Candidate division SR1 and gracilibacteria code
{{Short description|Alternative genetic code found in the genome of some bacteria}}
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.{{Cite journal|last1=Davis|first1=James P.|last2=Youssef|first2=Noha H.|last3=Elshahed|first3=Mostafa S.|date=June 2009|title=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|journal=Applied and Environmental Microbiology|volume=75|issue=12|pages=4139–4148|doi=10.1128/AEM.00137-09|issn=1098-5336|pmc=2698373|pmid=19395567|bibcode=2009ApEnM..75.4139D}} The difference to the standard and the bacterial code is that UGA represents an additional glycine codon and does not code for termination.
A survey of many genomes with the codon assignment software Codetta,{{cite journal |last1=Shulgina |first1=Yekaterina |last2=Eddy |first2=Sean R. |date=9 November 2021 |title=A computational screen for alternative genetic codes in over 250,000 genomes. |journal=eLife |volume=10 |doi=10.7554/eLife.71402|doi-access=free |pmid=34751130 |pmc=8629427 }} analyzed through the GTDB taxonomy system {{cite journal |last1=Parks |first1=Donovan H. |last2=Chuvochina |first2=Maria |last3=Chaumeil |first3=Pierre-Alain |last4=Rinke |first4=Christian |last5=Mussig |first5=Aaron J. |last6=Hugenholtz |first6=Philip |date=September 2020 |title=A complete domain-to-species taxonomy for Bacteria and Archaea. |journal=Nature Biotechnol. |volume=38 |issue=9 |pages=1079–1086 |doi=10.1038/s41587-020-0501-8 |pmid=32341564 }} (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".
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
| class="wikitable" style="border: none; text-align: center;" |
| DNA codon
! RNA codon ! This code (25) ! style="border: none; width: 2px;" | ! Standard code (1) |
|---|
| {{mono|TGA}}
| {{mono|UGA}} | style="background-color:#ffe75f;" | {{mono|Gly (G)}} | style="border: none; width: 2px;" | | style="background-color:#B0B0B0;" | {{mono|1=STOP = Ter (*)}} |
Initiation codons
- AUG, GUG, UUG
Systematic range
References
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