A new family of yeast vectors and S288C-derived strains for the systematic analysis of gene function

Recombinant multicopy plasmids in yeast – interactions with the endogenous 2 μm

Flp-mediated site specific intramolecular recombination in Saccharomyces cerevisiae is considered responsible for amplification of the endogenous 2 μm plasmid. For YEp-type vectors, a similar mechanism can be imagined by which such plasmids achieve high copy numbers, a trait desired for many research applications and necessary for industrial production. We have cultivated yeast carrying one of six isomeric YEp-type model expression plasmids under two different conditions and back transformed the shuttle vectors into Escherichia coli. Our analysis of 586 ampR clones represents a high-resolution snapshot of plasmid forms present in the transformed yeast cells with a detection limit of structural changes of <2%. Altered forms summed up to about 11%, constituting likely a lower limit. We have observed two categories of recombination events. One is Flp based, with products of intermolecular recombination with the 2 μm, likely intermediates that are prerequisites for YEp-type plasmid amplification. The other type is based on Flp-independent homologous recombination leading to oligomerization of such plasmids also in a 2μm-free [cir°] strain, i.e. in the absence of Flp. Beyond the general maintenance and its functional sequences, only the gene of interest and its expression might have an impact on the physiology of the host.

Impact of plasmid architecture on stability and yEGFP3 reporter gene expression in a set of isomeric multicopy vectors in yeast

Multicopy episomal plasmids in yeast, used whenever elevated levels of foreign or homologous gene expression are necessary, are known to be less stable compared to the endogenous 2-μm plasmid they are based on, at least without selective pressure. Considering that rich medium favors growth rate and, simultaneously, is less expensive than selective medium, enhancing stability in non-selective medium is extremely desirable. In this study, we changed the architecture of a multicopy model expression plasmid, creating six isoforms (same size, same DNA content but different positions and orientations of the expression block) and studied mitotic stability, copy number, as well as reporter yEGFP3 expression between isoforms. With one isoform being significantly more stable than the others and another one exhibiting elevated plasmid copy numbers in rich medium, we show that consideration of the arrangement of the plasmid elements might be crucial for productivity employing Saccharomyces cerevisiae as a host. We strongly believe that the ideal architecture has to be assessed for each case and assembly strategy has to begin by evaluating the stability of the vector backbone before insertion of the desired gene. For the plasmid set studied, yEGFP3 reporter production depends more on mitotic stability than on elevated plasmid copy numbers in a small number of cells retaining the plasmid under non-selective conditions.

A set of isomeric episomal plasmids for systematic examination of mitotic stability in Saccharomyces cerevisiae

Yeast episomal shuttle vectors (YEp type) are commonly used in fundamental research and biotechnology whenever elevated product levels are desired. Their instability, however, poses an impediment not only in industrial scale fermentation. In order to analyse instability which might be linked to plasmid structure, a series of YEp type plasmids that are identical in size has been assembled, differing only in the overall arrangement of the fragments used. The performance of the eight plasmid isoforms was studied with respect to mitotic stability. While transformation efficiency in two laboratory strains of Saccharomyces cerevisiae does not differ dramatically between the eight plasmids, the plasmids do not, however, perform equally well in terms of segregational stability. Although stable at about 90% plasmid-bearing cells in selective medium, under non-selective conditions, three plasmid forms performed better than the other five with an up to 5.7-fold higher stability as compared with the least favourable isoform. In a subset of four plasmids (including stable and unstable isoforms) copy numbers were determined. Furthermore the functionality of the selection marker was characterized with respect to plasmid-derived relative HIS3 transcript levels. No significant differences in HIS3 transcript levels could be observed between strains carrying any one of the four plasmids. Ruling out copy number and performance of HIS3, the results indicate nevertheless that plasmid architecture has an impact on mitotic segregation in yeast and that construction of an expression vector should take into account that the plasmid backbone itself might already show a more or less favourable arrangement of its segments. © 2017 The Authors. Yeast published by John Wiley & Sons, Ltd.

The yeast telomerase RNA, TLC1, participates in two distinct modes of TLC1-TLC1 association processes in vivo

Telomerase core enzyme minimally consists of the telomerase reverse transcriptase domain-containing protein (Est2 in budding yeast S. cerevisiae) and telomerase RNA, which contains the template specifying the telomeric repeat sequence synthesized. Here we report that in vivo, a fraction of S. cerevisiae telomerase RNA (TLC1) molecules form complexes containing at least two molecules of TLC1, via two separable modes: one requiring a sequence in the 3′ region of the immature TLC1 precursor and the other requiring Ku and Sir4. Such physical TLC1-TLC1 association peaked in G1 phase and did not require telomere silencing, telomere tethering to the nuclear periphery, telomerase holoenzyme assembly, or detectable Est2-Est2 protein association. These data indicate that TLC1-TLC1 associations reflect processes occurring during telomerase biogenesis; we propose that TLC1-TLC1 associations and subsequent reorganization may be regulatory steps in telomerase enzymatic activation.

New and Redesigned pRS Plasmid Shuttle Vectors for Genetic Manipulation of Saccharomycescerevisiae

We have constructed a set of 42 plasmid shuttle vectors based on the widely used pRS series for use in the budding yeast Saccharomyces cerevisiae and the bacterium Escherichia coli. This set of pRSII plasmids includes new shuttle vectors that can be used with histidine and adenine auxotrophic laboratory yeast strains carrying mutations in the genes HIS2 and ADE1, respectively. Our pRSII plasmids also include updated versions of commonly used pRS plasmids from which common restriction sites that occur within their yeast-selectable biosynthetic marker genes have been removed to increase the availability of unique restriction sites within their polylinker regions. Hence, our pRSII plasmids are a complete set of integrating, centromere and 2μ episomal plasmids with the biosynthetic marker genes ADE2, HIS3, TRP1, LEU2, URA3, HIS2, and ADE1 and a standardized selection of at least 16 unique restriction sites in their polylinkers. Additionally, we have expanded the range of drug selection options that can be used for PCR-mediated homologous replacement using pRS plasmid templates by replacing the G418-resistance kanMX4 cassette of pRS400 with MX4 cassettes encoding resistance to phleomycin, hygromycin B, nourseothricin, and bialaphos. Finally, in the process of generating the new plasmids, we have determined several errors in existing publicly available sequences for several commonly used yeast plasmids. Using our updated sequences, we constructed pRS plasmid backbones with a unique restriction site for inserting new markers to facilitate future expansion of the pRS series.

Synthetic cooperation in engineered yeast populations

Cooperative interactions are key to diverse biological phenomena ranging from multicellularity to mutualism. Such diversity makes the ability to create and control cooperation desirable for potential applications in areas as varied as agriculture, pollutant treatment, and medicine. Here we show that persistent cooperation can be engineered by introducing a small set of genetic modifications into previously noninteracting cell populations. Specifically, we report the construction of a synthetic obligatory cooperative system, termed CoSMO (cooperation that is synthetic and mutually obligatory), which consists of a pair of nonmating yeast strains, each supplying an essential metabolite to the other strain. The behavior of the two strains in isolation, however, revealed unintended constraints that restrict cooperation, such as asymmetry in starvation tolerance and delays in nutrient release until near cell death. However, the joint system is shown mathematically and experimentally to be viable over a wide range of initial conditions, with oscillating population ratio settling to a value predicted by nutrient supply and consumption. Unexpectedly, even in the absence of explicitly engineered mechanisms to stabilize cooperation, the cooperative system can consistently develop increased ability to survive reductions in population density. Extending synthetic biology from the design of genetic circuits to the engineering of ecological interactions, CoSMO provides a quantitative system for linking processes at the cellular level to the collective behavior at the system level, as well as a genetically tractable system for studying the evolution of cooperation.

New 'marker swap' plasmids for converting selectable markers on budding yeast gene disruptions and plasmids

Marker swap plasmids can be used to change markers for genes disrupted with nutritional markers in the yeast Saccharomyces cerevisiae. We describe 18 new marker swap plasmids, and we also review other plasmids available for marker conversions. All of these plasmids have long regions of flanking sequence identity, and thus the efficiency of homologous recombination mediated by marker conversion is very high. Marker swaps allow one to easily perform crosses to construct double mutant strains even if each of the disrupted strains contains the same marker, as is the case with the KanMX marker used in the yeast knockout collection. Marker swaps can also be used to change the selectable marker on plasmids, eliminating the need for subcloning.