While the genetic code is classically taught as being unambiguous, and indeed may largely be so, we now know this is an oversimplification. Since the original discovery of the standard genetic code, alternative translational interpretations of codons have been found, most notably in the use of the UGA codon for selenocysteine incorporation, in the context of special mRNA stem-loops in the UTRs of a small number of protein-coding genes Nasim et al.
An additional form of codon ambiguity, translational readthrough of stop codons, is now also recognized as pervasive, but usually weak, in eukaryotes, occurring at a few percent or less compared to the non-readthrough form e. Translational readthrough usually gives rise to short protein extensions, e. Readthrough is enabled by near-cognate pairing of tRNAs to codons, with either the first or third anticodon base noncanonically paired Blanchet et al.
Although the options for engineering of new genetic codes with artificial amino acids have been proliferating Lemke, , many important questions about natural genetic codes remain unresolved.
Among these questions, are basic ones of how codons are recognized in variant genetic codes with stop codon reassignments and whether there is competition between eRF1 and stop-cognate tRNAs for the same codons.
Experimental evidence attempting to address the former problem has been conflicting, supporting either loss or ongoing recognition of reassigned stop codons by eRF1 Eliseev et al. With extensive sequence data spanning a wide range of eukaryotes, including ciliates, now available, uncertain genetic codes may be properly determined, and consequently, the proposed basis for nuclear genetic code diversification is also ripe for reinvestigation.
We present the new genetic codes we discovered in the course of screening a large collection of eukaryotic transcriptomes, how codons may have multiple meanings in two of these codes, and the consequences of tolerance of genetic code ambiguity for genetic code evolution. We found that like Bembidion americanum , Bradyrhizobium japonicum uses UGA as a tryptophan codon, although it does so at low levels 0.
Thus, given this reassignment and previous experimental results Eliseev et al. Homo sapiens standard genetic code is an outgroup. Bootstrap support for every node is shown. Scale bar indicates amino acid substitutions per site. UGA codons were previously found in the coding sequences of Blepharisma americanum and were predicted to encode tryptophan Eliseev et al.
Experimental assays in Blepharisma japonicum suggest its eRF1 recognizes all three standard stop codons Eliseev et al. B Predicted C. Stop codons are highlighted in orange. Predicted amino acids are those with maximal heights. See also Figure S1 and Table S1. Predicted Codon Translations of Parduczia sp. Stop codons in the standard genetic code are highlighted by orange rectangles.
Coding sequence codon usage is listed below each codon in percentage. Codon usage for Parduczia sp. As the remaining C. Hence, the question is if and how translation termination occurs given these codes. Because the UGA codon usage in C.
In-frame UGA codons are present in critical genes, such as C. Substitution rates of genes such as these support the hypothesis of functionality since they indicate strong purifying selection, e.
Standard genetic code stop codons are shown with stars, with larger stars for UGA. C Histone H4 C-termini and stop codons gray arrow, coding sequence from C.
Poly A tails are visible at C. Histone H4. D RPFs mapped to histone H4. See also Figure S2. K Stop codon readthrough. See the Supplemental Experimental Procedures for the manner in which readthrough was measured. To investigate the nature of translation termination in C.
With respect to the conserved C-terminal amino acid of histone H4 homologs in other eukaryotes, each of the C. The coding sequence of the single histone H4 in the Parduzcia sp.
With respect to aligned homologs from other organisms, all the Parduczia sp. From the sequence alignments, we therefore infer that C. Sense and Stop Codons in C. Parduczia sp. B A putative UAA terminated gene encoding a cyclophilin protein is shown with mapped poly A -tailed reads. Note that from multiple sequence alignments alone it is uncertain which of the UAAs after the indicated CDS is a stop.
A downstream transcript overlaps with the upstream transcript, but, as indicated by paired-end reads, these transcripts are completely separate Data S1 S and S1T. C RPFs mapped to the transcript corresponding to a transcript of the gene in B showing that termination exclusively occurs at the first of the two UAA codons. Light blue graph shows the coverage by RPFs, shown on a log scale. E Multiple sequence alignment of thioredoxin reductase homologs. In mammals and other eukaryotes the penultimate sense codon in the multiple sequence alignment encodes a catalytic selenocysteine Lee et al.
The position of the thioredoxin selenocysteine codon in C. To test whether translation termination occurs at the putative histone H4 stop codons, we used ribosome profiling ribo-seq. For C. In general, translation terminating C. Consequently, both the primary and secondary H4. A RPFs 25—32 nt mapped to histone H4.
B RPF read length distribution and frame distribution. Putative ribosomal P- and A-site locations of translation terminating RPFs situated at stop codons, based on that predicted for other eukaryotic ribosomes Chung et al.
See also Figure S3. While readthrough is conventionally classified as translation of stop codons by near-cognate tRNAs, in C.
Therefore, for the sake of simplicity, in C. It should be noted that in C. As a consequence, if extensions result from readthrough they are typically expected to be very short. Even though multiple possible stop codons exist, examples of imprecise termination as in H4.
Thus, overall readthrough is quite low, e. The small amount of readthrough that does occur is most readily detected when the ribosome occupies downstream stops Figure 3 E. Although we found a comprehensive set of tRNAs in our C. Given the high sequence coverage of the C. Ciliates possess both a micronuclear and a macronuclear genome, with the former predominantly unsequenced in our C.
It is also unlikely that tRNA Trp UCA s have gone undetected because they are micronuclear genome-encoded: although these genomes are transcriptionally active during ciliate sexual development they are generally inactive during vegetative growth Chen et al.
Bonds shown are predicted by the RNAfold web server Lorenz et al. See also Figure S4. Thus, to determine whether C. C represents two macronuclear genome-encoded tryptophan tRNAs with CCA anticodons with a single base difference between the forms. Judging from our assemblies there may be more than three C.
The selenocysteine tRNA is found in the draft C. In standard genetic code organisms, readthrough UGA stop codons are preferentially translated as tryptophan e. We assessed two hypotheses for how sense codons are distinguished from stop codons in ambiguous codes: 1 that there are sequence-specific features motifs allowing discriminating protein factors to bind nearby sense and stop codons, and 2 that proximity to transcript ends results in recognition of stops.
A Sequence logos of regions surrounding C. For the central sense codon itself the underlying base frequencies are shown, not bit scores as for the surrounding bases. B Sequence logos of regions surrounding C. For the central stop codon itself the underlying base frequencies are shown.
C Graphs like those of Figure 5 for Parduczia sp. Transcript ends begin, and include 0, 1, or 2 nucleotides of the poly A tail position 0 to maintain reading frame. Because poly A tails of certain C. Because the ribosome occupies 11 or 12 nucleotides downstream of C. B Length distribution of C. Lengths are from the putative primary stop in the 60 nt window upstream of poly A sites and exclude the stop and poly A tail lengths. Poly A tail-ending reads mapped to the genomic region encoding this gene are shown, and no other reads extend beyond the poly A addition site.
See also Figure S6. The very low readthrough levels detected in C. Given the low tolerance of either readthrough or premature translation termination, the prediction is that when codons recognized inefficiently as either stop or sense arise in coding sequences, they are deleterious. Codons counted are those in the poly A -tailed single gene, single isoform Trinity assembled transcripts. A—C The top three subgraphs are drawn in decreasing order of ordinate limits. In the genetic codes of C.
UGA is a codon triality codon duality is reviewed in Atkins and Baranov, , because in addition to being interpreted as a tryptophan codon and a stop codon, it also serves as a selenocysteine codon in the context of SECIS elements. Ribosome position and the protected mRNA span are illustrated as inferred from C.
Three prior observations favor this hypothesis: 1 PABP overexpression enhances translation termination when it is weak, implying that PABPs may be involved in translation termination Cosson et al. From their distribution throughout coding sequences, it is evident that most reassigned codons in ciliates arose from substitutions of codons that were already normally translated, rather than from readthrough stop codons. Upon acquisition of a stop cognate tRNA, a shift in balance from translation termination to readthrough at stop codons is expected.
Normally this acquisition would immediately be deleterious, due to the creation of aberrant C-terminal peptide signals or the triggering of non-stop mRNA decay Frischmeyer et al. By enforcing proper translation termination close to transcript ends, ciliates with ambiguous genetic codes provide a way of getting around these problems.
Given that we detected no new genetic codes in diverse non-ciliate eukaryotic species from MMETSP, the abundance of alternative genetic codes within ciliates is all the more striking. Two hypotheses for the origin of genetic codes in ciliates are that they were enabled by codon capture or eRF1 mutations. To date, all sequenced ciliate genomes are AT rich Aeschlimann et al. This suggests that the diversification of genetic codes from the standard one could have followed UAG and UGA stop codon depletion in ancestral ciliates with AT rich genomes.
For example, in Euplotes sp. A Multiple sequence alignment underlying the phylogeny in Figure 1 A; sequences obtained from UniProt; downloaded Feb 22, Only the N-terminal half of the alignment is shown. Since these providers may collect personal data like your IP address we allow you to block them here. Please be aware that this might heavily reduce the functionality and appearance of our site. Changes will take effect once you reload the page.
Pronunciation: [ koh -don]. Definition A Sequence. To specify the genetic code for a protein. Use in clinical context Changes to the bases within a codon can have a variety of effects on the resulting amino acid and polypeptide. Other changes can insert or delete bases that can affect several codons at once, significantly impacting the final Protein. A large molecule composed of one or more chains of amino acids, the sequence of which is determined by DNA.
Related terms Amino acids Bases Protein. Discover more Learning opportunities Online course. Public Health Masterclass in Genomics Up to 3 hours. These mutations are like fruit machines: getting one bell is easier than getting a row of three cherries to show.
You need to play more often and for longer to get the difficult combinations. It is included to show two things. That most amino acids can be made from more than one combination of bases. That some mutations are easy and some are difficult. Easy mutations only need one letter to change.
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