Synthetic Genomics From a Yeast Perspective

Abstract

Synthetic Genomics focuses on the construction of rationally designed chromosomes and genomes and offers novel approaches to study biology and to construct synthetic cell factories. Currently, progress in Synthetic Genomics is hindered by the inability to synthesize DNA molecules longer than a few hundred base pairs, while the size of the smallest genome of a self-replicating cell is several hundred thousand base pairs. Methods to assemble small fragments of DNA into large molecules are therefore required. Remarkably powerful at assembling DNA molecules, the unicellular eukaryote Saccharomyces cerevisiae has been pivotal in the establishment of Synthetic Genomics. Instrumental in the assembly of entire genomes of various organisms in the past decade, the S. cerevisiae genome foundry has a key role to play in future Synthetic Genomics developments.

Synthesis and assembly of full-length cyanophage A-4L genome

“…We explored ORFs located between B-fragments ( Supplementary Table S2 ), which were deleted as designed ( Table 1 ). S. cerevisiae can stitch together multiple DNA sequences efficiently and with high fidelity [ 5 ]. Recombinant plasmids with pRS415 as backbone were assembled via TAR in yeast and transferred into E. coli ( Fig.…”

“…Synthetic biology has advanced to the point of synthesizing the entire genome, including Mycoplasma genome [ 1 ], yeast chromosome [ 2 ], Escherichia coli genome [ 3 ] and mouse mitochondrial genome [ 4 ]. Large assemblies may be unstably maintained in E. coli but can be easily completed in yeast [ 5 ]. Viral genomes [ 6 ] have also been constructed, including poliovirus, simian immunodeficiency virus, coxsackievirus, adenovirus, tobacco mosaic virus, human endogenous retrovirus, coronavirus, as well as bacteriophage ɸ X174, T7, AP205 and G4 [ 7 ].…”

Cross-species microbial genome transfer: a Review

“…However, due to the slow growth rate, insufficient DNA recombination ability, and low transformation efficiency of the organisms, the tools and methods cannot always be performed directly in the original species. Therefore, it is necessary to transfer the genome into model organisms such as Saccharomyces cerevisiae , Escherichia coli , or Bacillus subtilis ( Blount, 2015 ; Nielsen, 2019 ; Errington and Aart, 2020 ; Koster et al, 2022 ; Malci et al, 2022 ). Model organisms have the advantages of a short life cycle, a clear genetic background, easy cultivation, and a simple experimental procedure, making them very suitable as a platform for genome synthesis.…”

Automation protocol for high-efficiency and high-quality genomic DNA extraction from Saccharomyces cerevisiae

“…Unlike many eukaryotes, S. cerevisiae prefers to repair DNA by homologous recombination, which enables the incorporation of custom genetic sequences into the genome with as little as *50 bp of homology flanking a sequence [1,2]. This feature has been used for decades to insert custom sequences into the genome for a wide array of biotechnology applications, including the assembly of whole genomes from kilobase-sized fragments [3], and the assembly of custom plasmid sequences from linear DNA [4]. Although plasmids are flexible tools for assembling transcriptional units [5], there is greater variability in gene expression from plasmids versus from genes in the genome [5][6][7], and plasmids are not stably inherited if selection is not maintained [8].…”