Candidate division SR1 and gracilibacteria code

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The candidate division SR1 and gracilibacteria code (translation table 25) is used in two groups of (so far) uncultivated bacteria found in marine and fresh-water environments and in the intestines and oral cavities of mammals among others. [1] The difference to the standard and the bacterial code is that UGA represents an additional glycine codon and does not code for termination. [2] A survey of many genomes with the codon assignment software Codetta, [3] analyzed through the GTDB taxonomy system [4] (release 220) shows that this genetic code is limited to the Patescibacteria order BD1-5, not what are now termed Gracilibacteria, and that the SR1 genome assembly GCA_000350285.1 for which the table 25 code was originally defined is actually using the Absconditibacterales genetic code and has the associated three special recoding tRNAs. Thus this code may now be better named the "BD1-5 code".

Contents

The code

    AAs = FFLLSSSSYY**CCGWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = ---M-------------------------------M---------------M------------
  Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
 Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
 Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Bases: adenine (A), cytosine (C), guanine (G) and thymine (T) or uracil (U).

Amino acids: Alanine (Ala, A), Arginine (Arg, R), Asparagine (Asn, N), Aspartic acid (Asp, D), Cysteine (Cys, C), Glutamic acid (Glu, E), Glutamine (Gln, Q), Glycine (Gly, G), Histidine (His, H), Isoleucine (Ile, I), Leucine (Leu, L), Lysine (Lys, K), Methionine (Met, M), Phenylalanine (Phe, F), Proline (Pro, P), Serine (Ser, S), Threonine (Thr, T), Tryptophan (Trp, W), Tyrosine (Tyr, Y), and Valine (Val, V).

Difference from the standard code

DNA codonRNA codonThis code (25) Standard code (1)
TGAUGAGly (G)STOP = Ter (*)

Initiation codons

Systematic range

See also

References

This article incorporates text from the United States National Library of Medicine, which is in the public domain. [5]

  1. ↑ Davis, James P.; Youssef, Noha H.; Elshahed, Mostafa S. (June 2009). "Assessment of the diversity, abundance, and ecological distribution of members of candidate division SR1 reveals a high level of phylogenetic diversity but limited morphotypic diversity". Applied and Environmental Microbiology. 75 (12): 4139–4148. Bibcode:2009ApEnM..75.4139D. doi:10.1128/AEM.00137-09. ISSN   1098-5336. PMC   2698373 . PMID   19395567.
  2. ↑ J. H. Campbell; O'P. Donoghue; A. G. Campbell; P. Schwientek; A. Sczyrba; T. Woyke; D. Söll; M. Podar (2 April 2013). "UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota". Proc Natl Acad Sci U S A. 110 (14): 5540–5. Bibcode:2013PNAS..110.5540C. doi: 10.1073/pnas.1303090110 . PMC   3619370 . PMID   23509275.
  3. ↑ Shulgina, Yekaterina; Eddy, Sean R. (9 November 2021). "A computational screen for alternative genetic codes in over 250,000 genomes". eLife. 10 e71402. doi: 10.7554/eLife.71402 . PMC   8629427 . PMID   34751130.
  4. ↑ Parks, Donovan H.; Chuvochina, Maria; Chaumeil, Pierre-Alain; Rinke, Christian; Mussig, Aaron J.; Hugenholtz, Philip (September 2020). "A complete domain-to-species taxonomy for Bacteria and Archaea". Nature Biotechnol. 38 (9): 1079–1086. doi:10.1038/s41587-020-0501-8. PMID   32341564.
  5. ↑ 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.
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