Re: Please educate me

R. Joel Duff (
Tue, 16 Dec 1997 09:08:58 -0600 (CST)

I had said,
>I won't try to explain the proposed mechanisms for tRNA changes off the top
>of my head but will try find the papers tomorrow.

Naturally I can't find the paper I was thinking of but I did run accross a
few other interesting ditties on the way.
Of the examples of the non-universal code listed on the web page previously
listed, most are indeed real examples of an incorrect code. By this I mean
that the amino acid sequence, DNA sequence and the mRNA and tRNAs have all
been examined to show difinitively that the code is different. There have
been cases in the past though were changes in the universal code have been
proposed because it certainly appeared that the code had changed. For
example in plant chlroplasts and mitochondria there are times when stop
codons are found in the DNA sequence of various protein coding genes but it
was known from previous work that a normal amino acid seqeunce was
produced. Is this a case of the stop codon actually coding for an amino
acid. Nope. It is actually a case of RNA editing by which the transcribed
DNA is edited (U converted to a C) before being translated. Thus, this
gives the appearance of the code being changed. (BTW, this can cause real
problems with molecular phylogeneies based only on comparative DNA
sequences and can explain some anomylous positioning of some taxa when when
one taxon is edited while another is not).

In another odd example, intermediate tRNAs have been found in marsupials
(Morl et al 1995). The second position of the anticodon of the tRNA for
aspartic acid is changed post-transcriptionally such that the translational
machinery recognizes it as a uracil rather than the cytosine residue encode
in the gene. So this isn't a case of the code being completely changed by
is changed in the process of translation. Even more interesting is the
fact that postlabeling nucleotide analyis showed that the "cytosine residue
is converted to a conventional uracil residue in an RNA editing event that
effects approximately half of the tRNA molecules.." Furthermore Morl et al
(1995) identified three different tRNA(Asp) species which all carry three
pseiudouridines and two methylations but have the anticodons GCC, GUC and
QUC (not a typo, its the rare nucleotide base Queuine) respectively. This
allows them to describe a likely sequential order of modification of the
tRNA (Asp). In these cells then you have a mixture of tRNAs with different
anticodons. Unfortunately, as yet it is not known what the effect of such
mixture is.


A very interesting paper on the evolution of RNA editing is:

Arts G.J. and R. Benne. 1996. Mechanism and evolution of RNA editing in
kinetoplastida. Biochimica et Biophysica Acta 1307: 39-54

Cavalier-Smith Tom. 1997. Cell and genome coevolution: facultative
anaerobiosis, glycosomes and kinetoplastan RNA editing.

Morl, M, Dorner, M., and S. Paabo. 1995. C to U editing and modifications
during the maturation of the mitchondrial tRNA(Asp) in marsupials.

A good survey of mitochondrial evolution (gene content, universal code, rna
editing, sybiosis) is:
Origin and evolution of mitochondria: what have we leart from red algae?
Current Genetics 31: 193-207.

Joel and Dawn Duff / | ' \ Spell Check?
Carbondale IL 62901 ( ) 0
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