Worm Breeder's Gazette 8(1): 36

These abstracts should not be cited in bibliographies. Material contained herein should be treated as personal communication and should be cited as such only with the consent of the author.

Codon Choice in C. elegans

T. Blumenthal, E. Zucker, K. Denison, J.Spieth

Figure 1

It has been found that when synonymous codons are available to code 
for a particular amino acid, most organisms use some codons more 
frequently than they use others.  This asymmetry in codon choice 
varies considerably both in which choices are made and in the degree 
of asymmetry from organism to organism.  Also, genes which encode 
abundant proteins show greater asymmetry than those for less abundant 
proteins [Grantham et al., NAR 9, r42 (1981)].  We present below the 
codon utilization table for the approximately 3.5 kb of two of the 
yolk protein genes which we have sequenced so far.  Codon usage is 
extremely asymmetric in these genes.  Furthermore, we have examined 
published sequences of the collagen, myosin, and actin genes and have 
found the same high degree and type of asymmetry.  Although yeast and 
bacteria also show high (albeit different) codon asymmetries, most 
metazoans are not this selective about codon choice.
There are several implications of these 
1.  It is very easy to identify reading frames used for coding 
abundant proteins in C.  elegans DNA.  This can be a great aid in 
interpretation of ambiguous sequence data.
2.  In principle, members of gene families which are pseudogenes can 
be so identified by comparison of codon usage between the hypothetical 
pseudogene and a legitimate gene.  Pseudogenes will accumulate rarely 
used codons.  This sort of analysis suggests that all five yolk 
protein genes are legitimate genes, even though we have been able to 
unequivocally assign mRNA to only two of them.
3.  C.  elegans seems to prefer some codons which are very rare in E.
coli (for instance GGA for glycine).  This may result in low level 
synthesis of C.  elegans proteins in E.  coli from clones in 
expression vectors.  In fact, we failed to detect expression from 
several yolk protein DNA fragments cloned in lambda gt11 even though 
they were in the correct orientation and reading frame.  We don't know,
however, if slow translation of certain codons is responsible for 
this failure.  The high degree of asymmetry suggests that there is 
strong selection for efficient translation of abundant proteins in C.  
elegans.  In the case of yolk proteins, mutation to a less frequently 
used codon, almost anywhere in the gene, presumably results in reduced 
fecundity even though the amino acid at that position is unchanged and 
even though there are other genes coding for nearly identical proteins.

Figure 1