Isn'T A Prokaryotic Gene Continuous..?

Question

[SRKR]

I work on E. coli genomes and while going through the various genes present it, I have seen that in the coordinates area of the description it is suggested to join different regions of genome.

join(1463416..1465928,1467265..1467317,1468541..1472037)

I was wondering why is this so? Isn't a gene sequence meant to be continuous.

Another thing that I am not clear about is the difference between a gene and CDS - I see cases in E. coli (based on NCBI annotation file in FTP site) where mutiple CDS are present with gene, some times they overlap also. And in most of the cases the gene and the corresponding CDS have the same coordinates.

Please somebody clarify me regarding these two things.

Answer 1

[skymningen]

The gene in your link is only a pseudogene, that has been interrupted by transposases. (Gene on NCBI) In this (or similar) cases, also a procaryotic gene without introns can be joint from several locations.

[SRKR]

Yeah I realized that my gene is a pseudogene. I am working with a prokaryotic genome, which does not contain introns. So didn't got what you said in the second sentence.

[skymningen]

I just looked up, what is in the space included. (In this case, transposes.) This often gives you an idea. Functional genes in procaryotes shouldn't be interrupted, though.

Answer 2

[KCC]

The CDS is the coding DNA sequence, meaning it's the part of the genetic sequence that gets directly translated into a protein. Since a single gene can code for multiple proteins, there can be multiple CDS regions. For genes, that contain introns which do not code for protein sequence, this means the CDS may not be continous.

[Sudeep]

AFAIK isn't a prokaryotic gene intron free ? http://www.emunix.emich.edu/~rwinning/genetics/transcr.htm

[Devon Ryan]

No, they can have introns and there can even be splicing (though much less and most/all of the splicosomal pathway is missing).

[Sudeep]

Thanks, I looked it up after your answer and even found a publication ~30 years old (http://www.pnas.org/content/80/11/3309.full.pdf) , but what I don't understand is why do some texts and webpages say there are no introns in prokaryotes.

[Neilfws]

Some texts and webpages are simply wrong :) Just remember that biology is the science where every rule has an exception. Another example: the bacterial genus Gemmata, which has cellular compartmentalization.

[Devon Ryan]

To rephrase what Neilfws said, always remember that biology is messy :)