They are unsuitable because eukaryotic proteins before they are synthesized through transcription giving rise to mRNA and translation to proteins undergo various modifications such as splicing (removal of introns and joinimg of the exons) etc due to the presence of introns in the eukaryotic genome which is absent in bacteria.
Thus, bacteria does not have machinery that will perform this functions as it has little to no introns and the products do not have to undergo modifications like eukaryotic genome.
Thus, without this, some functional proteins will not be expressed using the bacteria expression system.
They are not really suitable because of the reason that eukaryotic proteins before being synthesized through transcription giving rise to mRNA and the translation of proteins have to undergo many modifications, due to the presence of introns in eukaryotic genome which is not present in the bacteria. Eukaryotic is a simple form of gene which can be introduced in bacteria. Bacteria usually do not have capability to perform functions. The product does not undergo Eukaryotic genome modification as it contains linear DNA chromosomes. Unlike prokaryotic, eukaryotic have exon intron proteins of coding genes which has repetitive DNA.
