Deletion of Budding Yeast MAD2 Suppresses Clone-to-Clone Differences in Artificial Linear Chromosome Copy Numbers and Gives Rise to Higher Retention Rates.

Scott C Schuyler,Lin-Ing Wang,Yi-Shan Ding,Hsin-Yu Chen,Yi-Chieh Lee

doi:10.3390/microorganisms8101495

Scott C Schuyler, Lin-Ing Wang + Show 3 more

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https://doi.org/10.3390/microorganisms8101495

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Abstract

Our goal was to investigate the changes in artificial short-linear chromosome average copy numbers per cell arising from partial or full loss of Mitotic Arrest-Deficient 2 (MAD2) spindle checkpoint function in budding yeast Saccharomyces cerevisiae. Average artificial linear chromosome copy numbers in a population of cells, as measured by quantitative polymerase chain reactions (qPCR), and retention rates, as measured by fluctuation analyses, were performed on a total of 62 individual wild type and mad2∆ mutant haploid and diploid clones. Wild type cells, both haploids and diploids, displayed phenotypically unique clone-to-clone differences: one group of 15 clones displayed low-copy numbers per cell and high retention rates, were 1 clone was found to have undergone a genomic integration event, and the second group of 15 clones displayed high copy numbers per cell and low retention rates, with the latter values being consistent with the previously published results where only a single clone had been measured. These chromosome states were observed to be unstable when propagated for 10 days under selection, where high copy-low retention rate clones evolved into low copy-high retention rate clones, but no evidence for integration events was observed. By contrast, mad2∆ haploid and mad2∆/mad2∆ diploids displayed a suppression of the clone-to-clone differences, where 20 out of 21 clones had mid-level artificial linear chromosome copy numbers per cell, but maintained elevated chromosome retention rates. The elevated levels in retention rates in mad2∆ and mad2∆/mad2∆ cells were also maintained even in the absence of selection during growth over 3 days. MAD2/mad2∆ heterozygous diploids displayed multiple clonal groups: 4 with low copy numbers, 5 with mid-level copy numbers, and 1 with a high copy number of artificial linear chromosomes, but all 10 clones uniformly displayed low retention rates. Our observations reveal that MAD2 function contributes to the ability of yeast cells to maintain a high number of artificial linear chromosomes per cell in some clones, but, counter-intuitively, mad2∆ suppresses clone-to-clone differences and leads to an improvement in artificial linear chromosome retention rates yielding a more uniform and stable clonal population with mid-level chromosome copy numbers per cell.

Highlights

There is broad interest in using budding yeast artificial short-linear chromosomes as a tool to study the mechanisms of chromosome segregation in mitosis and as a technology to carry large fragments of exogenous DNA for recombinant protein expression, for bioengineering of entire metabolic pathways, where all of the pathway enzymes are carried on a single large artificial chromosome, or for amplification of exogenous DNA clones, such as fragments of the human or mouse genomes or other organisms [1,2]
Artificial linear chromosomes have the advantage of containing telomeres, a centromere, and an origin of replication all of which can contribute to a high rate of chromosome segregation fidelity relative to other smaller circular plasmids that lack all of these elements [3,4,5,6,7]
Our initial goal was to investigate the potential role of the mitotic checkpoint gene Mitotic Arrest-Deficient 2 (MAD2) in the maintenance of artificial linear chromosomes

Summary

Introduction

There is broad interest in using budding yeast artificial short-linear chromosomes as a tool to study the mechanisms of chromosome segregation in mitosis and as a technology to carry large fragments of exogenous DNA for recombinant protein expression, for bioengineering of entire metabolic pathways, where all of the pathway enzymes are carried on a single large artificial chromosome, or for amplification of exogenous DNA clones, such as fragments of the human or mouse genomes or other organisms [1,2]. Artificial linear chromosomes have the advantage of containing telomeres, a centromere, and an origin of replication all of which can contribute to a high rate of chromosome segregation fidelity relative to other smaller circular plasmids that lack all of these elements [3,4,5,6,7] These chromosome elements allow artificial linear chromosomes to maintain a presence in a population of yeast even in the absence of selection, at least for short durations of time. Average linear chromosome numbers in populations of yeast cells have been measured for individual clones in the past using Southern blots with an external piece of plasmid DNA as a reference standard, and retention rates, as measured by classic fluctuation analyses [6,7]. These quantitative studies were performed in wild-type yeast cell backgrounds containing all mitotic and cell cycle regulatory pathways which, in principle, should maximize chromosome segregation fidelity, but were limited to single clones [6,7]

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