Confusion over orthologues of Drosophila stress-sensitive B

[amym]

Hi,

I have posted the below in the general forum, but so far no replies. It is related to a discussion also going on in the vectorbase forum, see here:

http://www.vectorbase.org/sections/Foru ... 5&p=21#p21

I'd be most grateful if anyone could explain a bit more about the relationship between Drosophila SesB and the orthologous ANTs in other insects.

Many thanks,
Amy

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Confusion over synonyms for Drosophila stress-sensitive B

Postby amym on Wed Sep 24, 2008 10:34 am
Hello,

I am working on a gene that has been annotated as ANT2 (adenine nucleotide translocator isoform 2) in the mosquito Anopheles gambiae. As there is still a dearth of functional information on some An. gambaie genes, I frequently refer to work that has been done on the corresponding Drosophila orthologues.

According to the ensembl link, the Drosophila orthologue of ANT2 is stress-sensitive B (sesB). However, when reading the literature on sesB, most authors seem to refer to it as being a synonym for ANT1, not ANT2.

To make matters even more confusing, the vertebrate literature on ANT genes contains 3 isoforms, ANT1, ANT2 and ANT3 - of these, ANT2 has very low abundance in vertebrates and is restricted to certain tissues (heart mainly). This does not fit the mosquito ANT2 picture I have, since mosquito ANT2 mRNA is relatively abundant and present in fatbodies, midgut and ovaries.

Lastly, the Drosophila orthologue of the Anopheles gambiae gene that has been annotated as ANT1 is also sesB.

So my question is, what is sesB - is it ANT1 or ANT2?

Also do the designations "1" and "2" refer to different things in Drosophila than they do in vertebrates? I gather that Drosophila ANT1 and ANT2 are alternatively spliced transcripts of the same gene, whereas this clearly isn't how the numbers are being used in An. gambiae, since Ag.ANT1 and Ag.ANT2 are presented as two separate genes. In vertebrates I get the impression that they are separate genes also.

I'd be most grateful if anyone could shed some light on this conundrum.

Many thanks,
Amy

[Josh Goodman]

Hi Amy,

Here is a reply from one of our curators.

Josh

Dear Amy,

Speaking as a FlyBase curator/annotator (with no specific expertise related to these genes) ....

Since both Anopheles ANT1 and ANT2 show higher similarity to sesB than to Ant2, I'm not sure it is valid to try to decide which is orthologous to which. Plus, they map to different areas of the genomes (not adjacent, as in flies). I don't see any obvious synteny relative to flies, but if you look more closely you may be able to make an argument based on a syntenic relationship.

Some information about expression can be gleaned from the sources of the ESTs and cDNAs that correspond to sesB and Ant2. For sesB, there are many many ESTs from diverse sources. For Ant2, all the ESTs are from testis libraries, with one exception (GM13259), which is from an ovary library.

FlyBase considers sesB and Ant2 to be 2 separate genes, since they do not share any part of their protein-coding sequences. There is one EST (GM13259, again, as it happens) that suggests they share 5' UTR sequences (and presumably promoter sequences) in some tissues. This is what makes it look like they are alternative transcripts of one gene (but keep in mind that this is one EST among dozens, it may represent a rare transcript).

--Lynn

[amym]

Hi Lynn,

Many thanks for your reply. I was also just wondering, what does the "2" in Drosophila ANT2 refer to / come from?

Best wishes,
Amy

[Josh Goodman]

Hi Amy,

Writing as myself now. The ANT2 name originates from http://flybase.org/reports/FBrf0111529.html and appears to be so named because it was the second ANT gene discovered in Drosophila.

Cheers,
Josh