Bacterial, archaeal and plant plastid code

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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.

Contents

The code

Amino-acid biochemical propertiesNonpolarPolarBasicAcidicTermination: stop codon
Standard genetic code (NCBI table 1) [1]
1st
base		2nd base3rd
base
UCAG
UUUU(Phe/F) Phenylalanine UCU(Ser/S) Serine UAU(Tyr/Y) Tyrosine UGU(Cys/C) Cysteine U
UUCUCCUACUGCC
UUA(Leu/L) Leucine UCAUAA Stop (Ochre) [B] UGA Stop (Opal) [B] A
UUG [A] UCGUAG Stop (Amber) [B] UGG(Trp/W) Tryptophan G
CCUUCCU(Pro/P) Proline CAU(His/H) Histidine CGU(Arg/R) Arginine U
CUCCCCCACCGCC
CUACCACAA(Gln/Q) Glutamine CGAA
CUGCCGCAGCGGG
AAUU(Ile/I) Isoleucine ACU(Thr/T) Threonine AAU(Asn/N) Asparagine AGU(Ser/S) Serine U
AUCACCAACAGCC
AUAACAAAA(Lys/K) Lysine AGA(Arg/R) Arginine A
AUG [A] (Met/M) Methionine ACGAAGAGGG
GGUU(Val/V) Valine GCU(Ala/A) Alanine GAU(Asp/D) Aspartic acid GGU(Gly/G) Glycine U
GUCGCCGACGGCC
GUAGCAGAA(Glu/E) Glutamic acid GGAA
GUG [A] GCGGAGGGGG
A Possible start codons in NCBI table 1. AUG is most common. [2] The two other start codons listed by table 1 (GUG and UUG) are rare in eukaryotes. [3] Prokaryotes have less strigent start codon requirements; they are described by NCBI table 11.
B ^ ^ ^ The historical basis for designating the stop codons as amber, ochre and opal is described in an autobiography by Sydney Brenner [4] and in a historical article by Bob Edgar. [5]

As in the standard code, initiation is most efficient at AUG. In addition, GUG and UUG starts are documented in archaea and bacteria. [6] [7] [8] [9] [10] [11] [12] In Escherichia coli , UUG is estimated to serve as initiator for about 3% of the bacterium's proteins. [13] CUG is known to function as an initiator for one plasmid-encoded protein (RepA) in E. coli. [14] 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. [15] [16] [10] [17] 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. [18]

The NCBI raw format is as follows, with UUG, CUG, AUU, AUC, AUA, AUG, and GUG marked as possible initiators: [19] 

   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. [20]

See also

References

This article incorporates text from the United States National Library of Medicine, which is in the public domain. [19]

  1. ↑ Elzanowski A, Ostell J (7 January 2019). "The Genetic Codes". National Center for Biotechnology Information. Archived from the original on 5 October 2020. Retrieved 21 February 2019.
  2. ↑ 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.
  3. ↑ Asano, K (2014). "Why is start codon selection so precise in eukaryotes?". Translation (Austin, Tex.). 2 (1): e28387. doi:10.4161/trla.28387. PMID   26779403.{{cite journal}}: CS1 maint: article number as page number (link)
  4. ↑ Brenner S. A Life in Science (2001) Published by Biomed Central Limited ISBN   0-9540278-0-9 see pages 101-104
  5. ↑ Edgar B (2004). "The genome of bacteriophage T4: an archeological dig". Genetics. 168 (2): 575–82. PMC   1448817 . PMID   15514035. see pages 580-581
  6. ↑ 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. PMC   281560 . PMID   6343825.
  7. ↑ Fotheringham, IG; Dacey, SA; Taylor, PP; Smith, TJ; Hunter, MG; Finlay, ME; Primrose, SB; Parker, DM; Edwards, RM (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. PMC   1146613 . PMID   3521591.
  8. ↑ 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. PMC   177430 . PMID   7592355.
  9. ↑ 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. PMC   176905 . PMID   7730278.
  10. 1 2 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.
  11. ↑ 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.
  12. ↑ 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.
  13. ↑ Blattner, FR; Plunkett G, 3rd; Bloch, CA; Perna, NT; Burland, V; Riley, M; Collado-Vides, J; Glasner, JD; Rode, CK; Mayhew, GF; Gregor, J; Davis, NW; Kirkpatrick, HA; Goeden, MA; Rose, DJ; Mau, B; Shao, Y (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.{{cite journal}}: CS1 maint: numeric names: authors list (link)
  14. ↑ 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. PMC   207463 . PMID   1447126.
  15. ↑ 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.
  16. ↑ 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.
  17. ↑ 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.
  18. ↑ 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.
  19. 1 2 Elzanowski A, Ostell J, Leipe D, Soussov V. "The Genetic Codes". Taxonomy browser. National Center for Biotechnology Information (NCBI), U.S. National Library of Medicine. Retrieved 19 March 2016.
  20. ↑ 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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