Because proteins produced by eukaryotes are not processed by bacteria in the same way.
What are recombinant proteins?
Foreign genes are transfected into a host cell to create recombinant proteins. Recombinant proteins are frequently used to create pharmaceutical goods, protein-based polymers for drug administration, antibodies and enzymes for the treatment of diseases, protein scaffolds for tissue engineering, and a variety of other applications.
A major obstacle to these expressions is the absence of post-translational machinery and the creation of inactive protein as a result of inclusion body formation.
Being a prokaryote, E. coli lacks the membrane-bound nucleus (and other organelles) seen in eukaryotic cells, which is a drawback when utilizing it to express eukaryotic proteins. Accordingly, some eukaryotic genes may not operate as they would in E. coli, which can make it difficult to isolate them using selection processes that rely on gene expression. Additionally, it is difficult to guarantee that the prokaryotic host produces a completely functional protein if the goal of a cloning experiment is to make eukaryotic protein.
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