Biology:Bacterial, archaeal and plant plastid code

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Short description: The genetic code found in genomes of bacteria, archaea, and plant plastids

The bacterial, archaeal and plant plastid code (translation table 11) is the DNA code used by bacteria, archaea, prokaryotic viruses and chloroplast proteins. It is essentially the same as the standard code, however there are some variations in alternative start codons.

The code

Amino acids biochemical properties nonpolar polar basic acidic Termination: stop codon
Standard genetic code
1st
base 		2nd base 3rd
base
U C A G
U UUU (Phe/F) Phenylalanine UCU (Ser/S) Serine UAU (Tyr/Y) Tyrosine UGU (Cys/C) Cysteine U
UUC UCC UAC UGC C
UUA (Leu/L) Leucine UCA UAA Stop (Ochre)[B] UGA Stop (Opal)[B] A
UUG[A] UCG UAG Stop (Amber)[B] UGG (Trp/W) Tryptophan     G
C CUU CCU (Pro/P) Proline CAU (His/H) Histidine CGU (Arg/R) Arginine U
CUC CCC CAC CGC C
CUA CCA CAA (Gln/Q) Glutamine CGA A
CUG[A] CCG CAG CGG G
A AUU (Ile/I) Isoleucine ACU (Thr/T) Threonine         AAU (Asn/N) Asparagine AGU (Ser/S) Serine U
AUC ACC AAC AGC C
AUA ACA AAA (Lys/K) Lysine AGA (Arg/R) Arginine A
AUG[A] (Met/M) Methionine ACG AAG AGG G
G GUU (Val/V) Valine GCU (Ala/A) Alanine GAU (Asp/D) Aspartic acid GGU (Gly/G) Glycine U
GUC GCC GAC GGC C
GUA GCA GAA (Glu/E) Glutamic acid GGA A
GUG GCG GAG GGG G
A The codon AUG both codes for methionine and serves as an initiation site: the first AUG in an mRNA's coding region is where translation into protein begins.[1] The other start codons listed by GenBank are rare in eukaryotes and generally codes for Met/fMet.[2]
B ^ ^ ^ The historical basis for designating the stop codons as amber, ochre and opal is described in an autobiography by Sydney Brenner[3] and in a historical article by Bob Edgar.[4]

As in the standard code, initiation is most efficient at AUG. In addition, GUG and UUG starts are documented in archaea and bacteria.[5][6][7][8][9][10][11] In Escherichia coli, UUG is estimated to serve as initiator for about 3% of the bacterium's proteins.[12] CUG is known to function as an initiator for one plasmid-encoded protein (RepA) in E. coli.[13] In addition to the NUG initiations, in rare cases bacteria can initiate translation from an AUU codon as e.g. in the case of poly(A) polymerase PcnB and the InfC gene that codes for translation initiation factor IF3.[14][15][9][16] The internal assignments are the same as in the standard code though UGA codes at low efficiency for tryptophan in Bacillus subtilis and, presumably, in Escherichia coli.[17]

The NCBI raw format is as follows, with UUG, CUG, AUU, AUC, AUA, AUG, and GUG marked as possible initiators:[18] 

   AAs  = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
 Starts = ---M------**--*----M------------MMMM---------------M------------
 Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
 Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
 Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Initiation at AUC and AUA is not addressed in the NCBI description text, but both are indeed known to occur in E. coli.[19]

See also

References

This article incorporates text from the United States National Library of Medicine, which is in the public domain. [18]

  1. ↑ Nakamoto T (March 2009). "Evolution and the universality of the mechanism of initiation of protein synthesis". Gene 432 (1–2): 1–6. doi:10.1016/j.gene.2008.11.001. PMID 19056476. 
  2. ↑ Blattner, F. R.; Plunkett g, G.; Bloch, C. A.; Perna, N. T.; Burland, V.; Riley, M.; Collado-Vides, J.; Glasner, J. D. et al. (1997). "The Complete Genome Sequence of Escherichia coli K-12". Science 277 (5331): 1453–1462. doi:10.1126/science.277.5331.1453. PMID 9278503. 
  3. ↑ Brenner S. A Life in Science (2001) Published by Biomed Central Limited ISBN:0-9540278-0-9 see pages 101-104
  4. ↑ "The genome of bacteriophage T4: an archeological dig". Genetics 168 (2): 575–82. 2004. PMID 15514035.  see pages 580-581
  5. ↑ Kozak, M (March 1983). "Comparison of initiation of protein synthesis in procaryotes, eucaryotes, and organelles.". Microbiological Reviews 47 (1): 1–45. doi:10.1128/MMBR.47.1.1-45.1983. PMID 6343825. 
  6. ↑ Fotheringham, IG; Dacey, SA; Taylor, PP; Smith, TJ; Hunter, MG; Finlay, ME; Primrose, SB; Parker, DM et al. (15 March 1986). "The cloning and sequence analysis of the aspC and tyrB genes from Escherichia coli K12. Comparison of the primary structures of the aspartate aminotransferase and aromatic aminotransferase of E. coli with those of the pig aspartate aminotransferase isoenzymes.". The Biochemical Journal 234 (3): 593–604. doi:10.1042/bj2340593. PMID 3521591. 
  7. ↑ Golderer, G; Dlaska, M; Gröbner, P; Piendl, W (October 1995). "TTG serves as an initiation codon for the ribosomal protein MvaS7 from the archaeon Methanococcus vannielii.". Journal of Bacteriology 177 (20): 5994–6. doi:10.1128/jb.177.20.5994-5996.1995. PMID 7592355. 
  8. ↑ Nölling, J; Pihl, TD; Vriesema, A; Reeve, JN (May 1995). "Organization and growth phase-dependent transcription of methane genes in two regions of the Methanobacterium thermoautotrophicum genome.". Journal of Bacteriology 177 (9): 2460–8. doi:10.1128/jb.177.9.2460-2468.1995. PMID 7730278. 
  9. ↑ 9.0 9.1 Sazuka, T; Ohara, O (31 August 1996). "Sequence features surrounding the translation initiation sites assigned on the genome sequence of Synechocystis sp. strain PCC6803 by amino-terminal protein sequencing.". DNA Research 3 (4): 225–32. doi:10.1093/dnares/3.4.225. PMID 8946162. 
  10. ↑ Genser, KF; Renner, G; Schwab, H (8 October 1998). "Molecular cloning, sequencing and expression in Escherichia coli of the poly(3-hydroxyalkanoate) synthesis genes from Alcaligenes latus DSM1124.". Journal of Biotechnology 64 (2–3): 125–35. doi:10.1016/S0168-1656(98)00093-5. PMID 9821671. 
  11. ↑ Wang, G; Nie, L; Tan, H (2003). "Cloning and characterization of sanO, a gene involved in nikkomycin biosynthesis in Streptomyces ansochromogenes.". Letters in Applied Microbiology 37 (6): 452–7. doi:10.1046/j.1472-765x.2003.01426.x. PMID 14633098. 
  12. ↑ Blattner, FR; Plunkett G, 3rd; Bloch, CA; Perna, NT; Burland, V; Riley, M; Collado-Vides, J; Glasner, JD et al. (5 September 1997). "The complete genome sequence of Escherichia coli K-12.". Science 277 (5331): 1453–62. doi:10.1126/science.277.5331.1453. PMID 9278503. 
  13. ↑ Spiers, AJ; Bergquist, PL (December 1992). "Expression and regulation of the RepA protein of the RepFIB replicon from plasmid P307.". Journal of Bacteriology 174 (23): 7533–41. doi:10.1128/jb.174.23.7533-7541.1992. PMID 1447126. 
  14. ↑ Polard, P; Prère, MF; Chandler, M; Fayet, O (5 December 1991). "Programmed translational frameshifting and initiation at an AUU codon in gene expression of bacterial insertion sequence IS911.". Journal of Molecular Biology 222 (3): 465–77. doi:10.1016/0022-2836(91)90490-w. PMID 1660923. 
  15. ↑ Liveris, D; Schwartz, JJ; Geertman, R; Schwartz, I (1 September 1993). "Molecular cloning and sequencing of infC, the gene encoding translation initiation factor IF3, from four enterobacterial species.". FEMS Microbiology Letters 112 (2): 211–6. doi:10.1111/j.1574-6968.1993.tb06450.x. PMID 8405963. 
  16. ↑ Binns, N; Masters, M (June 2002). "Expression of the Escherichia coli pcnB gene is translationally limited using an inefficient start codon: a second chromosomal example of translation initiated at AUU.". Molecular Microbiology 44 (5): 1287–98. doi:10.1046/j.1365-2958.2002.02945.x. PMID 12068810. 
  17. ↑ Hatfield, D; Diamond, A (March 1993). "UGA: a split personality in the universal genetic code.". Trends in Genetics 9 (3): 69–70. doi:10.1016/0168-9525(93)90215-4. PMID 8488562. 
  18. ↑ 18.0 18.1 Elzanowski, Andrzej; Ostell, Jim; Leipe, Detlef; Soussov, Vladimir. "The Genetic Codes". Taxonomy browser. National Center for Biotechnology Information (NCBI), U.S. National Library of Medicine. https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=tgencodes#thetop. 
  19. ↑ Romero, A; García, P (1 December 1991). "Initiation of translation at AUC, AUA and AUU codons in Escherichia coli.". FEMS Microbiology Letters 68 (3): 325–30. doi:10.1016/0378-1097(91)90377-m. PMID 1687139. 



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