Hi all,
I have a question regarding coding regions in bacterial genomes: can genes be encoded on both strands like this ?
If so, which one is considered as the sense strand ?
Thank you so much for your help!
Yes genes can be encoded on both strands, not only in bacteria but also in viruses and eukaryotes.
The "sense" strand is relative to each gene. So it will be the top strand for the genes on the top strand (also called the Whatson or "+" strand) and vice-versa for the genes on the bottom strand (also called the Crick or "-" strand).
yes, for example ryeA/ryeB on E Coli K12:
If so, which one is considered as the sense strand ?
I think it's meaningless
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Thank you so much Carlo Yague for your reply.
So, if I understood correctly, this can be schematically represented like this:
Do you have any article or references that say that "the sense strand is relative to each gene"?
From wikipedia: "Wherever a gene exists on a DNA molecule, one strand is the coding strand (or sense strand), and the other is the noncoding strand (also called the antisense strand,[3] anticoding strand, template strand or transcribed strand)."
With this as a ref: Lewin, Benjamin (2008). Genes IX. Oxford University Press. p. 129, 235. ISBN 978-0-7637-4063-4.
Any textbook of the very basics of molecular biology and transcription.
Thank you for your response. Do you have any examples, please?
Molecular Biology of the Celland similar books, it's really undergrad course knowledge, you likely will not find a paper in the classical sense of original article that contains one single referenceable line, it's something that is common knowledge and will be covered in any undergrad course that teaches transcription. Take any book and go to the transcription chapter.It really is a logical consequence of the fact that DNA is a double-strand, directional and transcription starts from a single strand, resulting in single-stranded (m)RNA, hence the orientation of transcription is directed and therefore the orientation of a gene is relative to the strand that the transcription start site is located on.
Thank you very much for these clarifications.
For DNA regions that do not contain any genes, we can not determine which strand is the sense strand, correct?
A_heath it might be helpful to remember that, as @ATpoint points out, DNA is directional - each strand has a 5' to 3' directionality (these refer to the unique moieties placed on specific positions of the carbon for sugar molecules found at each end), and the strands are anti-parallel. DNA is read from 5' to 3' on each strand. By convention, the top strand is read left to right, and if it codes for a gene, this is the sense strand. The bottom strand is read right to left, and if it codes for a gene, this would be the sense strand. If there is no gene on either strand - there is nothing to make "sense" of, therefore there would be no sense strand. No different than asking which lines on a blank page make sense.
Thank you for your help. I am wondering this because I am designing PCR primers and would like to attribute the forward and reverse sequences correctly. Sometimes, I am targetting intergenic regions, hence my question.
You should consult someone with experience to double-check your design. While not rocket science PCR can be tricky depending on what you want to do and some guidance helps with that. It can teek weeks debugging a non-working PCR, and you want to be sure it's not a rookie mistake in the primer design. Or if you do not have anyone to consult you may ask in molecular biology-focused fora for a quick review of your plan. Maybe reddit or so.