Introduction: Prokaryotic vectors are good to express the proteins of eukaryotic or prokaryotic origin but in few specific cases, they are not well suited. Such as, eukaryotic protein is unstable, require special environment for folding or losses its the biological activity. In few cases especially in the case of production of therapeutic proteins, cross contamination of bacterial products may cause clinical problems in humans. Eukaryotic vector system is designed to clone and express gene in eukaryotic cells such as yeast (saccharomyces cerevisiae), insect and mammalian cell lines. There are two different types of eukaryotic vectors-

1. Vector as extrachromosomal DNA- These vectors remains in eukaryotic cell as extrachromosomal DNA and express the protein.
2. Integration Vector- These vectors carry an integration site to facilitate recombination medited integration into the chromosomal DNA of the host cell.
In general, eukaryotic vector contains origin of replication from bacteria and eukaryotic cells. In addition, they also contain different selectable markers for prokaryotic and eukaryotic cells. These modifications allow to use and perform easy cloning procedure in bacterial host system to generate recombinant construct containing foreign DNA in vector. The basic features required for a vector discussed previously for prokaryotic system is also required for eukaryotic vector as well.  
Saccharomyces cerevisiae vector system-There are 3 types of yeast vector system. These all have couple of similar features such as presence of MCS, shuttle vector (origin of replication for E.coli and Yeast) and presence of selectable markers.     

1. Episomal vector- Yeast episomal vector are constructed by combining bacterial plasmid either with yeast 2µ origin of replication or with autonomous replication sequence (ARS). The yeast vector containing ARS are high copy number plasmid but they are unstable in the absence of selection pressure. This can be over-come by adding centromeric sequence (CEN) but it affects the plasmid copy number and as a result it become a low copy number plasmid. ARS based yeast plasmids are not very popular for expression of protein. In contrast, 2µ based vector are very popular for heterologous protein expression. A representative 2µ based episomal yeast vector is shown in Figure 19.1. It is a 6.3kb plasmid with a copy number in the range of 50-100 per cell. These plasmids are much more stable than ARS based plasmids.