Synthetic Yeast Chromosome Manipulation

13th August 2018

Tom Drake

Singer Instruments, Roadwater, Somerset, TA23 0RE, UK.


Saccharomyces cerevisiae has long been utilised as a model organism due to the replicable nature of eukaryotic processes. Recent advances in genome editing, with tools such as CRISPR becoming more efficient and controlled, have enabled further advances into the manipulation of S. cerevisiae including modifications to the karyotype. Recent publications in Nature from Shao et al.1 and Luo et al.2 have done just this and opened the door to further research in chromosome biology and the evolutionary nature of chromosome development and function.



S. cerevisiae

Wild type S. cerevisiae contains 16 chromosomes, each with a distinct set of genes, a centromere and a telomere at each end. How this species came to have 16 chromosomes is a question not fully understood. For example, we know some of our closest ancestors in primates have 24 pairs of chromosomes, yet we only have 23 pairs. This is due to an ancestral fusion in what we now know as Chromosome 23. The number of chromosomes that a species has is unlikely to be chance, and more likely to be a product of an evolutionary advantage, but what happens if a species had less chromosomes?

Two groups simultaneously investigated what would happen to S. cerevisiae if they reduced the number of chromosomes, without removing any essential genes.

The two groups; from Institute for Systems Genetics, NYU Langone Health, USA, and Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, China both published their results in Nature on August 1st 2018. Both groups simultaneously worked on reducing the number of chromosomes whilst maintaining the genome of S. cerevisiae. Utilising CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), which is one of the most aggressive engineering strategies, Luo et al. removed telomeres and one centromere at a time to reduce the number of chromosomes from n=16 stepwise to n=2. This process produced a variety of strains with varying chromosomal numbers which are beneficial for further genotype and phenotype research.

Fusing yeast chromosomes

Shao et al. created a single linear chromosome containing each of the 16 chromosomes, through successive end-to-end fusions and centromere removal. Interestingly, Luo et al. were unable to produce a stable yeast with only one chromosome, yet Shao et al. were. This is potentially due to the differing techniques used to edit the genome, or something as simple as the order of the fusions contributing to the success of the strain. Further research into this would prove interesting as this may suggest why one method was more successful.

Great, now we have n=1 and n=2, so what?

Now the strains had been engineered to only contain one, or two, chromosomes, the question was to investigate what difference this made compared to the wild type (n=16). As the role that chromosomes can play in the regulation of genes is not yet fully understood, they were careful to investigate gene expression in their new strains. Surprisingly, there was very little difference identified in the transcriptome or phenome of the n=1 strain and n=16. The other group, with n=2, reported modest transcriptomic changes although growth was shown with no major defects. This research suggests that a reduction in karyotype may have much less of an impact than first thought.

What if they mate?

S. cerevisiae grows as a haploid, meaning it only has one copy of each chromosome – humans are diploid, in that we have two copies of each chromosome. Haploid yeast can grow asexually, and continue to be clonal, or they can mate sexually and form diploid yeast before sporulating into haploid spores. This process transfers genomic material through genetic recombination. What happens if two strains with differentiating numbers of chromosomes mate sexually?

Luo et al. investigated this, and with varying results, showed that as the number of chromosomes drops below 16, the viability of spores decreases. When n=12, the viability of spores was less than 10%. When the wild type crossed with n=8, the viability of spores was less than 1%. Conversely, these strains could mate with others with the same number of chromosomes and produce viable tetrads and spores. This suggests that eight chromosome fusion events isolate these strains from reproducing and therefore enable isolated genetic evolution potentially leading to new species.


What have we learnt?

From the genetic engineering of S. cerevisiae chromosomes, reducing the total number from 16 to 1, we’ve seen that there are no major reductions in transcriptomes or phenomes. The reduction in chromosome number has also been investigated in terms of mating ability, with spore viability decreasing as the difference in chromosome number increases. Although, each strain could still mate with an identical chromosome number, and produce viable spores.

This research has created the basis for further investigation into the function, structure and purpose of chromosomes and the role that they play in a variety of essential processes in the cell. Alongside paving the way for the study of chromosome evolution and the significance of chromosome number within S. cerevisiae.

Jef Boeke and his laboratory at the Institute for Systems Genetics, NYU Langone Health, New York, USA, utilise an MSM tetrad dissection microscope to dissect spores, and have more recently added a SporePlay+ tetrad dissection microscope, a ROTOR HDA colony manipulation robot and a PhenoBooth colony counter to their laboratory.
Jef Boeke - Singer Instruments MSM 400 Tetrad Dissection ScopeJef Boeke - Singer Instruments MSM 400 Tetrad Dissection Scope



1. Yangyang Shao, Ning Lu, Zhenfang Wu, Chen Cai, Shanshan Wang, Ling-Li Zhang, Fan Zhou, Shijun Xiao, Lin Liu, Xiaofei Zeng, Huajun Zheng, Chen Yang, Zhihu Zhao, Guoping Zhao, Jin-Qiu Zhou, Xiaoli Xue & Zhongjun Qin. Creating a functional single-chromosome yeast. Nature (2018)
2. Jingchuan Luo, Xiaoji Sun, Brendan P. Cormack & Jef D. Boeke. Karyotype engineering by chromosome fusion leads to reproductive isolation in yeast. Nature (2018).
3. IJdo JW, Baldini A, Ward DC, Reeders ST, Wells RA. Origin of human chromosome 2: an ancestral telomere-telomere fusion. Proc Natl Acad Sci U S A. (1991);88(20):9051-5.


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