Most editing in plants corrects T to C mutatons at first or second
nonsynonymous base postions, and the overall effect is an mRNA and protein
sequence that differs from that predicted by the DNA, although I have not
seen in any papers anyone that has actually done the aminoacid sequence to
determine if in fact the amino acids are the ones that are those predicted
by the altered mRNA strand.
>Having spent the first 6 years of my career in the digital signal
>processing part of my profession, one thing I learned was that information
>does not appear out of nowhere. Somewhere there must be a set of
>instructions for these repairs. If there is truly no instruction for this
>in the genome then we are witnessing a miracle where God himself changes
>the appropriate cytosines.
My only limited experience in this area is with plants although I believe
that there are many forms of editing that have been described among other
organisms that each may have different mechanisms. The mechanism for the T
to C seems to be a rather simple site specific conversion of the C to a U
rather than an insertion deletion phenomena which has been proposed in
other cases (an actually clipping out and replacement of individual
nucleotides). The latter is probably necessary for editing of other
nucleotides which cannot be as easily altered as Cytidines can.
Yu. Wei, and W. Schuster. 1995 Evidence for a site-specific
Cytidine Deamination Reaction Involved in C to U RNA editing of plant
mitochondria.
Jour. Biol. Chemistry. 270: 18227-18233.
Also last night I was writing from the top of my head and I didn't
think that all that many site were really edited but now I have a paper in
front of me that states that coxIII (a protein coding gene - I think that
does somthing int he electron transport chain) is edited at 9.2% of the 391
bp in gymnosperms while only 2.4% in angiospers. It is unedited in
Bryophytes (see below for more details). Apparently these are all C-U
conversions but again not all Cs are converted.
>
>Since I don't think God is doing this, I would like to see what is wrong
>with the following suggestion. This depends upon the existence of some
>info storage location. Lineages which lost the correct sequence but which
>also had a fortuitous correction mechanism were able to continue living
>and reproducing. Those that didn't have it, died.
Another intersting side note to my previous post is found in:
Hiesel, R., Combettes, B., and A. Brennicke. 1994 Evidence for RNA
editing in mitochondria of all major groups of land plants except the
Bryophyta. Proc. Nat. Acad. Sci. 91: 629-633
It is reported here that all vascular plants appear to have RNA editing in
their mitochondrial CoxIII gene but that no evdence for editing can be
found in Bryophytes (mossses in general) or in the algea examined. Only a
single editing site was found in Lycopodium (representative of the Lycopods
considered to be the oldest extant group of vascular plants). Editing
increases in the ferns is greatest in some relictual groups of gmynospers
such as the Ginkgos and is found in all flowering plants studies to date.
At all the different sites edited in other plant species, the lycopsid and
bryophyte genomic sequences encode nucleotides corresponding to the edited
sequences. Interestingly edited sites correlate quite well to established
phylogenetic groupings. Also three cases here of U-C editing were found in
two ferns for which no mechanism has been proposed.
>Now are there fortuitous, pre-existing correction mechanisms? What about
>those that change the cytosine in the 3rd location with no effect on amino
>acid sequence? Is that possibly evidence of such a function?
These are the big questions and I wish I had the answers. The real
question as it relates to the previous thread ""Black" days for evolution"
is:
Are processes such as this just too amazing to ever believe that
such a fortuitous event occurred allowing for the development of a
correction mechanism to correct incorrect bases rather than the more
parsimonious evolutionary answer which is let those indiduals with mutated
bases die and preserve the ones with the correct sequence! or
is this simply a case of We Are Amazed now but further investigation
will relieve those concerns. Maybe I'm amazed because I just don't
understand yet.
It is known that there is a process by which multicopy genes such as the
ribosomal DNA genes are found in many copies in the nuclear genome and two
copies in the cpDNA genome and studies have shown that they all have the
same sequence. One particular copy is being used somehow as a control
template by which the rest are compared and edited at the DNA level to
maintain the original code (thus the remarkable conservation of these
sequences in all living things). This concerted evolutionary mechanism was
a complete mystery for some time but at least now there are some hypotheses
for how it might occur and some good evidence supporting some of them.
(this is way out of my field now so I will quit before I go too far).
Joel
R. Joel Duff
Dpt. Plant Biology
Southern Illinois University
Carbondale, IL 62901-6509
e-mail: Duff@siu.edu
office: 618-453-3823