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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,

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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.

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  • $\begingroup$ 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, 2016 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, 2016 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, 2016 at 14:16

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