The bacterial, archaeal and plant plastid code (translation table 11) is the DNA code used by

bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...

archaea Archaea ( ) is a Domain (biology), domain of organisms. Traditionally, Archaea only included its Prokaryote, prokaryotic members, but this has since been found to be paraphyletic, as eukaryotes are known to have evolved from archaea. Even thou ...

, prokaryotic

virus A virus is a submicroscopic infectious agent that replicates only inside the living Cell (biology), cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Viruses are ...

es and chloroplast proteins. It is essentially the same as the standard code, however there are some variations in alternative

start codon The start codon is the first codon of a messenger RNA (mRNA) transcript translated by a ribosome. The start codon always codes for methionine in eukaryotes and archaea and a ''N''-formylmethionine (fMet) in bacteria, mitochondria and plastids. ...

The code

As in the standard code, initiation is most efficient at AUG. In addition, GUG and UUG starts are documented in archaea and bacteria. In ''

Escherichia coli ''Escherichia coli'' ( )Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. is a gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Escherichia'' that is commonly fo ...

'', UUG is estimated to serve as initiator for about 3% of the bacterium's proteins. CUG is known to function as an initiator for one plasmid-encoded protein (RepA) in ''E. coli''. In addition to the NUG initiations, in rare cases bacteria can initiate translation from an AUU

codon Genetic code is a set of rules used by living cells to translate information encoded within genetic material (DNA or RNA sequences of nucleotide triplets or codons) into proteins. Translation is accomplished by the ribosome, which links prote ...

as e.g. in the case of poly(A) polymerase PcnB and the InfC gene that codes for translation initiation factor IF3. The internal assignments are the same as in the standard code though UGA codes at low efficiency for

tryptophan Tryptophan (symbol Trp or W) is an α-amino acid that is used in the biosynthesis of proteins. Tryptophan contains an α-amino group, an α-carboxylic acid group, and a side chain indole, making it a polar molecule with a non-polar aromat ...

in ''Bacillus subtilis'' and, presumably, in ''Escherichia coli''. The NCBI raw format is as follows, with UUG, CUG, AUU, AUC, AUA, AUG, and GUG marked as possible initiators: 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''.

References

{{Reflist, refs= {{cite journal, last1=Kozak, first1=M, title=Comparison of initiation of protein synthesis in procaryotes, eucaryotes, and organelles., journal=Microbiological Reviews, date=March 1983, volume=47, issue=1, pages=1–45, pmid=6343825, pmc=281560, doi=10.1128/MMBR.47.1.1-45.1983 {{cite journal, last1=Fotheringham, first1=IG, last2=Dacey, first2=SA, last3=Taylor, first3=PP, last4=Smith, first4=TJ, last5=Hunter, first5=MG, last6=Finlay, first6=ME, last7=Primrose, first7=SB, last8=Parker, first8=DM, last9=Edwards, first9=RM, title=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., journal=The Biochemical Journal, date=15 March 1986, volume=234, issue=3, pages=593–604, pmid=3521591, doi=10.1042/bj2340593, pmc=1146613 {{cite journal, last1=Golderer, first1=G, last2=Dlaska, first2=M, last3=Gröbner, first3=P, last4=Piendl, first4=W, title=TTG serves as an initiation codon for the ribosomal protein MvaS7 from the archaeon Methanococcus vannielii., journal=Journal of Bacteriology, date=October 1995, volume=177, issue=20, pages=5994–6, pmid=7592355, doi=10.1128/jb.177.20.5994-5996.1995, pmc=177430 {{cite journal, last1=Nölling, first1=J, last2=Pihl, first2=TD, last3=Vriesema, first3=A, last4=Reeve, first4=JN, title=Organization and growth phase-dependent transcription of methane genes in two regions of the Methanobacterium thermoautotrophicum genome., journal=Journal of Bacteriology, date=May 1995, volume=177, issue=9, pages=2460–8, pmid=7730278, doi=10.1128/jb.177.9.2460-2468.1995, pmc=176905 {{cite journal, last1=Sazuka, first1=T, last2=Ohara, first2=O, title=Sequence features surrounding the translation initiation sites assigned on the genome sequence of Synechocystis sp. strain PCC6803 by amino-terminal protein sequencing., journal=DNA Research, date=31 August 1996, volume=3, issue=4, pages=225–32, pmid=8946162, doi=10.1093/dnares/3.4.225, doi-access=free {{cite journal, last1=Genser, first1=KF, last2=Renner, first2=G, last3=Schwab, first3=H, title=Molecular cloning, sequencing and expression in Escherichia coli of the poly(3-hydroxyalkanoate) synthesis genes from Alcaligenes latus DSM1124., journal=Journal of Biotechnology, date=8 October 1998, volume=64, issue=2–3, pages=125–35, doi=10.1016/S0168-1656(98)00093-5, pmid=9821671 {{cite journal, last1=Wang, first1=G, last2=Nie, first2=L, last3=Tan, first3=H, title=Cloning and characterization of sanO, a gene involved in nikkomycin biosynthesis in Streptomyces ansochromogenes., journal=Letters in Applied Microbiology, date=2003, volume=37, issue=6, pages=452–7, pmid=14633098, doi=10.1046/j.1472-765x.2003.01426.x, doi-access=free {{cite journal, last1=Blattner, first1=FR, last2=Plunkett G, first2=3rd, last3=Bloch, first3=CA, last4=Perna, first4=NT, last5=Burland, first5=V, last6=Riley, first6=M, last7=Collado-Vides, first7=J, last8=Glasner, first8=JD, last9=Rode, first9=CK, last10=Mayhew, first10=GF, last11=Gregor, first11=J, last12=Davis, first12=NW, last13=Kirkpatrick, first13=HA, last14=Goeden, first14=MA, last15=Rose, first15=DJ, last16=Mau, first16=B, last17=Shao, first17=Y, title=The complete genome sequence of Escherichia coli K-12., journal=Science, date=5 September 1997, volume=277, issue=5331, pages=1453–62, pmid=9278503, doi=10.1126/science.277.5331.1453, doi-access= {{cite journal, last1=Spiers, first1=AJ, last2=Bergquist, first2=PL, title=Expression and regulation of the RepA protein of the RepFIB replicon from plasmid P307., journal=Journal of Bacteriology, date=December 1992, volume=174, issue=23, pages=7533–41, pmid=1447126, doi=10.1128/jb.174.23.7533-7541.1992, pmc=207463 {{cite journal, last1=Polard, first1=P, last2=Prère, first2=MF, last3=Chandler, first3=M, last4=Fayet, first4=O, title=Programmed translational frameshifting and initiation at an AUU codon in gene expression of bacterial insertion sequence IS911., journal=Journal of Molecular Biology, date=5 December 1991, volume=222, issue=3, pages=465–77, pmid=1660923, doi=10.1016/0022-2836(91)90490-w {{cite journal, last1=Liveris, first1=D, last2=Schwartz, first2=JJ, last3=Geertman, first3=R, last4=Schwartz, first4=I, title=Molecular cloning and sequencing of infC, the gene encoding translation initiation factor IF3, from four enterobacterial species., journal=FEMS Microbiology Letters, date=1 September 1993, volume=112, issue=2, pages=211–6, pmid=8405963, doi=10.1111/j.1574-6968.1993.tb06450.x, doi-access=free {{cite journal, last1=Binns, first1=N, last2=Masters, first2=M, title=Expression of the Escherichia coli pcnB gene is translationally limited using an inefficient start codon: a second chromosomal example of translation initiated at AUU., journal=Molecular Microbiology, date=June 2002, volume=44, issue=5, pages=1287–98, pmid=12068810, doi=10.1046/j.1365-2958.2002.02945.x, doi-access=free {{cite journal, last1=Hatfield, first1=D, last2=Diamond, first2=A, title=UGA: a split personality in the universal genetic code., journal=Trends in Genetics, date=March 1993, volume=9, issue=3, pages=69–70, pmid=8488562, doi=10.1016/0168-9525(93)90215-4 Molecular genetics Gene expression Protein biosynthesis

The code

See also

References