2
$\begingroup$

I was wondering if someone knows the answer to this quenstion, because I can't find a clear answer, maybe there isn't a clear answer :).

question Which of these two is right? or maybe both influence each other

  • GC% determines codon bias
  • codon bias determines GC%

Thankyou,

$\endgroup$
2
$\begingroup$

Think about it this way, the G-C content is averaged over the entire genome, and varies between different species. Whether you are dealing with prokaryotes, with relatively compact genomes, or with eukaryotes, with lots of non-coding regions, the open reading frames will, in general, be influenced by the average G-C content across the genome. Therefore we would predict that in species with lower G-C their open reading frames would be biased to using the codons in the genetic code that are higher in A-T. N.B. this also means that their tRNAs should also favour anticodons higher in A-T. In contrast, we would predict that in species with high G-C content, the open reading frames would be biased, in general, to using codons that are higher in G-C. That is all G-C bias in codons is; for some amino acids like Met and Trp, there is only a single codon, but for other amino acids there can be up to six codons that can each encode the same amino acid side chain. It is in these ones with a higher number of degenerate codons that you are going to see the effect of codon bias.

$\endgroup$
  • $\begingroup$ Thankyou for the answers, it cleared up a lott, but there is one thing I still don't get: I thought the GC bias is determined by the availibility of tRNA, so if a gene needs to be transcribed and translated to a protein very often like ribosomes, it prefers codons of which al lot of tRNA availible for, what am i missing here? @mdperry $\endgroup$ – KingBoomie Apr 5 '16 at 7:59
  • $\begingroup$ This may be debatable (the cause of GC bias). If the abundance, or cellular concentration, of individual tRNAs is fixed, or pre-determined, then over many generations the individuals in the population who use more of the corresponding codons would be able to replicate faster, and over time, the G+C% of the species would appear to change. However, it is difficult for me to imagine a mechanism that would fix, or pre-determine, the concentrations of individual tRNAs in the cell. The concentrations are a combination of the rate of synthesis and the rate of decay. There is probably feedback. $\endgroup$ – mdperry Apr 5 '16 at 11:39
  • $\begingroup$ Maybe the codon bias is determined by the GC% of the whole genome, so favoring the most GC rich codons. Futher, de codon usage is maybe determined by the availibility of tRNA, It's just what I think? @mdperry $\endgroup$ – KingBoomie Apr 5 '16 at 14:16

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.