why 16S rRNA?

Bill_A_Nussbaumer at ms.bd.com Bill_A_Nussbaumer at ms.bd.com
Mon Oct 4 16:23:32 EST 1999





Bill A Nussbaumer at BDX
10/04/99 12:47 PM

No you're not wrong at all.  In fact you've pretty much got your answer right
there.  I probably didn't phrase my question quite right but what I was after is
found in your statement that the molecule is highly conserved.  The 16S rRNA
molecule can actually be found in all bacteria with relatively few modifications
when compared with mutation rates of other molecules in the bacteria (that's
what I meant by other parts).  In fact, even usually critical molecules such as
cytochrome C used in cellular respiration cannot be found in all bacteria, and
even when it is, the differences from one species (or phyla) to another may vary
so widely as to make a relational comparison between the two species almost
impossible.  The important thing to think about here is the implications on
phylogenetic analysis.  In other words, knowing what you know, why would the 16S
molecule be so helpful in designing a bacterial family tree?  Pay particular
attention to what you read about the mutations being located in characteristic
divergent regions.   I think your conclusion is correct.  It makes biochemical
sense that these mutations would affect certain regions. That information
becomes helpful when you relate it to the phenotypic characteristics of the
organism.  The key word here is "divergent".  You're close in saying that you
could differentiate between strains, but given the rate of mutation in the 16S
rRNA, how likely do you think it is you would be able to reliably use this as a
separator for so closely related organisms?  I don't actually know the answer to
this question (this might be possible) but my point would be to think larger.

Hopefully what I've said has been helpful without just giving you an answer to
copy down (I'm assuming this is a homework problem since you didn't say
otherwise so forgive me if it's not).  And also keep in mind that this is not
exactly "my area" so you've really made me think about exactly how to respond.
I'm sure of one thing.  We don't give our teachers enough credit in what they
do.  :-)

Bill





Please correct me if I am wrong. The 16S rRNA molecule is involved in the
conversion
of DNA sequences into functional protein and this is a process which is similar
in
all organisms. The DNA sequence which encodes this molecule is highly conserved
and
mutations which occur does not affect the function of the 16S rRNA molecule. I
read
that the mutations are usually located in characteristic divergent regions. Does
this mean that the mutations only affect specific regions of the molecule for
all
organisms? that means by analysing these specific regions, one is able to
differentiate, let's say, different strains of bacteria?  but well, I have not
figured out  what sets 16S rRNA apart from the other parts of bacteria for
analysis.
Any hints?

rowyna






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