Codon usage

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Codon usage (Engl. Codon usage ), and codon bias , describes the phenomenon that variants of the universal genetic code of different species are used with varying frequency. Certain codons of the degenerate code are preferred, which ultimately corresponds to the tRNA concentration within the cell. Codon usage plays a major role in regulating protein biosynthesis . Rarely used codons can slow down translation , while frequently used codons can speed up translation.

application

In the genetic engineering production of human proteins in bacteria (which is often preferred for reasons of cost), attention is paid to the fact that the bacterium, for example E. coli , has a different codon usage than humans. It is genetically modified so that the bacteria can read the alien human gene quickly and efficiently for translation just like their own genes. The result is an adapted gene sequence which largely corresponds to the codon usage repertoire of the bacterial strain, but still codes for the same protein. Another possibility is codon optimization , whereby the expression rate can be increased in the production of a recombinant protein by using only those 20 amino acid codons that are most strongly expressed in the respective species.

Codon Usage Table

The following table shows the frequency of use of a specific codon per 1000 codons of a DNA sequence. The codon bias of the E. coli safety strain K12 was compared with that of baker's yeast and that of humans.

amino acid Codon E. coli K12 S. cerevisiae H. sapiens amino acid Codon E. coli K12 S. cerevisiae H. sapiens
Valine (V) GUU 16.8 22.1 11.0 Alanine (A) GCU 10.7 21.2 18.4
GUC 11.7 11.8 14.5 GCC 31.6 12.6 27.7
GUA 11.5 11.8 7.1 GCA 21.1 16.2 15.8
GUG 26.4 10.8 28.1 GCG 38.5 6.2 7.4
Leucine (L) CUU 11.9 12.3 13.2 Proline (P) CCU 8.4 13.5 17.5
CUC 10.5 5.4 19.6 CCC 6.4 6.8 19.8
CUA 5.3 13.4 7.2 CCA 6.6 18.3 16.9
CUG 46.9 10.5 39.6 CCG 26.7 5.3 6.9
Leucine (L) UUA 15.2 26.2 7.7 Serine (S) UCU 5.7 23.5 15.2
UUG 11.9 27.2 12.9 UCC 5.5 14.2 17.7
Phenylalanine (F) UUU 19.7 26.1 17.6 UCA 7.8 18.7 12.2
UUC 15.0 18.4 20.3 UCG 8.0 8.6 4.4
Isoleucine (I) AUU 30.5 30.1 16.0 Threonine (T) ACU 8.0 20.3 13.1
AUC 18.2 17.2 20.8 ACC 22.8 12.7 18.9
AUA 3.7 17.8 7.5 ACA 6.4 17.8 15.1
Methionine (M) AUG 24.8 20.9 22.0 ACG 11.5 8.0 6.1
amino acid Codon E. coli K12 S. cerevisiae H. sapiens amino acid Codon E. coli K12 S. cerevisiae H. sapiens
Aspartic acid (D) GAU 37.9 37.6 21.8 Glycine (G) GGU 21.3 23.9 10.8
GAC 20.5 20.2 25.1 GGC 33.4 9.8 22.2
Glutamic acid (E) ATM 43.7 45.6 29.0 GGA 9.2 10.9 16.5
GAG 18.4 19.2 39.6 GGG 8.6 6.0 16.5
Tyrosine (Y) UAU 16.8 18.8 12.2 Cysteine (C) UGU 5.9 8.1 10.6
UAC 14.6 14.8 15.3 UGC 8.0 4.8 12.6
stop UAA 1.8 1.1 1.0 stop UGA 1.0 0.7 1.6
stop UAG 0.1 0.5 0.8 Tryptophan (W) UGG 10.7 10.4 13.2
Asparagine (N) AAU 21.9 35.7 17.0 Serine (S) AGU 7.2 14.2 12.1
AAC 24.4 24.8 19.1 AGC 16.6 9.8 19.5
Lysine (K) AAA 33.2 41.9 24.4 Arginine (R) AGA 1.4 21.3 12.2
AAG 12.1 30.8 31.9 AGG 1.6 9.2 12.0
Histidine (H) CAU 15.8 13.6 10.9 Arginine (R) CGU 21.1 6.4 4.5
CAC 13.1 7.8 15.1 CGC 26.0 2.6 10.4
Glutamine (Q) CAA 12.1 27.3 12.3 CGA 4.3 3.0 6.2
CAG 27.7 12.1 34.2 CGG 4.1 1.7 11.4

Codon Adaptation Index (CAI)

The Codon Adaption Index (CAI, "Codon Adaptation Index") describes how well the codons of a heterologously expressed gene correspond to the codon usage of the host organism. A CAI of 1.0 would be optimal, a CAI> 0.9 is very good, ie it allows a high level of expression.

swell

  1. ↑ E. Kotsopoulou, VN Kim, AJ Kingsman, SM Kingsman, KA Mitrophanous: A Rev-independent human immunodeficiency virus type 1 (HIV-1) -based vector that exploits a codon-optimized HIV-1 gag-pol gene. In: J Virol. (2000), Vol. 74 (10), pp. 4839-52. PMID 10775623 ; PMC 112007 (free full text).
  2. ↑ Data from the Codon Usage Database , which in turn uses the NCBI GenBank data.

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