Codons for termination of translation UAA(ochre), UAG(amber), UGA(opal) For the genes identified in E. coli UAA is used for 2705 genes UGA is used for 1257 genes UAG is used for 326 genes
Codons for termination of translation • UAA (ochre), UAG (amber), UGA (opal) • For the genes identified in E. coli: UAA is used for 2705 genes. UGA is used for 1257 genes. UAG is used for 326 genes
4. Genetic code is univeral(almost) all organisms so far examined use the code as originally deduced We can produce a human protein by using E coli over-expression system! The standard genetic code is widespread but not universal, e. g in rna derived from mitochondrial dna
4. Genetic code is univeral (almost) • All organisms so far examined use the code as originally deduced • We can produce a human protein by using E. coli over-expression system! • The standard genetic code is widespread but not universal, e.g. in RNA derived from mitochondrial DNA
Alterations of the universal code Usual Use Alternate Use Where Alternate Use Occurs AGA 8 Stop, Ser Some animal mitochondria. some AGG protozoans Ile Met Mitochondria CGG 8 Trp Plant mitochondria CUU Yeast mitochondria CUc CUA CUG AOU Start(N-fMet) Some prokaryote GUG val UUG Leu UAA Stop u Some protozoans UAG UGA Stop T Mitochondria, mycoplasmas s代半肥酸Eao "Depends on context of message, other factors
硒代半胱氨酸 Alterations of the universal code
5. Differential codon usage Some codons are used much more frequently than others to encode a particular amino acid The pattern of codon usage varies between species and even among tissues within a species Correlates with trNa abundance Pattern of codon usage can be a predictor of level of expression of a gene Preferred codon usage is a help in reverse genetics
5. Differential codon usage • Some codons are used much more frequently than others to encode a particular amino acid. • The pattern of codon usage varies between species and even among tissues within a species. • Correlates with tRNA abundance. • Pattern of codon usage can be a predictor of level of expression of a gene. • Preferred codon usage is a help in reverse genetics
Differential codon usage Codon usage database TABLE I Extra Copies of tRNA Genes in BL2 ]-Codon Plus Strains Host strain tRNA genes(codon recognition of gene product) Antibiotic BL21-Codon Plus(DE3)-RIPL strain argU (AGA, AGG), ileY (AUA), proL(CCC), leuw BL21-CodonPlus(DE3)-RILstroinargU (AGA, AGG), ileY (AUA), leuW(CUAC BL21-CodonPlus(DE3)-RIL-XstrainargU (AGA, AGG), ileY (AUA), leUW(CUA) BL2 -Codon Plus-RP strain argU(AGA, AGG), proL(CCC) BL21-CodonPlus(DE3)-RP strain argU (AGA, AGG), proL(CCC) BL21-CodonPlus(DE3)-RP-X strain argU (AGA, AGG), proL (CCC)
Differential codon usage • Codon usage database: http://www.kazusa.or.jp/codon/