John Solum

A while back in this thread Dr.GH provided a link to the following paper:

Johnson, W. E., and Coffin, J. M. Constructing primate phylogenies from ancient retorvirus sequences. PNSA, vol. 96, pp. 10254-10260. 1999.

<a href="http://www.pnas.org/cgi/content/full/96/18/10254#Top" target="_blank">http://www.pnas.org/cgi/content/full/96/18/10254#Top</a>

I'm making my way through the paper, but it's slow going since I am but a simple structural geologist.

I'd appreciate it if people more-knowledgeable than I am when it comes to biology could help me out with the following questions:

1) If the retrovirus is incorporated into a cell's genome how do you distinguish between the retrovirus and the "regular" genome?

2) What's an immortalized cell line? I assume it's samples of DNA from various animals that are used as standards. If so, how do you ensure that the immortalizaed cell line is representative of the species?

3) Johnson and Coffin go over three ways to determine the age of insertion of a retorvirus. I understand the first two (distribution of the retrovirus among primates and comparison of the mutations in the retrovirus), but I don't understand the third. Here's a quote from the text:

4) What are 5 and 3 LTRs?

thanks a lot,

John

theyeti

I believe certain consensus sequences that are unique to retroviruses. I can't tell you what they are off-hand, but I can look them up later. I imagine that the presence of reverse transcriptase and integrase are among them though.

An immortalized cell line is one that won't senese and die out after about 50 divisions. Cancer cell lines are immortal, as are all useful cell lines that are cultured. Whatever it is that causes apoptosis is turned off in an immortal cell line. Other than that, they sould be normal. Non immortal cell lines are mostly useless for culturing.

Like the quote says, LTRs are long terminal repeats. They are sequences that flank the protein coding sequences, and they contain important promoter regions. The 5' (five prime) is at the "beginning" of the sequence, where as the 3' is at the "end". (Of course, there is a complementary strand, but when you see a sequence written out, the 5' is almost always on the left and the 3' on the right, thus corresponding to the way that we in the westren world read first to last. Replication and transciption takes place 5' --&gt; 3'). LTRs in retroviruses are between about 250 and 600 bp. They are characteristic of integrated retroviruses and are necessary for the viral life-cycle. They are also present in retrotransposons. I would imagine that number of muatations corresponds to the time that has passed since the sequence became unable to replicate itself. Thus, "newer" ones should have fewer mutations.

theyeti

theyeti

One more thing. IIRC, the LTRs are what's most important for determing whether or not the provirus can replicate. The internal protein sequences can actually become broken and the virus will still replicate, because other proviruses are proving the necessary reverse transcriptase, integrase, etc. Penty of "broken" retrotansposons have been picked up and inserted elsewhere in the genome this way. So the only way to know the time of insertion is to look at the LTRs and not the internal sequences. Don't take that as gospel verse though.

theyeti

MortalWombat

This page has a nice review of retroviruses:

<a href="http://www-micro.msb.le.ac.uk/335/Retroviruses.html" target="_blank">http://www-micro.msb.le.ac.uk/335/Retroviruses.html</a>

lpetrich

And a very nice result is that the family trees found from these incorporated retroviruses agree with those found using other data.

[code]
|---Human
|-|-|-Chimp
|-| |-Bonobo
| |-----Gorilla
|-|-------Orangutan
| |-------Gibbon
|
|-|-------African Green Monkey
|-|-----Baboon
|--|--Cynomolgus Macaque
|--Rhesus Macaque
</pre>[/quote]

ps418

Regarding how endogenous retrovirii (sp?) are identified, the following is from Ed Max's <a href="http://www.talkorigins.org/faqs/molgen/" target="_blank">Plagiarized errors and molecular genetics:</a>

Infectious retroviruses were discovered as agents of human disease and have been intensively studied. They ... all contain two identical non-coding Long Terminal Repeats (LTRs) at their ends as well as three genes known as gag, pol and env. These genes are encoded in the virus not by DNA but by RNA. The pol gene encodes reverse transcriptase, and may also encode additional enzymatic activities. The env gene encodes proteins that coat the outside surface (envelope) of the infectious virus. The gag gene encodes additional proteins necessary for processing the viral components. The structure common to all retroviruses is thus LTR-gag-pol-env-LTR. The "left" LTR includes regulatory sequences that can initiate RNA transcription towards the right, into the gag-pol-env-LTR; the "left" LTR is then recopied from the "right" LTR by a complex mechanism.

More links:

<a href="http://biology.uark.edu/dmcnabb/genvirol/lect22/lecture22.html" target="_blank">An Introduction to the Retroviridae</a>

<a href="http://www.ultranet.com/~jkimball/BiologyPages/R/Retroviruses.html" target="_blank">Retroviruses</a>

[ February 11, 2002: Message edited by: ps418 ]</p>

Valentine Pontifex

John,

If you are interested in phylogeny of primates you might look at this paper:

<a href="http://www.pnas.org/cgi/content/full/97/20/11130" target="_blank">http://www.pnas.org/cgi/content/full/97/20/11130</a>

You know the problem, molecules say gorilla is the outgroup of human-chimp-gorilla while morphology "obviously" says humans are the outgroup. The researchers tested this with soft-body characteristics by going to the library and finding studies of ape morphology that were not done for the purposes of evolutionary biology. When the characters that were known for all the apes and humans and differered for at least one of them were put into a computer to generate a cladogram, the same evolutionary relationships as what the molecules said was found.

pangloss

Or you could check out some of those listed here:
<a href="http://www2.norwich.edu/spage" target="_blank">http://www2.norwich.edu/spage</a>

Not that I like to toot my own horn now and then...

John Solum

Thanks a lot to everyone who's replied. I'll read the material you've linked to, and if I'm still confused I'll post my questions.

John