ARC Centre of Excellence in Synthetic Biology

Synthetic Biology


3, Apr 2024

Highs and lows of creating world-first chromosomes

A decade-long quest to create chromosomes for the world’s first entirely synthetic yeast is nearly complete for Macquarie University researchers.

‘Would we have started this if we knew it was going to take 10 years? I don’t know,’ says Professor Paulsen, Director of the Australian Research Council Centre of Excellence in Synthetic Biology. ‘But we sure have learned a lot about designing and building a genome.’

Centre researchers at Macquarie University are a few tweaks away from completing Australia’s role in the global Yeast 2.0 project to produce the first-ever complex synthetic organism – a version of the common baker’s yeast, Saccharomyces cerevisiae.

Macquarie University has been working with nine other institutions, including New York University, Tsinghua University, Imperial College, University of Edinburgh and the National University of Singapore. Each university took responsibility for designing and building one or more of the 16 chromosomes that will make up the engineered version of the industrial workhorse used in baking, brewing and wine-making for thousands of years.

Macquarie is responsible for the construction of two chromosomes, SynXIV and synXVI. These chromosomes are now fully assembled, although Syn XVI is undergoing some final debugging. The complete synthetic chromosome Syn XIV has now been published in Cell Genomics. ‘In building this synthetic chromosome, the design accidentally introduced several severe growth defects and we were able to identify and fix these defects through a combination of rational debugging and evolution experiments,’ says Dr Tom Williams, lead author of the paper.

In addition to rebuilding yeast into a synthetic version, Macquarie researchers have been working on proof of principle that it’s possible to build on a genome scale. A genome is an organism’s complete set of DNA, a set of instructions that’s carefully organised into paragraphs (genes) and chapters (chromosomes). Being able to build on this level opens up possibilities for creating suites of new-to-nature chromosomes or ‘neochromosomes’.

Macquarie University researchers have been involved in the construction of three neochromosomes. The first of these projects was done in collaboration with the Australian Wine Research Institute. Unique genomic sequences from a range of yeast strains – including those used in wine, sake and biofuel production – were assembled into a completely new chromosome in the laboratory strain. This additional genetic material imparted new characteristics, such as allowing the laboratory strain to ferment sugars it normally can’t use, widening the feedstocks available for industrial purposes. This work was published in Nature Communications in 2022.

Dr Roy Walker, who was at the University of Edinburgh until joining Macquarie University, played a major role in designing and building the tRNA neochromosome. The genes for tRNAs – small RNA molecules that play a key role in protein synthesis – have been relocated from native chromosomes and placed onto a single synthetic designer chromosome. In future, this will eventually be added to a host yeast cell with a fully synthetic genome. The 10-year project to build the tRNA neochromosome was recently published in Cell in collaboration with researchers at the University of Manchester and the Max Planck Institutes. Roy shared co-first-authorship with Dr Daniel Schindler. More recently Macquarie University PhD student Tom Collier has designed and built another new-to-nature chromosome, this time for producing fats.

‘Taking something that exists and redesigning it is a nightmare because you accidentally break things all the time,’ says Professor Paulsen. ‘Building something new and putting them inside a cell doesn’t have the same troubleshooting problems. ‘It’s like putting an extension on a house instead of pulling out all the wiring and plumbing of a house and building it from scratch while  blindfolded.’

Building a wholly synthetic yeast genome will be an amazing accomplishment but it is just the beginning, says Macquarie University Project Lead and Deputy Vice Chancellor (Research), Professor Sakkie Pretorius. ‘This is history in the making as all previous ground rules for research in biology are being rewritten. ‘Once we can synthesise the full genetic blueprint of a yeast we can then apply the same techniques to increasingly more complex organisms. The possibilities in medicine or the environment, for example, are truly mind-blowing.’

He is hoping to use a yeast strain to produce triacylglycerides, the types of oils found in cosmetics and common household products. The hope eventually is to replace the production of unsustainable vegetable oils that are leading to widespread deforestation.

The main challenge of Yeast 2.0, Professor Paulsen says, has not been to build a synthetic chromosome. That can be done in six months. ‘It’s because we’ve inadvertently made changes that made the cell sick. Working out what made it sick has been the work of years and years,’ he says.

‘This trouble shooting, fixing the defects, has been a challenging journey. If we had our time again, we’d design it very differently. Parts of the design caused 95 percent of the problems.’ Professor Paulsen says building the new-to-nature chromosomes has been far less problematic.