Worm Breeder's Gazette 9(3): 70

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Potential Secondary Structures at the 5' Ends of Vitellogenin mRNAs

E. Zucker and T. Blumenthal

Figure 1

We asked the computer to find the most stable potential secondary 
structures that the 5' ends of the vitellogenin mRNA's could fold into.
It found quite stable structures ( G congruent to -24 Kcal/mol) in 
the first 70 bases of vit-2, vit-5 and vit-6.  The 
same region of vit-1, which we know is a pseudogene, could not be 
folded into a structure of equivalent stability.  In each case, the 
AUG at which translation initiates is involved in a hydrogen bonded 
structure.  Do these structures actually form and, if so, what are 
they for?  We have three lines of evidence that they have been 
selected for and therefore presumably perform some function.
(1.)  We have sequenced the equivalent regions of the C.  briggsae 
genes and found that the proposed stem-forming regions have been 
highly conserved.  Most base pair changes between C.  elegans and C.  
briggsae are in unpaired regions; while the unpaired regions have 
diverged by about 20%, approximately the same as the rest of the 
coding regions we have sequenced, the sequences proposed to be 
involved in stem formation have diverged by only 2%.  Furthermore, the 
few changes in the stems that have occurred would not result in 
alteration of stem stability.
(2.)  Although vit-1 is a pseudogene in C.  elegans, it is 
apparently an expressed gene in C.  briggsae and, in the latter, a 
stable stem-loop structure is predicted.  There are far more base 
changes between the two species in vit-1 than in the other gene pairs, 
but even in vit-1 a preponderance of the changes are in unpaired 
regions.  This may reflect the fact that vit-1 became a pseudogene in 
C.  elegans relatively recently.
(3.)  We have noted before (Spieth, et. al., 1985, Nucleic Acids Res.
13, 7129) that the 5' most 70 bases of all of the vit genes contain a 
much higher frequency of rare codons than do the rest of the coding 
regions.  Although we originally had no satisfactory explanation for 
this finding, we believe it can be understood in the context of the 
step-loop structures.  It turns out that the great majority of third-
position bases which result in the presence of a rare codon are 
predicted to be involved in stem formation.  In most cases, if these 
bases were changed to ones resulting in common codons, the stems would 
be significantly destabilized.  Thus, it appears that selective 
pressure to maintain the ability to form the stem-loop structures is 
greater than the pressure to utilize certain codons.
We have two hypotheses for what functions the stems might 
First, they might be responsible for mRNA stabilization.  Although 
we don't know whether the nematode vitellogenin mRNA's are especially 
stable, it has been shown that their close relatives, the Xenopus 
vitellogenin mRNA's are quite stable as long as estrogen is present.  
Interestingly, we have found that structures very similar to those 
shown in the Figure can be drawn for the 5' ends of all of the 
vertebrate vitellogenin mRNA's.
The second possibility is that the proposed secondary structures are 
involved in regulation of vitellogenin translation.  It may be that 
under some conditions, starvation for instance, that it makes sense to 
cease banking such a large quantity of amino acids for the next 
generation, but it doesn't make sense to destroy the large amount of 
vitellogenin RNA already synthesized.  Thus, it may be that the system 
is designed to modulate vitellogenin translation as a response to 
environmental conditions, perhaps by formation of secondary structures 
close enough to the 5' end to prevent ribosome loading.  Experiments 
to test these fantasies are in progress.
[See Figure 1]

Figure 1