Synthetic genome engineering forging new frontiers for wine yeast

Abstract

Over the past 15 years, the seismic shifts caused by the convergence of biomolecular, chemical, physical, mathematical, and computational sciences alongside cutting-edge developments in information technology and engineering have erupted into a new field of scientific endeavor dubbed Synthetic Biology. Recent rapid advances in high-throughput DNA sequencing and DNA synthesis techniques are enabling the design and construction of new biological parts (genes), devices (gene networks) and modules (biosynthetic pathways), and the redesign of biological systems (cells and organisms) for useful purposes. In 2014, the budding yeast Saccharomyces cerevisiae became the first eukaryotic cell to be equipped with a fully functional synthetic chromosome. This was achieved following the synthesis of the first viral (poliovirus in 2002 and bacteriophage Phi-X174 in 2003) and bacterial (Mycoplasma genitalium in 2008 and Mycoplasma mycoides in 2010) genomes, and less than two decades after revealing the full genome sequence of a laboratory (S288c in 1996) and wine (AWRI1631 in 2008) yeast strain. A large international project -the Synthetic Yeast Genome (Sc2.0) Project -is now underway to synthesize all 16 chromosomes ($12 Mb carrying $6000 genes) of the sequenced S288c laboratory strain by 2018. If successful, S. cerevisiae will become the first eukaryote to cross the horizon of in silico design of complex cells through de novo synthesis, reshuffling, and editing of genomes. In the meantime, yeasts are being used as cell factories for the semi-synthetic production of high-value compounds, such as the potent antimalarial artemisinin, and food ingredients, such as resveratrol, vanillin, stevia, nootkatone, and saffron. As a continuum of previously genetically engineered industrially important yeast strains, precision genome engineering is bound to also impact the study and development of wine yeast strains supercharged with synthetic DNA. The first taste of what the future holds is the de novo production of the raspberry ketone aroma compound, 4-[4-hydroxyphenyl]butan-2-one, in a wine yeast strain (AWRI1631), which was recently achieved via metabolic pathway engineering and synthetic enzyme fusion. A peek over the horizon is revealing that the future of "Wine Yeast 2.0" is already here. Therefore, this article seeks to help prepare the wine industry -an industry rich in history and tradition on the one hand, and innovation on the other -for the inevitable intersection of the ancient art practiced by winemakers and the inventive science of pioneering "synthetic genomicists". It would be prudent to proactively engage all stakeholders -researchers, industry practitioners, policymakers, regulators, commentators, and consumers -in a meaningful dialog about the potential challenges and opportunities emanating from Synthetic Biology. To capitalize on the new vistas of synthetic yeast genomics, this paper presents wine yeast research in a fresh context, raises important questions and proposes new directions. ARTICLE HISTORY

Advances in Metabolic Engineering of Saccharomyces cerevisiae for the Production of Industrially and Clinically Important Chemicals

“…Resveratrol is a polyketide derivative with potent antioxidant properties and it has been recently brought to market as a bio-product [72]. Earlier reports on the production of resveratrol were based on bioconversion of aromatic precursors such as p-coumaric acid and tyrosine by engineered S. cerevisiae strains [73,74].…”

Conducting Wine Symphonics with the Aid of Yeast Genomics

“…The goals of this large international project -the Synthetic Yeast Genome Project (referred to as the Yeast 2.0 or Sc2.0 project) include answering a broad spectrum of "profound questions about fundamental properties of chromosomes, genome organisation, gene content, function of RNA splicing, the extent to which small RNAs play a role in yeast biology, the distinction between prokaryotes and eukaryotes, and questions relating to genome structure and evolution" while recognising that "the eventual 'synthetic yeast' being designed and refined could ultimately play an important practical role" (www.syntheticyeast.org). The early learnings from the Yeast 2.0 project are already starting to forge new frontiers for wine yeast development (Pretorius, 2016).…”

“…Those who research in the emerging field of synthetic genomics have to work relentlessly to engage all stakeholders, including fellow scientists, industry practitioners, policymakers, regulators, commentators and consumers [23]. It is important for researchers to explain that the development of 'synthetic' yeast models in the laboratory would help yeast researchers to further expand their understanding of the biological fundamentals, limitations and potential of existing wine yeastsmuch like what the physicist Richard Feynman meant when he famously said "What I cannot create, I do not understand".…”

“…Once the best candidate strains have been identified, yeast researchers employ hybridisation, mutagenesis, genetic engineering or genome engineering techniques to genetically improve the oenological properties of selected strains (Figure 14). Improved mutants and hybrids are routinely used in commercial winemaking whereas genetically modified (GM) strains generated through genetic and genome engineering are largely reserved for research purposes at this stage [13,[17][18][19][20][21][22][23]. Researchers are investigating non-GM strategies, including hybridisation, mutagenesis and adaptive laboratory evolution, to circumvent the current anti-GM constraints from consumers facing comestible food products generated through bioengineering strategies [24].…”

“…Figure 22. The construction of a 'synthetic' wine strain of Saccharomyces cerevisiae capable of producing raspberry aroma in Chardonnay (adapted from [23]). This is the first wine yeast containing a 'synthetic DNA circuit' coding for raspberry ketone formation.…”