talking to organelles

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Allan Adler - 13 Dec 2004 08:45 GMT

Let me warn readers in advance that I don't know anything and that this
will be evident from what I am about to write. Basically, I was thinking
over some things I had heard at different times and trying to make sense
of them. I came up with something that makes a little sense to me but
which is probably wrong in some important ways and maybe right in some
other ways.

It's like this: I'm under the impression that mitochondria, nuclei and other
cell organelles evolved from cells that developed a symbiotic relationship
with other cells that they eventually resided inside of and lost their
independence from. I'm aware that there are some chemical modes of
communication between cells, but that cells can also be controlled
by invading viruses which are, among other things, basically snippets
of RNA or DNA. On the other hand, there is internal communication inside
a cell involving some chemical control but also stuff like messenger RNA.
To my uninformed brain, there seems to be at least a superficial resemblance
in these descriptions of internal and external modes of communication.

What I'd like to know is:
(1) Whether the internal modes of communication inside a cell evolved from
external modes of communication among cells and between cells and
viruses?
(2) Assuming an affirmative answer to (1), whether one can compare the
internal and external modes in such a way as to place the evolution
of internal from external modes in evidence?
(3) Assuming an affirmative answer to (1) and (2), whether some examples
have been published in which some details are worked out or at least
suggested for specific organisms?
(4) Assuming an affirmative answer to (1)-(3), where I might read about
this or, assuming all these speculations are entirely without merit,
where I should read about the right way to look at this stuff?

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Ignorantly,
Allan Adler <ara@zurich.csail.mit.edu>
* Disclaimer: I am a guest and *not* a member of the MIT CSAIL. My actions and
* comments do not reflect in any way on MIT. Also, I am nowhere near Boston.

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Bob - 16 Dec 2004 04:51 GMT

>Let me warn readers in advance that I don't know anything and that this
>will be evident from what I am about to write. Basically, I was thinking
[quoted text clipped - 13 lines]
>To my uninformed brain, there seems to be at least a superficial resemblance
>in these descriptions of internal and external modes of communication.

Well ok, I'll bite.

Let's take what you wrote above as generally ok.

I think it would help to be more specific. What kind of communication?
Specific examples? I think it would also help to leave viruses out of
the story, since they are not an integral part of basic cellular
processes.

In some general sense, all communication events involve molecular
interactions, such as protein-protein or protein with small molecule.
Proteins have specific shape, thus allowing them to recognize other
specific molecules.

As to #1 below, my intuition would be the opposite, that intracellular
communication came first. Simple first, then complex (intercellular
communication inevitably involves more steps, some of which are at
membranes). But I'm not sure my generality is any better than yours.
So better to see if you can refine/focus.

bob

>What I'd like to know is:
>(1) Whether the internal modes of communication inside a cell evolved from
[quoted text clipped - 9 lines]
> this or, assuming all these speculations are entirely without merit,
> where I should read about the right way to look at this stuff?

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Allan Adler - 17 Dec 2004 17:51 GMT

> Let's take what you wrote above as generally ok.

> I think it would help to be more specific. What kind of communication?
> Specific examples? I think it would also help to leave viruses out of
> the story, since they are not an integral part of basic cellular
> processes.

I wish I could be more specific. I really don't know much. Regarding
viruses: before leaving them out of the picture, maybe you can clarify
one point about intracellular communication. I was under the impression
that messenger RNA was used to control the mitochondria. I don't know
where I got that impression. That was the basis for wondering whether
it was a refinement of the way viruses take control of a cell, the
cell in this case being the mitochondria (which used to be a cell
at an earlier evolutionary stage).

> As to #1 below, my intuition would be the opposite, that intracellular
> communication came first. Simple first, then complex (intercellular
> communication inevitably involves more steps, some of which are at
> membranes). But I'm not sure my generality is any better than yours.
> So better to see if you can refine/focus.

Why do you think intracellular communication came first? Let's say that
there are two cells, A and B, way back before cells started living inside
other cells. Let's say that A takes up residence in B and manages to survive
in that environment. Let's say that this becomes a common arrangement between
cells of these two types and together they evolve symbiotically into a
cell C in which A has become a mere organelle.

I could be misunderstanding your use of the term "intracellular". Maybe
you would include in it communication between A and B while A is residing
inside B. I'm restricting it to mean the communications between, say,
the nucleus and the mitochondria (I don't know what else participates
in communication inside cells these days). The old communication between
A and B while A is living inside B is something I would classify as
intercellular communication which, for reasons that might be more
favorable inside the cell, is more successful than it might be if
A were not living inside B. If B leaks something outside the cell,
it is more likely to be diluted and not affect an external A as
much as if A lives inside the cell.

Well, I'm reading Betsy Dexter Dyer's book, "A field guide to bacteria"
at the moment. There are pictures of cells living on the surface of other
cells. For her, cells are little chemical factories that metabolize some
chemicals into other chemicals. So, I guess the lowest level of intercellular
communication is that A likes to eat B's waste products. That seems like
it is more likely to precede any other mode of communication. Possibly
A likes B's cooking so much, A decides to move in.

On the other hand, maybe merely being a cell implies having internal modes
of communication, just to get the work done of being a cell. In that sense,
intracellular modes might be prior.

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Bob - 21 Dec 2004 03:12 GMT

>> Let's take what you wrote above as generally ok.
>
[quoted text clipped - 10 lines]
>that messenger RNA was used to control the mitochondria. I don't know
>where I got that impression.

Not sure what that means. That is, it is a generality, and specifics
would be more useful. In general, the role of mRNA is to code for
proteins. In some sense then, mRNA controls everything, but I don't
think that is too helpful.

>That was the basis for wondering whether
>it was a refinement of the way viruses take control of a cell, the
>cell in this case being the mitochondria (which used to be a cell
>at an earlier evolutionary stage).

Viruses are very diverse. There are no good generalities about how a
virus takes control of a cell. In fact, some viruses do not take
control, but basically co-exist. OTOH, some will interfere with the
use of host mRNA.

Note that the co-existence case is more relevant to the mito.

>> As to #1 below, my intuition would be the opposite, that intracellular
>> communication came first. Simple first, then complex (intercellular
[quoted text clipped - 20 lines]
>it is more likely to be diluted and not affect an external A as
>much as if A lives inside the cell.

Ok, we are dealing with terminology here. By intracellular, I meant
any communication/regulation within a single cell. Obviously, this
occurs (and presumably occurred) in primitive cells before there were
any mito.

Your Q is quite reasonable, but I do not know of any good term for it.
Perhaps we could be specific and suggest nuclear-mito communication.

My bias stated earlier is not relevant, then, to your Q, so I withdraw
it.

>Well, I'm reading Betsy Dexter Dyer's book, "A field guide to bacteria"
>at the moment. There are pictures of cells living on the surface of other
[quoted text clipped - 3 lines]
>it is more likely to precede any other mode of communication. Possibly
>A likes B's cooking so much, A decides to move in.

There are other scenarios, some variations of that.

For example, the products of B might inhibit A. Thus we might
generalize that the products of B affect the growth of A, either + or
-. Then we might consider attract/repel.

As to the events preceding establishment of the organelle... It is
also likely that cell B simply takes up A, with the intent of eating
it. But somehow A manages to survive. Events of this type can be shown
with modern organisms. Whether that reflects on the early events
relevant to establishment of (say) mito is unknown (unknowable?).

Rather than look for generalities, I suspect it would be more
productive to look for specifics. What kinds of communication are
there between mito and nucleus? We know that mito replicate in step
with the cells, so there must be some regulation. I do not know what
is known on that. This type of regulation may well not have occurred
until the mito began to take shape.

Regulation of mito activity (energy generation) is done via transport
of small molecules. This type of regulation occurs within any cells.

Each example would have to be examined on its own merit.

bob

>On the other hand, maybe merely being a cell implies having internal modes
>of communication, just to get the work done of being a cell. In that sense,
>intracellular modes might be prior.

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Allan Adler - 21 Dec 2004 05:15 GMT

Bob, thanks for taking the time to deal with my ignorant questions.
I think I need to do some reading before I pursue this any further.
For example, I apparently had a very fundamental misconception of
the function of mRNA.

I think the idea of organelles as cells that never left is due to
Lynn Margulis. At any rate, I think she did a lot to develop the
idea. What is the basic reference on this theory?

Apart from that, I think I need to read about how a cell works.
That includes the daily life of a cell and the precise mechanisms
by which different parts of the cell are controlled. I have the
following books:
(1) Ayala and Kiger, Modern Genetics (1980)
(2) James D. Watson, Molecular Biology of the Gene, 2nd ed. (1970)
(3) Albert L. Lehninger, Bioenergetics, 2d ed. (1973)
(4) Lehninger, Biochemistry 2d ed. (1979)
(5) Stryer, Biochemistry, 2d ed. (1981)
(6) Davis, Dulbecco, Eisen, Ginsberg, Microbiology 3d ed. (1980)
(7) Ariel G. Loewy and Philip Siekevitz, Cell Structure and Function,
2d ed. (1969)

I've looked at all of them at one time or another but haven't had time
to commit to reading them from cover to cover. I started reading (7),
thinking it looked like the easiest of the lot, but got very distracted
by an error I found early in the book. I showed it to a doctor in training
who, after I explained the error and its probable origin, told me that books
like (7) are written for doctors, who don't (he said) worry about details
like the one I found. The error occurs on pp.34-36, where they take an
inventory of the contents of the bacterium Dialister pneumonsintes and
try to do some computations. After that, I kind of lost confidence in
the book and didn't want to invest the effort in reading it. But maybe
it won't do me any harm to at least turn all of the pages. I probably
won't be more badly misinformed than I wound up by not reading anything.

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Natural Science Forum / Biology / Biology / December 2004

talking to organelles