[Ontology-editors] forward and reverse transcription

[Karen Christie]

Hmmm, a tricky question...

Reading through the whole thread so far, I have several comments.

1. Based on the current defs of "RNA-dependent DNA replication" (which 
includes the phrase 'RNA-dependent DNA polymerases (e.g. reverse 
transcriptase)' and of "transcription, RNA-dependent" which has 'reverse 
transcriptase' as a synonym, these two terms do seem to be identical.

However, it seems to me that the reverse transcription (txn) step is only 
half of "RNA-dependent DNA replication" because reverse txn only makes a 
ssDNA copy. This ssDNA then serves as the template for production of 
dsDNA (going off my old biology book). So, perhaps the def of 
"RNA-dependent DNA replication" needs to be broader to encompass the whole 
process, and "transcription, RNA-dependent" could have a part_of 
relationship to such a redefined/new term.

2. Harold's example of "A negative-sense ssRNA virus genome is copied by 
an RNA polymerase to form positive-sense RNA" is currently outside the 
scope of the question at hand, since this is not included in either form 
of transcription represented in GO by current defs:
- txn, RNA-dependent =  ssDNA copy from RNA template
- txn, DNA-dependent = ssRNA copy from DNA template

I'm definitely not an expert on all the ways viruses can do things, so it 
may be that we need to represent making a ssRNA copy from an RNA template, 
but this is currently not included in the def of "txn, RNA-dependent".

3. While I see where Harold is going in the idea that it's "all in what 
the copy is used for", I'm not sure that we can use this to distinguish. 
In terms of how enzymologists think of reverse transcriptase, it's the 
enzyme that makes a ssDNA copy from an RNA template.

4. Thinking about the question "Should "txn, RNA-dependent", e.g. reverse 
txn be uder "gene expression", I talked to my coworker Julie, who is more 
knowledgable about viruses than I am, and we weren't sure that "reverse 
txn" could be classified as always "gene expression" or as always 
"RNA-dependent DNA replication"; it seems that reverse txn is used in both 
contexts. In addition, once you start considering viral life cycles, is it 
always true that "txn, DNA-dependent" is part of "gene expression" or are 
there viruses that use DNA intermediates in the process of making an RNA 
genome?

-Karen




On Mon, 1 Dec 2008, Harold Drabkin wrote:

> It's all in what the copy is used for I think:
>
> I suppose an RNA dependent RNA polymerase  vs a DNA dependent RNA 
> polymerase... vs ....
>
> In the case of some single strand viral genomes:
>
> A negative-sense ssRNA virus  genome is copied by  an RNA polymerase to form 
> positive-sense RNA. This means that the virus must bring along with it the 
> RNA-dependent RNA polymerase enzyme. The positive-sense RNA molecule then 
> acts as viral mRNA, which is translated into proteins by the host ribosomes.
>
> A positive-sense ssRNA viruse genome is directly used as an mRNA, making a 
> single protein which is modified by host and viral proteins to form the 
> various proteins needed for replication. One of these includes RNA-dependent 
> RNA polymerase, which copies the viral RNA to form a double-stranded 
> replicative form, in turn this directs the formation of new virions.
>
> Both processes use an RNA template and make an RNA. one is transcription, the 
> other replication.
>
> hjd
>
> Midori Harris wrote:
>> Wait, I'm confused now about what you guys favor. RNA-dependent synthesis 
>> of RNA isn't transcription at all; it's RNA replication.
>> 
>> Transcription is the interconversion of DNA and RNA by synthesizing one on 
>> a template made of the other. Synthesis of RNA on a DNA template is 
>> considered "forward" because it's by far the more common direction.
>> 
>> m
>> 
>> On Mon, 1 Dec 2008, David Hill wrote:
>> 
>>> I agree with Harold.  Reverse transcription refers to the process of 
>>> reversing the transcription process, not a type of transcription.
>>> 
>>> Harold Drabkin wrote:
>>>> Hmm, from  the def of 64101, the term name really doesn't fit, since to 
>>>> me, RNA -dependent transcription would be a process whereby an RNA 
>>>> template is transcribed to create another RNA molecule. As it's defined, 
>>>> it is "reverse" transcription.
>>>> Based on the def, I would vote to merge them.
>>>> Posted to SF also
>>>> 
>>>> 
>>>> Midori Harris wrote:
>>>>> Hi,
>>>>> 
>>>>> A couple of questions have come up in SF 2354289:
>>>>> 
>>>>> 1. Should these terms be merged?
>>>>>
>>>>>   id: GO:0006278
>>>>>   name: RNA-dependent DNA replication
>>>>>   def: "The process whereby new strands of DNA are synthesized, using 
>>>>> RNA
>>>>>   as a template for RNA-dependent DNA polymerases (e.g. reverse
>>>>>   transcriptase) that synthesize the new strands."
>>>>>
>>>>>   id: GO:0006410
>>>>>   name: transcription, RNA-dependent
>>>>>   namespace: biological_process
>>>>>   def: "The synthesis of DNA on a template of RNA."
>>>>> 
>>>>> 2. Should reverse transcription be considered part of gene expression 
>>>>> (at present it is, by transitivity, but if it shouldn't be, it's easy to 
>>>>> change)?
>>>>> 
>>>>> Comments here or on the SF item much appreciated.
>>>>> 
>>>>> https://sourceforge.net/tracker/index.php?func=detail&aid=2354289&group_id=36855&atid=440764 
>>>>> Midori
>
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