Endogenous Retroviruses II

[BGoodForGoodSake]

OK I'm good with that Phoenix integrates in a petri dish with the exact signature of existing HERV-K elements. IT is not clear how the sequences would change in a living human. Many changes to the sequence would result from transposition and interaction with specific substrates, transposases, recombinases, and other cellular mechanisms. Many of the mutations visible in existing HERV-K sequnces could happen during reverse transcription to the RNA intermediary during retrotranslocation.

We are not discussing retrotranslocated elements per se. The reconstruction is base on HERV-K proviruses.
The signature may include these other elements, but we can differentiate between these different elements. Otherwise a reconstruction would not have been possible.
"To construct a consensus HERV-K(HML2) provirus, we assembled all of the complete copies of the 9.4-kb proviruses that are human specific (excluding those with the 292-nt deletion at the beginning of the env gene) and aligned their nucleotide sequence to generate the consensus in silico, taking for each position the most frequent nucleotide."(1)

The same sequence was not located in that cells DNA in the same spot as we find that sequence in the human genome.

Yes, I hope this clarifies insertion affinity in general.

It would be unwise to generalize from one instance in the laboratory. Again it has been shown that a proviral element can insert in a specific place on a specific chromosome. Clearly the mechanism exists.

Again please site the source of this information.

We are not talking about activity after integration when discussing integration sites. Also retroviruses have not shown exact integration preference, in any experiments I know of. Additionally this phenemonen is not unique to this paper. I am certainly not generalizing from a single instance.(2)(3)(4)

Remember that shortly after integration a retrovirus becomes a provirus. There are site specific recombinases and integrases as well.

Please site an instance of a retroviral integrase which is site specific to the level you have just described. The same for recombinases. Now, lets answer the question is this the general pattern we find among retroviruses?
Also would not a virus which can target multiple integration sites have an advantage?

What is meant by this, we have a fairly good understanding of how the viral material finds its way into the genome.

I agree but that is where the understanding gets cloudy. The propagation once inserted is a bit more fuzzy. This is a young field compared to many other areas of science, but we are gaining knowledge rapidly. IF we are patient perhaps many of our contentious points will be more clearly demonstrated in the coming years.

I don't think our contentions are in these areas, we are specifically focused on integration sites, and not on recombinatorial elements afterwards.

You asked how I can question the Viral Origin of HERV-K. It very well may be viral in origin. Phoenix simply took information that naturally exists in the human genome and packaged it in a retrovirus and inserted it through that mechanism. Nearly half of the human functioning genome is reverse transcribed. IT is becoming more and more clear that these are important elements of our life. Further I would point out again that most retroelements don't have naturally occurring exogenous retroviruses.

Is it not significant that the pattern of insertion by phoenix matches the patterns found in the human genome?
What is the significance that half the genome(your figure, not significant) resulted from retrotransposons?
From your knowledge of retroviruses, does the method of insertion (not to be confused with insertion into the genome) into the host cell matter in this discussion?
There may be some instances where ERV's are implicated in human related function, but certainly this does not apply to the majority of cases.
HERV-K activity for instance has been observed in teratocarcinoma.(5)
Finally why would you expect a homologous exogenous retrovirus if the conclusion is that this insertion occurred <5 million years ago?

I would ask a question in response. What observations demonstrate that HERV-K must be from a virus?

The method by which the material was inserted into the host cell does not matter. Once inside the envelope material is no longer part of the insertion process.
The methodology use to reconstruct the virus was purely statistical. (see below)
The signature of phoenix is identical to the pattern of HERV-K.
The distribution of HERV-K is consistent with that of viral infection and reinfection inter uterine.

Methodology used to reconstruct the viral RNA.
"To construct a consensus HERV-K(HML2) provirus, we assembled all of the complete copies of the 9.4-kb proviruses that are human specific (excluding those with the 292-nt deletion at the beginning of the env gene) and aligned their nucleotide sequence to generate the consensus in silico, taking for each position the most frequent nucleotide
...
Based on this in silico reconstruction, we then generated a molecular clone corresponding to the consensus DNA proviral sequence that we named Phoenix, using the related K108 and K109 proviruses (which we had previously cloned from a commercial human BAC library) as a backbone, and a commercial kit to introduce single nucleotide mutations at each position required to match the consensus."(1)

1. Dewannieux, M, Harper, F, Richaud, A, Letzelter, C, Ribet, D, Pierron, G & Heidmann, T. (2006) Genome Res 16, 1548—1556.
2. Boeke, J.D. and Stoye, J.P. 1997. Retrotransposons, endogenous retroviruses, and the evolution of retroelements. In Retroviruses (eds. J.M. Coffin, et al.), pp. 343—435. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
3.Brown, P.O. 1997. Integration. In Retroviruses (eds. J.M. Coffin, et al.), pp. 161—204. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
4. Bushman, F.D. 2003. Targeting survival. Integration site selection by retroviruses and LTR-retrotransposons. Cell 115: 135—138.
5. Dewannieux et al. Genome Res..2006; 16: 1548-1556

[BGoodForGoodSake]

The next point I would like to adddress is the following. Mentioned several times but the three examples below should suffice.

The problem here is that the insertion is found in every individual of a species with nearly identical sequences. Not withstanding the identical insertion points between species. I see this as more problematic for common ancestry hypothesis and perhaps even for the generally accepted label of many of these sequences as ERVs. Common ancestry would say that many of these infections are well over 100,000 generations old. Given the highly error prone process of reverse transcription and the instability of retroviral sequences I would wonder how you account for the remarkable stability of these sequences and how phoenix can show the same sequence today? IT would appear that remarkable few mutations have occoured and that these insertions seem to have happened very recently.

Retroviral signatures have remained extraordinarily fixed in light of the instability of proviral DNA especially caused by the reverse transcription of the retroviral RNA. If one accepts millions of years it would seem they need to either doubt the time period, or question the observations showing the extraordinary ability of retroviral RNA and proviral DNA to mutate rapidly.

IT is not clear how the sequences would change in a living human. Many changes to the sequence would result from transposition and interaction with specific substrates, transposases, recombinases, and other cellular mechanisms. Many of the mutations visible in existing HERV-K sequnces could happen during reverse transcription to the RNA intermediary during retrotranslocation.

It seems here you are attributing the behaviour of retrotransposons and similar elements, to all proviral material in general.

This also ignores that the original insertion is not what is mutating in the case of retrotransposons. This point is very important.

Lets say the the original insertion does contain a retrotransposon.
It will then replicate itself and insert into another section of DNA.
We now have the original insertion and the duplicated retrotransposon.

You are correct in that the replicated copy is error prone. But the original copy at the original insertion point has not undergone any mutations.

Think of the original insertion as a cookie cutter.

Here is a visual illustration

DNA____________________________________________________
Retrovirus o.o.o.o
After insertion
____________________________o.o.o.o__________________

Retrotransposon (over simplification)
o.o.i.o
____________________________o.o.o.o__________________

Insertion
_________o.o.i.o___________________o.o.o.o__________________

As you can see the original copy is at the same insertion point and maintains the same sequence.

In fact the inserted material will collect mutations at a far slower rate than the exogenic material. Thus the question why the sequences can be so similar between species if they are the result of separate infections.

[NewCreature]

Adeno associated provirus. This virus goes beyond site specific, and is able to find an exact location on an exact chromosome. Most proviral insertions are able to integrate at various sites since specific sequences appear in more than one location. There is a myriad of mechanisms at play in retroviral propagation throughout the genome; these involve deletions, translocated insertions by cut and paste and copy and paste, mutations, and a host of poorly understood interactions. Here are a few snippets that address recombinases/integrases. I have been a bit busy, but will try to address other points in the thread later.

http://www.jbc.org/cgi/content/full/272/13/8361
The results indicate that the domain responsible for target site selection resides in the central core region of integrase.
The mechanism for target site selection is not well understood.
integration into some sites occurs at a frequency several hundred times random
integrases from different retroviruses have different target site preferences
the cleavage site on the DNA substrate is not entirely random, and different integrases exhibit different preferred cleavage sites
Analysis of the preferred target sites may provide information on the interaction between integrase and the sequence and structure of target DNA.

http://www.springerlink.com/content/envn4nurmjhxv0kf/
It is a bit difficult to explain the high frequency of integrations into the same gene using a random model of retroviral integration, and there has been evidence for decades that retroviral integrations may not be random.

http://www.virologyj.com/content/2/1/68
The specific pressures that influence site selection for retroviral integration remain incompletely understood.
Evidence is accumulating to indicate that proviral integration is not random, and that the secondary structure of DNA plays a major role in integration site selection

It is interesting to note that most of the identified site specific recombinases belong to the superfamily of retroviral integrases.

http://www.ncbi.nlm.nih.gov/books/bv.fc ... figgrp.882
Transpositional site-specific recombination by a retrovirus or a retroviral-like retrotransposon.

http://www.biology.usu.edu/courses/biol ... _notes.doc
Many viruses use transpositional site-specific recombination. [Retrovirus like HIV are a given example]

http://www.tribunes.com/tribune/edito/8-3z.htm
Whenever DNA segments are moved around the genome, e.g., plasmids, transposable elements, transduction, and reverse transcription, they are moved by enzymes that may be controlled in the same way as in site specific recombination.
Recently molecular biology has revealed several mechanisms by which genes are controlled. Reverse transcriptase (5, p.254) is a protein which modifies DNA (genes) in a non random way, which is forbidden by the dogma of the deaf gene. There many more examples: site-specific recombination enzymes move special DNA sequences in and out of the genome (5, p. 246); retrovirus integration (5, p. 254); transposable elements are mobile DNA sequences that are integrated by special enzymes, transposases (5, p. 255). Elements may replicate when moving, amplifying DNA segments (5, p. 256). Some move within chromosomes directly as DNA, while others via an RNA intermediate (5, p. 605). As transposable elements move, they cause a variety of short additions and deletions in nucleotide sequences (5, p. 606). Recombinant DNA technology exploits natural processes of the cell that defy the "deaf gene" dogma., e.g., plasmids (5, p. 259).

http://www.nature.com/nsmb/journal/v8/n ... 1_302.html
Although there are several classes of transposition proteins, the best understood are members of the transposase/retroviral integrase superfamily. These proteins are responsible for the movement of most DNA elements and the virus-like (LTR) retrotransposons, as well as for retroviral integration. The new millennium has brought the first structure of a transposase−DNA complex, as well as several new retroviral integrase structures and the structure of a transposase-associated nuclease. These data, along with recent biochemical experiments, reveal sophisticated new views on the mechanisms used by transposases to assemble multimeric protein−DNA complexes and catalyze recombination.

[BGoodForGoodSake]

These are all very interesting links and we will return to them from time to time.
It appears that you focused on key terms such as non-random integration and site-specific. The problem is this does not indicate exact insertion.

However let's say for arguments sake that a virus is able to integrate into an exact location across multiple species. (although the evidence does not show this, we will return to this later.)

What explanation can be given for the similarities in sequences of these insertions?

[NewCreature]

However let's say for arguments sake that a virus is able to integrate into an exact location across multiple species. (although the evidence does not show this, we will return to this later.)

What explanation can be given for the similarities in sequences of these insertions?

OF course the evidence shows this. We do in fact find integration into exact locations across multiple species. After we hypothisize about proviral integration and look to the observations we do find a large amount of evidence showing exact insertion points.

As to the similarity in sequences that is a function of a pandemic where many individuals get infected by the same retrovirus.

Why do you continue to question the varied hypotheses here? Did you have some better explanations? While, sure it is helpful to hone the hypotheses to a certian extent, I'm not sure what the use would be to contend the points further. While I feel that it is clear that proviral integration into the genome is not that well understood, I think that I have been clear in proposing the mechanisms by which the hypotheses might work.

Perhaps it would be best to move on to other hypotheses. I feel that there is some plausibility to the pandemic model of retroviral integration that might yield a small percentage of similar integrations in similar locations. Sure there is variability in location and sequence to an extent and we do indeed find quite a bit of variation in retroviral signatures as a whole. But it seems clear that the process is not completely random and as such and by definition we should see patterns and distributions resulting from the guided processes involved.

I will have little more to say about my stance on retroviral integration as it seems we will be circleing over the same ground again, but if you would like to address or propose any number of other hypotheses I would be interested in exploring how they might answer the observations as well.

[BGoodForGoodSake]

OF course the evidence shows this. We do in fact find integration into exact locations across multiple species.

After we hypothisize about proviral integration and look to the observations we do find a large amount of evidence showing exact insertion points.

As to the similarity in sequences that is a function of a pandemic where many individuals get infected by the same retrovirus.

Why do you continue to question the varied hypotheses here? Did you have some better explanations? While, sure it is helpful to hone the hypotheses to a certian extent, I'm not sure what the use would be to contend the points further. While I feel that it is clear that proviral integration into the genome is not that well understood, I think that I have been clear in proposing the mechanisms by which the hypotheses might work.

Perhaps it would be best to move on to other hypotheses. I feel that there is some plausibility to the pandemic model of retroviral integration that might yield a small percentage of similar integrations in similar locations. Sure there is variability in location and sequence to an extent and we do indeed find quite a bit of variation in retroviral signatures as a whole. But it seems clear that the process is not completely random and as such and by definition we should see patterns and distributions resulting from the guided processes involved.

For the purposes of this discussion lets stick to one point and I will sumarize after all the queries have been resolved.

The evidence of exact insertion points is what lead to the hypothesis in the first place.
The matter of exact insertion points in this discussion is not yet resolved. The data does not show definitve evidence for exact insertion points.
However for the purposes of continuing this discussion I proposed that we assume that exact insertion points are the case.

That way we can continue the analysis of this hypothesis.

So now the matter is why the sequence similarity.
Let us assume that the viuses in question did indeed lead to the same insertion points across multiple species.
It is your assertion that sequence will fall into a pattern because of the type of animal being infected.

Does the original sequence of viral material have more of an impact on the sequence found in the exact insertion point?
Or does the type of animal being infected affect the sequence more?

The reason I ask this is because as you will recall the sequences of these insertions across species falls into a pattern.

Doesn't the sequence depend on the viral sequence itself?

I will have little more to say about my stance on retroviral integration as it seems we will be circleing over the same ground again, but if you would like to address or propose any number of other hypotheses I would be interested in exploring how they might answer the observations as well.

I beg to differ, we are only now beginning this discussion. We need to continue with analysis of your hypotheses. There are several unanswered questions. Lets us start by answering the question posed above, marked by an arrow.

[NewCreature]

I wanted to address this point you made, "This also ignores that the original insertion is not what is mutating in the case of retrotransposons. This point is very important."

Entire proviral integrations of a retrovirus are transposable elements.

I would have to disagree to an extent with your point. While I understad what you are saying, I think it oversimplifies the complexity of retroviral propagation throughout the genome. There are a myriad of processes involved some of which are poorly understood.

I would say that it is the orignial insertion that is mutating. While it is not clear how proviral segments are impacted by conservative transposition, our current understanding is that they most often move by replicative transposition.

The original retroviral insertion is copied to an RNA intermediary, and reverse transcribed with a likely mutation into a slightly different DNA provirus, and reintegrated elsewhere. The orginial insertion may not even exist in short order. Deletions, mutations, tranposition, recombination, it truly is a complex maze that we are only just begiing to understand in the last 25 years.

The point is with, HERV-K for instance, up to 1000 copies of elements from a particular retrovirus how are you able to determine that the initial insertion is even still in the genome? All that might be left of the initial insertion could be simply a "key" showing that a site specific recombinase or integrase has at some point copied the insertion at that site. The initial insertion is what is mutated and moved, often times insertions are selected against by deletions.

[NewCreature]

Doesn't the sequence depend on the viral sequence itself?

Yes I would say in large part it does, however there may be differences in the proteins and enzymes in different species involved in transcribing the RNA into a DNA provirus and its subsequent integration into the DNA substrate. Interestingly there is some evidence to suggest that the exact same DNA sequence in different species will result in a protein with a different shape and may quite possibly behave somewhat differently.

Perhaps it is a bit simplified to say so, but I would in one word answer YES.

The data does not show definitve evidence for exact insertion points.

OK well the data does show sequences in exact locations which would be a prediction of exact insertion points. I would modify that to clarify it a bit. Insertion point is a bit vague, as it could be construed as to mean the initial viral integration which of course might not even exist after a short time. I mean that we see that a viral signature has arrived in a specific location during propagation of the proviral sequence throughout the human genome be one or more of several mechanisms.

I am coming more and more to the conclusion that these elements of our DNA COULD have given rise to exogenous viruses rather than vice versa. There is some thinking within evolution along the lines that retroelements are predecessors of retroviruses; while there is some evidence to suggest that I don't come to the same conclusion myself with respect to some of the narrative involved in that particular theory.

I am weary of this discussion because it simply results in me reasserting my position over and over again. For instance exact insertions COULD result from mechanisms we have already been over more than once. There appears to be little reciprocity in this converstation from my perspective. I really don't have much more to say unless you address the issue by proposing a more likely or equally viable hypothesis for a particular observation. If you can't propose a mechanism for your point that seems more likely or fits the observation better, than you really have nothing.

Your method throughout this thread is a bit inane and bores me. IT seems to be more addressed like, "Prove this", "Prove that". That isn't how science works, it cannot be proven, and in the abscense of a better hypothesis for the observation, then pandemic origins answers fine. I have proposed a hypothesis and tried to demonstrate how it could be probable, but I have yet to see one shread of alternative hypothesis. I can't prove my hypothesis as that is not possible. IF you do have some alternative explanation that might be helpful. In short from within this thread it appears that my pandemic hypothesis is scientific "truth" unless something can be proposed that offers a more complete alternative that fits the data better.

Perhaps you are afraid of going on the defenseive, but I will try hard not to do that, as I am sure that it would be as tiring for you as it has been for me.

[BGoodForGoodSake]

Doesn't the sequence depend on the viral sequence itself?

Yes I would say in large part it does, however there may be differences in the proteins and enzymes in different species involved in transcribing the RNA into a DNA provirus and its subsequent integration into the DNA substrate.
...
Perhaps it is a bit simplified to say so, but I would in one word answer YES.

Bear with me here I am getting to a point.

So you answer yes that viral sequence has a large bearing on insertion sequence.

Do you agree that viral DNA is always changing.

Do you also agree that viral material mutates at a much higher rate than endogenous material?

----------------------------------------------------------------------

If on the other hand you are saying that viral material will integrate with a different sequence depending on the species it is infecting, the following must be addressed.
For the Phoenix viral reconstruction the retroviral insertion was identical across three species.

Based on what can you make the assertion that host genome has more influence on insertion sequence than the sequence of the virus itself?

Being familiar with retroviral insertion at what point does the host genome or host processes affect the genetic sequence of the integrase?

What significant differences exist between the cells of the various organisms(primates) in question to validate this assertion?

Interestingly there is some evidence to suggest that the exact same DNA sequence in different species will result in a protein with a different shape and may quite possibly behave somewhat differently.

We are not talking about proteins here, this is immaterial, do you not agree? ERV's are generally non-coding sections of DNA.

[NewCreature]

Do you agree that viral DNA is always changing.

Do you also agree that viral material mutates at a much higher rate than endogenous material?

Viral material is static. It is barely alive. I would agree that proviral material that is integrated into a genome has an amazing ability to move about and be deleted only showing a signature of their passage. So I suppose in a sense that it is changed by many separate recombination events. Changed viral particles can infect another cell or another individual with a slightly mutated version of a retrovirus.

Upon the initial delivery of a new virus and during a pandemic there will be many similar infections by a virus that hasn't been able to be mutated and changed significantly by the mechanisms of the host.

In addition to the pandemic hypothesis I would like to hypothesize that many of the "retroviruses" are intrinsic parts of the human mechanism. IT seems that if that were the case there would be few stable regions and that the translocation of these retroelements would happen in unique ways within the individual based on other genetic material and in conjunction with environmental influences. This hypothesis would espouse the idea that retroviruses are productions of pre existing retroelements. Perhaps it would be interesting to explore to see if that answers observations as well as pandemic integration of viruses. Of course the two hypotheses need not exclude each other becase a variety of different mechanisms and sources could be at play in providing the entirety of the transposable elements which make up 45% of the human mechanism.

If on the other hand you are saying that viral material will integrate with a different sequence depending on the species it is infecting, the following must be addressed.
For the Phoenix viral reconstruction the retroviral insertion was identical across three species.

Well I don't think this is cut and dried. It is clear that a virus can infect a host or a particular set of hosts. Now if the genetic structure of the potential host is different enough the virus may not be able to integrate at all. As Phoenix is a clear viral integration it seems to show that infection by a pandemic of Phoenix viruses will yield a pattern of integration. While retroviral integration seems to effect a cross section of similar hosts, It's uncertain how the unique combination of integrases, transposases, and recombinases between the host species will change the signature of the varied instances of transposition of the retrovirus and the retro elements that it spawns. IT is clear that there is a pattern of viral integrations where more similar species have more similar viral signatures. The pandemic model would expect that similar species infected by the same viral outbreak to show similar patterns of viral integration.

Based on what can you make the assertion that host genome has more influence on insertion sequence than the sequence of the virus itself?

I'm not sure I have claimed this to the extent that you state it here. Both the primary structure and secondary structure of the DNA influence proviral integration. Since there are unique properties to these structures in the disparate species of viable hosts we would have lots of basis to propose a statement not all that dissimilar from yours. After all I would estimate that 90%+ of proviral integrations do seem to not line up between the viable hosts. That could suggest that 10% of it is from the virus and 90% of it is from unique properties of host DNA and environmental influences.

[/quote]Being familiar with retroviral insertion at what point does the host genome or host processes affect the genetic sequence of the integrase?

I'm not sure what your question is trying to get at. The host genome effects the genetic sequence of the integrase during the process where reverse transcriptase and other protiens form the RNA into DNA. Translation and recombination are also mechanisms whereby the host genome can change the genetic structure of integrase. I'm not sure if this answers your question or not. Perhaps you were more interested in how integrase interacts with a particular hosts DNA. Site specific recombinases and integrases have a host of incarnations that behave in specific ways. Different integrases have different affinities based both on the primary and secondary structure of the hosts DNA. Actually integrases and recombinases could be viewed as a cross section of similar proteins.

What significant differences exist between the cells of the various organisms(primates) in question to validate this assertion?

The ability of specific integrases to work in a particular genome and not another. The primates are a great example of this. Apparently there are some differences between the cells that provide immunity in the case of one hosts DNA while the others do not.

We are not talking about proteins here, this is immaterial, do you not agree? ERV's are generally non-coding sections of DNA.

Well no that is not true. Retroviruses code for proteins, and there are a host of proteins involved in the propagation of retrelements throughout the hosts DNA, so I think the structure of the proteins involved is important especially in how the cellular mechanisms create that protein. IT is probable that some viruses are not capable of infecting a host because the genetic sequence doesn't yield a protein of the correct shape and function.

[zoegirl]

Just to pop in here, most viruses not static. They are very prone to mutation. HIV particles are different even between several states. (If I remember correctly that is one of the reasons developing a vaccine for them is so difficult, probably wrong here)

It's been a awhile for me (high school viruses, even in AP Bio, don't delve this deeply!), but Aren't these high mutation rates related to whether they are single stranded RNA, DNA virus families. Help me remember!

LIke reading about this. Bgood, and new creature... Do you a coulple of good resources (I will be convenient and hope there are web sites ) where I could brush up on this?

Thanks.

[BGoodForGoodSake]

Do you agree that viral DNA is always changing.

Do you also agree that viral material mutates at a much higher rate than endogenous material?

Viral material is static. It is barely alive. I would agree that proviral material that is integrated into a genome has an amazing ability to move about and be deleted only showing a signature of their passage. So I suppose in a sense that it is changed by many separate recombination events. Changed viral particles can infect another cell or another individual with a slightly mutated version of a retrovirus.

Upon the initial delivery of a new virus and during a pandemic there will be many similar infections by a virus that hasn't been able to be mutated and changed significantly by the mechanisms of the host.

How so? Every viral partical must originate individually from a host cell somewhere else. Therefore each viral partical must be slightly different in terms of sequence. When asking whether viral material mutates I am not asking whether retroviral RNA within one viral particle was changing, I was asking whether viral material itself changes as it propogates through host cells.

It's funny how in the case of viral genetic material you focus on the static material within an individual viral particle and ignore the rapidly changing sequence due to propogation.
While on the other hand you ignore the static sequence of an ERV and choose to focus on the rapidly changing retro transposal elements.
lol

I'll repeat the question, does retroviral RNA change as a function of time in a retroviral population faster than the genetic material known as ERV's?

In addition to the pandemic hypothesis I would like to hypothesize that many of the "retroviruses" are intrinsic parts of the human mechanism. IT seems that if that were the case there would be few stable regions and that the translocation of these retroelements would happen in unique ways within the individual based on other genetic material and in conjunction with environmental influences. This hypothesis would espouse the idea that retroviruses are productions of pre existing retroelements. Perhaps it would be interesting to explore to see if that answers observations as well as pandemic integration of viruses. Of course the two hypotheses need not exclude each other becase a variety of different mechanisms and sources could be at play in providing the entirety of the transposable elements which make up 45% of the human mechanism.

Lets not stray off of the topic. We are focusing on the ERV's and the pattern of differences exhibited by shared insertions.

Well I don't think this is cut and dried. It is clear that a virus can infect a host or a particular set of hosts. Now if the genetic structure of the potential host is different enough the virus may not be able to integrate at all. As Phoenix is a clear viral integration it seems to show that infection by a pandemic of Phoenix viruses will yield a pattern of integration. While retroviral integration seems to effect a cross section of similar hosts, It's uncertain how the unique combination of integrases, transposases, and recombinases between the host species will change the signature of the varied instances of transposition of the retrovirus and the retro elements that it spawnsIT is clear that there is a pattern of viral integrations where more similar species have more similar viral signatures. The pandemic model would expect that similar species infected by the same viral outbreak to show similar patterns of viral integration.

We are not talking about integration signature when we are discussiong shared ERV's. We are talking about sequence. A much more exact match.

After all I would estimate that 90%+ of proviral integrations do seem to not line up between the viable hosts. That could suggest that 10% of it is from the virus and 90% of it is from unique properties of host DNA and environmental influences.

How can you make this assertion? Are you saying that the difference in integration sites is soley due to properties of host DNA and environmental influences?
It seems as if your using the fact that integrations do not line up between different species 90%+ of the timethe this is due soley to the properties of the host cells.
This assumes that a virus will always integrate to the same exact spot every time correct?
Please explain if I misunderstood.

Also are there really significant differences between the host cells being discussed?

I'm not sure what your question is trying to get at. The host genome effects the genetic sequence of the integrase during the process where reverse transcriptase and other protiens form the RNA into DNA. Translation and recombination are also mechanisms whereby the host genome can change the genetic structure of integrase. I'm not sure if this answers your question or not. Perhaps you were more interested in how integrase interacts with a particular hosts DNA. Site specific recombinases and integrases have a host of incarnations that behave in specific ways. Different integrases have different affinities based both on the primary and secondary structure of the hosts DNA. Actually integrases and recombinases could be viewed as a cross section of similar proteins.

The question is, if I were to infect a chimpanzee and a human with the same retrovirus how much of the sequence of the insertions will be modified because of the type of cell it has infected?
a. 0%
b. up to 20%
c more thn 20%
We are not discussing integration patterns or even insertion sites, as we are assuming the the integration site is exact. The focu is on sequence.

What significant differences exist between the cells of the various organisms(primates) in question to validate this assertion?

The ability of specific integrases to work in a particular genome and not another. The primates are a great example of this. Apparently there are some differences between the cells that provide immunity in the case of one hosts DNA while the others do not.

Immunity is a separate subject and involves the interaction of envelope proteins of viruses and proteins found in the cell membrane. Please stay on topic.

We are not talking about proteins here, this is immaterial, do you not agree? ERV's are generally non-coding sections of DNA.

Well no that is not true. Retroviruses code for proteins, and there are a host of proteins involved in the propagation of retrelements throughout the hosts DNA, so I think the structure of the proteins involved is important especially in how the cellular mechanisms create that protein.IT is probable that some viruses are not capable of infecting a host because the genetic sequence doesn't yield a protein of the correct shape and function.

Now you are talking about ribosomes... Please site this information. Does this study show a difference in protein shape between mammal cells or between bacteria and and eukaryotic cells? If the latter please refrain from adding this to this discussion because it is very off topic.

It's been a awhile for me (high school viruses, even in AP Bio, don't delve this deeply!), but Aren't these high mutation rates related to whether they are single stranded RNA, DNA virus families. Help me remember!

Yes retroviruses are especially prone to mutations.

LIke reading about this. Bgood, and new creature... Do you a coulple of good resources (I will be convenient and hope there are web sites ) where I could brush up on this?

Thanks.

Try this one. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=rv.TOC

NewCreature,
Once we have settled this issue(meaning answered all the questions) there is one final issue to resolve, then I will post a summary to which you can respond. So please be patient.

[zoegirl]

Whoa, nice website....now I've got some digesting to do.

Thanks

[NewCreature]

Just to pop in here, most viruses not static. They are very prone to mutation. HIV particles are different even between several states. (If I remember correctly that is one of the reasons developing a vaccine for them is so difficult, probably wrong here)

Actually HIV shows about 1 mutation for every recombination event. In the course of a viral infection cells will usually block reinsertion of the viral sequnce that infected them. With HIV nearly every recombined viral particle is slightly different and a cell can become infected numerous times.

A particular virion has no ability to change, but as I mentioned before proviral material that is integrated into a genome has an amazing ability to move about, be deleted, mutated, and transcribed. So while an individual virion is completely static the sequence of that initial infection will be changed both in location and sequence both within the host genome and within subsequent viral particles.

Every viral particle must originate individually from a host cell somewhere else. Therefore each viral particle must be slightly different in terms of sequence.

Yes I agree that every virion must originate from a host cell. This would suggest that transposition of genetic material within hosts gave rise to retroviruses. In order to state this you would need to reject the idea that simple viruses evolved into more complex organisms. Yes I agree that there will be slight differences among various recombinations of a virus.

It's funny how in the case of viral genetic material you focus on the static material within an individual viral particle and ignore the rapidly changing sequence due to propogation.
While on the other hand you ignore the static sequence of an ERV and choose to focus on the rapidly changing retro transposal elements.

I'm glad to entertain. The rapidly changing sequence due to propagation and the effects of retrotransposition have an effect both on the sequence of the ERV and on future virions produced. Retroviruses have no ability to evolve except by a myriad of processes that involve the host genome. The host genome can change the virus, the virus can re-infect the host, the signature can be moved, deleted or mutated. The activity of the host upon the virus is communicated to future virions, and fed back through re-infections.

I'll repeat the question, does retroviral RNA change as a function of time in a retroviral population faster than the genetic material known as ERV's?

I'm not sure that it is a simple enough question to answer simply. Retroviral populations seem to have been more stable in retaining a working genetic structure, whereas most ERV sequences have been so changed by the many mechanisms involved that many of them no longer resemble a retrovirus all that closely. In large part all we have left is some marking indicators that let us know that at some point a retrotransposon, perhaps as a working retrovirus, has passed through a section of the DNA. Sometimes the change is so drastic that entire sequences are deleted, apparently. Many of these mobile reverse transcribed elements have functions, and there is no a priori reason to dictate that they are all viral insertions. Many of these elements could be intrinsic parts of the host's biological structure by design. I'm not sure how you would functionally separate the retroviral population from the proviral integrations, so perhaps they are so linked that they change nearly in unison.

After all I would estimate that 90%+ of proviral integrations do seem to not line up between the viable hosts. That could suggest that 10% of it is from the virus and 90% of it is from unique properties of host DNA and environmental influences.

How can you make this assertion? Are you saying that the difference in integration sites is soley due to properties of host DNA and environmental influences?
It seems as if your using the fact that integrations do not line up between different species 90%+ of the timethe this is due soley to the properties of the host cells.
This assumes that a virus will always integrate to the same exact spot every time correct?
Please explain if I misunderstood.

While retroviral integrases do show unique insertion point affinities, the secondary structure of the hosts DNA has a lot to do with the insertion point. The thing is that translocations, recombinations, and integrations after the initial infection are carried out be a range of proteins encoded by the host's genome. Transposition is partly due to environmental factors. Viruses usually integrate at the exact same sequence, but these sequences exist at various locations throughout the host genome. As mentioned in an earlier post in a cited study exact locations have been found to display integrations at several hundred times random. Retroviral integrase affinity is not the only process involved in site selection. Specific ERVs have up to 1000 integration sites, and since none of the processes are random we should see some kind of a pattern. Many of these mechanisms are functions of the host DNA. The 90% 10% ratio is admittedly arbitrary.

The question is, if I were to infect a chimpanzee and a human with the same retrovirus how much of the sequence of the insertions will be modified because of the type of cell it has infected?

IT is likely that the initial insertions would be similar, but it is unknowm how the propagation of the proviral integration will differ between the two hosts. There are differences between individuals let alone species. After all many insertions appear somewhat random. Many of the insertions are probably a result of the unique secondary structure of the individual host's DNA, and a result of the different structures of seperate host species.

Immunity is a separate subject and involves the interaction of envelope proteins of viruses and proteins found in the cell membrane. Please stay on topic.

Yes this is one factor involved in immunity; there are also others. Viral immunity has a great deal to do with the distribution of ERVs. This can account for infections in humans and chimps but not gorillas, and infections in gorillas and chimps not found in humans.

Now you are talking about ribosomes... Please site this information. Does this study show a difference in protein shape between mammal cells or between bacteria and and eukaryotic cells? If the latter please refrain from adding this to this discussion because it is very off topic.

Yes partly ribosomes in that they are involved in protein synthesis, but I was more talking the proteins themselves. Let's see if I can find an article with the relevant information for you.

the chimp and human genomes are very similar and encode very similar proteins. The DNA sequence that can be directly compared between the two genomes is almost 99 percent identical. When DNA insertions and deletions are taken into account, humans and chimps still share 96 percent of their sequence. At the protein level, 29 percent of genes code for the same amino sequences in chimps and humans.

This article is clearly talking about the similarity of chimps and humans and everything is slanted in that direction. The key point here is that DNA is ~2% different while proteins are 71% different. If 71% of the proteins are made up of different amino acid sequences we get proteins with different shapes. IF you would like to know more about protein folding and how these changes in shape effect the function and behavior of these proteins (including integrases, recombinases, transposases, etc) you can start with a couple of examples in this article "Protein Folding - How Three Dimensional Shape Affects Function”
http://members.aol.com/profchm/cutler.html

[BGoodForGoodSake]

Yes I agree that every virion must originate from a host cell. This would suggest that transposition of genetic material within hosts gave rise to retroviruses.

While possible origins of retroviruses are interesting, they are off topic. Your hypothesis deals specifically with targetted insertions. In the evaluation of this hypothesis the existance of retroviruses in this case are a given.

I'm glad to entertain. The rapidly changing sequence due to propagation and the effects of retrotransposition have an effect both on the sequence of the ERV and on future virions produced. Retroviruses have no ability to evolve except by a myriad of processes that involve the host genome. The host genome can change the virus, the virus can re-infect the host, the signature can be moved, deleted or mutated. The activity of the host upon the virus is communicated to future virions, and fed back through re-infections.

Let me restate the question. Which entity will collect more mutations during a given timespan, ERV's or the sequence of retroviral DNA within a retroviral "population"?

I'm not sure that it is a simple enough question to answer simply. Retroviral populations seem to have been more stable in retaining a working genetic structure, whereas most ERV sequences have been so changed by the many mechanisms involved that many of them no longer resemble a retrovirus all that closely.

How are you comparing the two? Are you assuming that ERV's are the result of a recent event? For example given the timespans accepted by the scientific community the ERV's themselves were far more stable than the genetic code of the original retrovirus. What sort of details are in your analysis?

What kinds of comparisons are you using? Please be more specific. Also why are we introducing the concept of working genetic structure? That is off topic isn't it? We were discussing sequence modification over time.

In large part all we have left is some marking indicators that let us know that at some point a retrotransposon, perhaps as a working retrovirus, has passed through a section of the DNA. Sometimes the change is so drastic that entire sequences are deleted, apparently. Many of these mobile reverse transcribed elements have functions, and there is no a priori reason to dictate that they are all viral insertions. Many of these elements could be intrinsic parts of the host's biological structure by design. I'm not sure how you would functionally separate the retroviral population from the proviral integrations, so perhaps they are so linked that they change nearly in unison.

We are working off of your hypothesis that ERV's are the product of targetted insertions. Please stay on focus. How can we analyze your hypothesis if it's always changing? We need to prevent the target from moving in order to properly evaluate a hypothesis.

Remember
Let us assume that the viruses in question did indeed lead to the same insertion points across multiple species.

The question is, if I were to infect a chimpanzee and a human with the same retrovirus how much of the sequence of the insertions will be modified because of the type of cell it has infected?

IT is likely that the initial insertions would be similar, but it is unknowm how the propagation of the proviral integration will differ between the two hosts. There are differences between individuals let alone species. After all many insertions appear somewhat random. Many of the insertions are probably a result of the unique secondary structure of the individual host's DNA, and a result of the different structures of seperate host species.

You seem to have misread the question, the question was about the sequence of the insertion.

If I were to infect a chimpanzee and a human with the same retrovirus how much of the sequence of the insertions will be modified because of the type of cell it has infected?

Yes this is one factor involved in immunity; there are also others. Viral immunity has a great deal to do with the distribution of ERVs. This can account for infections in humans and chimps but not gorillas, and infections in gorillas and chimps not found in humans.

While you do make some very good points, they do not apply to this particular discussion.
We are talking specifically of shared ERV's here. So this is off topic. We are discussing the ERV's shared by many primates at the same insertion point.