What's the difference between inserting a gene into a plasmid and inserting a gene into e coli's genome(not episome)?
I only know that e.coli has its own genome + episome/plasmid
when inserting a gene which I'd like to express, what's the differences in those two cases?
The plasmids use in molecular biology are different from the genome of the bacteria. They are recombinant and they contain at least an element for their replication such as oriP, an antibiobic resistance gene in order to only maintain bacteria that have integrated the plasmid and finally, the transcription unit coding the gene of interest. If the bacteria is only used for storage and amplification of the recombinant plasmid, but the expression of GOI is done in eukaryotic cells it can contains orther genetic elements such as a resistance gene for eukaryotic cells.
The main difference is stability. A plasmid is lost when you remove antibiotic selection while a chromosomaly integrated gene is maintained. For plasmid transformation you can use heat shock based transformation or electroporation. For chromosomal integration you can use either CRISPR or Lamda RED recombineering or P1 transduction. In case of the RED system and P1 you will need to have your gene linked to a a selective marker while with CRISPR it is not necessary.
There really are two notable differences, first is how you build the construct. As Hanna Alalam describes, it requires much more effort to build your construct in the chromosome than on a plasmid. But I think the major difference is copy number, or gene dosage. You will only have 1 copy if in the chromosome and perhaps hundreds if on a plasmid. So if you want high level expression, a plasmid is usually much better. If you want low lever expression, then the chromosome might be better.
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