Talk:Retrovirus

From Wikipedia, the free encyclopedia

	MCB Portal This article is within the scope of the Molecular and Cellular Biology WikiProject. To participate, visit the WikiProject for more information. The current monthly improvement drive is Signal transduction.
Article Grading: The article has not been rated for quality and/or importance yet. Please rate the article and then leave comments here to explain the ratings and/or to identify the strengths and weaknesses of the article..

Contents 1 Old discussion 2 DNA Evolution 3 storage for DNA? 4 Removed from article 5 Beneficial retrovirus? 6 Because reverse transcription lacks the usual proofreading of DNA transcription... 7 Role in Oncogenes 8 DNA specific slicing and unanswered Questions in the article

[edit] Old discussion

Does the reverse transcription occur in the host cytoplasm or in the virus? I want to clear up difference beetween viral insertion into host and viral DNA insertion into host DNA -rmhermen

---

The reverse transcription occurs in the host's cytoplasm. The virus is just a highly packed storage form. BTW, I think it is "reverse transcriptase", not "retrotranscriptase". --Magnus Manske

Should this article discuss endogenous retroviruses. I understand that they are a "retrovirus that has become dormant and exists as DNA copies in every cell in the body of its host and is passed down from generation to generation."

I have read that some endogenous retroviruses exist in human DNA. But what precisely does this mean? Wase entire geonome of a given retrovirus transcribed into DNA, and then spliced into a human chromosome? Parts of a retrovirus geonome? Does this occur in nuclear DNA, mtDNA, or both? JeMa

In response to JeMa's question about endogenous retroviruses:

The nuclear genomes of eukaryotes (that includes humans) contain indeed DNA segments that are mobilized by endogenous reverse transcriptase and are being copied into other spots in the genome. Some people call them endogenous retroviruses. Though I would reserve the term virus for a capsule that transfers nucleic acids between organisms and stay with the more accurate way of calling these DNA elements retroposons.

Retroposons differ from transposons in that they do not "jump" but that they are being copied when they insert elsewhere. There are two fundamentally different types of these retroposons: one type which carries the gene for reverse transcriptase and another type which does not encode reverse transcriptase but can nevertheless be mobilized by reverse transcriptase provided by one of the other elements.

The way retroposons get activated is that they are in DNA regions that are first transcribed into RNA which then serves as a substrate for reverse transcriptase. Upon being reversely transcribed into DNA these elements get simultaneously inserted somewhere else into the genome.

Since retrotransposition is a copying mechanism, retroposons obviously increase in number over time. The human genome, for example, contains over 1,000,000 copies of a primate-specific retroposon called Alu. Alu elements are roughly 300 bp long, the human genome consists of roughly 3,200,000,000 bp - therefore Alu elements amount to some 10% of the human genome. Another class of retroposons in the human genome, so-called LINE elements, are roughly 7,000 bp long. Contrary to Alu, LINE elements in fact carry a reverse transcriptase gene. The amount of DNA that goes to LINE elements in the human genome is about 25%.

I am not aware of any instance of finding retroposons in mtDNA. Nor transposons, for that matter.

However, retroposons resembling retroviruses and transposons resembling DNA viruses have been found across all kingdoms. As far as who came first, two theories are actually being dicussed. The first one, as mentioned by JeMa, that retroposons and transposons could be remnants of viruses that lost the ability to leave their host cells. The other theory is that nucleic acids first learned to move about while they were still contained in cells. Later, they acquired the capability to leave and, subsequently, to invade other cells. Talk about sucessful 'selfish genes'.

Hillibilly

• Endogenous retroviruses (ERVs) (Human engodenous retrovivuses are called HERVs) are distinct from retrotransposons (however they can be considered as a type of retrotransposon). They are viruses that are transmitted vertically through the germ-line. They are not infectious but reflect past exogenous retroviral infection in which proviral DNA has been integrated, passed on and retained/trapped within the genome (they still have a gag, pol and env genes and therefore genetically still look like viruses). Some workers call them fossil viruses and they constitute about 4·8% of the human genome. Their role in the genome isn't really understood, but they may be used be made use of by other viruses like HIV contributing to the pathology of the disease. HERVs are also transcribed in the placenta and one hypothesis is that this happens to suppress local immune recognition of the embryo, making them necessary for reproduction. If you have access to a university library I recommend

Nelson, P.N et al. 2004. Human endogenous retroviruses: transposable elements with potential?, Clinical & Experimental Immunology 138:1-9, and

Muir, A,. et al. 2003. Expression and Functions of Human Endogenous Retroviruses in the Placenta: An Update, Placenta 25, supplement 1, S16-S25--nixie 00:39, 6 Feb 2005 (UTC)

[edit] DNA Evolution

Should we insert a note regarding the possibility that DNA evolved initially from retroviruses and was subsequently adopted by cellular organisms? I will try to search for some documentation, but I am quite sure it is an accepted possibility.

Something along the lines of

Certain groups speculate that the processes followed by retroviruses (that is, RNA>DNA>RNA>Protein) may be the key to the evolution of DNA; thus, that in the "primordial soup," retroviruses evolved to create DNA and it was subsequently adopted by cellular organisms due to its increased stability.

Ickle

That great! just dont forget to quote it and put it in a different paragraph. :)( --Procrastinating@^talk2me 11:58, 30 December 2006 (UTC)

[edit] storage for DNA?

"The virus itself is just a storage form for its DNA." -- This confuses me, as the article previously says, I think, that the retrovirus (which I assume is "the virus" here) holds RNA, and then gets its host to manufacture DNA. So, I would have expected the (retro)virus to be just a storage for its RNA (not "for its DNA"). Maybe someone knowledgeable to help me understand?

Been fixed for a long time now. -- Ec5618 23:25, 4 December 2005 (UTC)

[edit] Removed from article

"Another feature common to all retroviruses is a lipid coating surrounding their capsid. It is essential for their propagation. This explains why retroviruses can be made inactive by just washing hands."

I'd like a cite for this, as I find this incredible. Washing hands? Wouldn't that also mean that HIV could be destroyed with any chemical base? -- Ec5618 23:25, 4 December 2005 (UTC)

Similarly, I'd like a cite for: "Certain groups speculate that the processes followed by retroviruses (that is, RNA>DNA>RNA>Protein) may be the key to the evolution of DNA; thus, that in the "primordial soup", retroviruses evolved to create DNA from the RNA templates, and it was subsequently adopted by cellular organisms due to the increased chemical stability of DNA."

Which 'certain groups'? These are weasel words. -- Ec5618 23:29, 4 December 2005 (UTC)

[edit] Beneficial retrovirus?

Is there a such thing as a beneficial retrovirus in the wild? Like, would there be a virus that would infect you and then you would become smarter or stronger or something?

You may want to see the Wikipedia Reference Desk for such questions in future. The answer is rather complicated I'm afraid, but in simplest terms, retroviruses change your DNA, in any possible way. It is theorised that a retrovirus first enabled mammals to give live birth (note that in a way, the child 'infects' the mother).

Still, please see the Reference Desk. -- Ec5618 21:32, 7 February 2006 (UTC)

[edit] Because reverse transcription lacks the usual proofreading of DNA transcription...

"Because reverse transcription lacks the usual proofreading of DNA transcription, this kind of virus mutates very often." I think this should refer to DNA replication rather than transcription - it is proofreading by DNA polymerase rather than RNA polymerase that maintains the integrity of cellular genomes. Does anyone agree? Peter Znamenskiy 19:30, 27 May 2006 (UTC)

In light of the woeful article existing currently on reverse transcrption I'm tempted to bypass that article altogether. For now I think it would be best to have it linking to Reverse transcriptase, as I will prioritise the re-write of that article. My last exam is tomorrow, so I should be able to start it... well, tomorrow ☺ -- Serephine ♠ talk - 06:12, 20 June 2006 (UTC)

[edit] Role in Oncogenes

I think that this article should make mention of the significant role of retroviruses in the discovery of oncogenes. I would do it, but I feel maybe someone else is more qualified?

[edit] DNA specific slicing and unanswered Questions in the article

• When a retrovirus enters the host's system in insert it self to the DNA using the host insertion mechanisms, yet frequently that insertion fails to produce a phenotype, thus naming it junk-DNA.

My question is - Is the insertion location pertinent to the implementation of the code segment, and if so is there a way for a virus to control the location, or is it just random chance?

• Also, in the process of reproduction some viruses kill the host, while other do not reproduce or reproduce in a non-lethal-to-host manner? The article does not say. --Procrastinating@^talk2me 12:04, 30 December 2006 (UTC)