In protein-coding genes, synonymous codon usage and amino acid .. In addition, we wished to assess the relationship between Fop and amino acid in and of. Specifically, the code defines a mapping between tri-nucleotide sequences called codons and amino acids; every triplet of nucleotides in a nucleic acid. In most cases, the relationships between the coded amino acids and their in this issue of Chemistry & Biology and in a recent issue of the Journal of the.
In fact, 61 of the 64 possible triplets specify particular amino acids and 3 triplets called stop codons designate the termination of translation.
Thus, for most amino acids, there is more than one code word. Because the code is highly degenerate, only tryptophan and methionine are encoded by just one triplet each. The other 18 amino acids are each encoded by two or more. Indeed, leucine, arginine, and serine are specified by six codons each. The number of codons for a particular amino acid correlates with its frequency of occurrence in proteins.
Codons that specify the same amino acid are called synonyms. Note that synonyms are not distributed haphazardly throughout the genetic code depicted in Table 5. An amino acid specified by two or more synonyms occupies a single box unless it is specified by more than four synonyms. Thus, most synonyms differ only in the last base of the triplet. The structural basis for these equivalences of codons will become evident when we consider the nature of the anticodons of tRNA molecules Section What is the biological significance of the extensive degeneracy of the genetic code?
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If the code were not degenerate, 20 codons would designate amino acids and 44 would lead to chain termination. The probability of mutating to chain termination would therefore be much higher with a nondegenerate code. Chain-termination mutations usually lead to inactive proteins, whereas substitutions of one amino acid for another are usually rather harmless.
Thus, degeneracy minimizes the deleterious effects of mutations. Degeneracy of the code may also be significant in permitting DNA base composition to vary over a wide range without altering the amino acid sequence of the proteins encoded by the DNA.
How is mRNA interpreted by the translation apparatus? These codons are read not by tRNA molecules but rather by specific proteins called release factors Section Binding of the release factors to the ribosomes releases the newly synthesized protein.
The start signal for protein synthesis is more complex.
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Polypeptide chains in bacteria start with a modified amino acid—namely, formylmethionine fMet. However, AUG is also the codon for an internal methio-nine residue, and GUG is the codon for an internal valine residue. Hence, the signal for the first amino acid in a prokaryotic polypeptide chain must be more complex than that for all subsequent ones. In bacteria, the initiating AUG or GUG codon is preceded several nucleotides away by a purine-rich sequence that base-pairs with a complementary sequence in a ribosomal RNA molecule Section Once the initiator AUG is located, the reading frame is established—groups of three nonoverlapping nucleotides are defined, beginning with the initiator AUG codon.
Initiation of Protein Synthesis. Start signals are required for the initiation of protein synthesis in A prokaryotes and B eukaryotes. The base sequences of many wild-type and mutant genes are known, as are the amino acid sequences of their encoded proteins. In each case, the nucleotide change in the gene and the amino acid change in the protein are as predicted by the genetic code.
The amino acid composition of proteins also appears to change with increasing expression levels Akashi ; Cutter et al.
Several reports have indicated that amino acid frequency in proteins encoded by highly expressed genes correlates to the most abundant tRNA in an organism, consistent with selection for speed and accuracy of translation Akashi ; DuretFurther, studies in some eukaryotes, including yeast, T. Thus, in those studies, abundant proteins, presumably encoded by highly transcribed genes, tended to be comprised of smaller less complex amino acids, which is not only predicted to minimize the biochemical energy costs of synthesis, but might also contribute to the stability of the protein structure and its conformation Cutter et al.
Expanding this molecular evolutionary research to non-traditional model organisms will help elucidate the breadth of this phenomenon and the role of evolution of amino acid preferences in promoting translational efficiency. In the present investigation, we study optimal codon and amino acid usage based on recently available large-scale RNA-seq data from three emerging models of arthropods, G.
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Using these data, we provide strong evidence that codon usage and amino acid frequency has been optimized in highly expressed genes of each of these organisms, with the strongest signals observed in G. Together, the results are consistent with a history of selection on synonymous codon usage and on amino acid frequency in highly transcribed genes to promote translational efficiency and accuracy across Pancrustacean genome evolution. Multistage embryos and ovaries comprise highly complex tissues, expressing a large component of genes in the genome Li et al.
Subramanian and Kumar The next-generation sequencing data are described in Table S1. We identified all assembled transcripts Zeng and Extavour without isoforms, to allow accurate mapping of reads to a specific single CDS to quantify expression.
For this gene set, we extracted all coding regions with a start codon, and lacking any unknown sites or internal stop codons. To quantify expression levels, we mapped reads to the CDS and calculated reads per million RPM using the non-normalized libraries that comprise the largest or only dataset per species Table S1 ; where read number directly reflects abundance; average read length was, and bp per species, respectively Zeng and Extavour Tools and software for measuring expression and codon and amino acid usage in the various datasets are described in File S3.
Results For our analyses, the number of CDS examined after excluding genes with isoforms, unknown sites, or internal stop codons for G. The nucleotide composition varied across all CDS among organisms: We first asked whether we could detect differences in codon usage relative to expression levels in all three study species.
The genetic code
A highly effective method to identify codon preferences is to compare these preferences between genes expressed at extremely high or extremely low levels Cutter et al. These trends indicate that AT3 codons are more common under high transcription in these insects. For all genes per species, we then assessed the effective number of codons ENCwherein values range from 20 when one codon is exclusively used to code for a given amino acid to 61 all codons used equallyand lower values denote greater biases in codon usage in a gene Wright Given these findings, we next assessed synonymous codon usage in every amino acid of the analyzed CDS, to test the hypothesis that AT3 in the insects, and GC3 in the amphipod, were optimal codons in these species.