeasts with enhanced capabilities for biotechnology applications.

“The synthetic yeast genome represents a quantum leap in our ability to engineer biology,” according to Briardo Llorente, PhD, CSO at the Australian Genome Foundry.

The construction of such a large synthetic chromosome was only possible using the robotic instrumentation in the Australian Genome Foundry, he pointed out.

“This achievement opens up exciting possibilities for developing more efficient and sustainable biomanufacturing processes, from producing pharmaceuticals to creating new materials,” continued Llorente.

The research provides valuable insights for future synthetic biology projects, including potential applications in engineering plant and mammalian genomes, explains the research team whose new design principles for synthetic chromosomes to avoid placing potentially disruptive genetic elements near important genes will help other researchers working on synthetic chromosomes.

source:www.genengnews.com