Find a gene map

[Mega]

Hello,

I was trying to find a gene map (all chromosomes) of Vitis vinifera
(the plat you make wine of)

what I found was for example http://www.plantgdb.org/VvGDB/ .
But for that you need a software called Genoscope.

Is there a website where you can have a look on it online (without
downloading any tools) ??

Best,

[Cathal Garvey]

The usual place is NCBI: www.ncbi.nlm.nih.gov - They store genomes in a
multitude of standard formats, principally "Genbank" format, which can
be read as plain text but contains gene annotation data.
That is, when you read genbank information, it starts with all the
"features", genes and such, listing them by location in the ensuing
sequence. Then it gives the entire uninterrupted sequence. Most good
programs will import genbank sequences and display annotations. For
example, GENtle will display genbank sequences as maps. It's the
program I used designing my plasmid, and I'd recommend it for its
features.. but save very often, because it's very unstable and crashes
often.

Here's V.vinifera's genome splashpage:
http://www.ncbi.nlm.nih.gov/genome/401
You can go from here to all the chromosomes and episomes of V.vinifera,
or you can search the whole genome by gene name, or you can use "BLAST"
to try and match any gene/sequence you like to possibly related
sequences in V.vinifera's genome.

Bonus; here's Agrobacterium vitis:
http://www.ncbi.nlm.nih.gov/genome/1215 - which causes crown-gall in
grapes. It's got a Ti plasmid like A.tumefasciens, enabling it to
genetically modify V.vinifera cells so they form crown galls and
secrete food for the bacteria. I don't know if A.tumefasciens mediates
plasmid transfer to grapes, but if it doesn't you could try using an
A.vitis derived system instead.

--
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[Mega]

So, downloaded GENtle.
Thank you for the hint, looks great!

Was easier than I thought, just click the .exe and several times
'ok' ;)


Then I just download the gene maps and open them in GENtle?


Is there some search function? I'm looking for the sequence that codes
for Isoflavones or Resveratrol or Proanthocyanidin.

[Cathal Garvey]

You don't actually need gentle, you can read genbank as plain text. But, it helps.

Mega <masters...@gmail.com> wrote:

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[rwst]

On Feb 23, 12:33 pm, Mega <masterstorm...@gmail.com> wrote:
> Is there some search function? I'm looking for the sequence that codes
> for Isoflavones or Resveratrol  or Proanthocyanidin.

Taking resveratrol as example you would first look up the pathway,
e.g. in Metacyc or from a paper:
http://metacyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-84

The last 3 steps for example are catalyzed by stilbene synthase and
resveratrol synthase. Using a simple text search like grep will find
you these proteins in your gene map IF the map is well enough
annotated.

What if not? The Metacyc resveratrol synthase is from Arachis hypogaea
which, although a different plant family, should be homologous to the
V.v. enzyme, so just blast a V.v. genome with the A.h. sequence.

If NCBI doesn't have it, always check at uniprot.org !

[Mega]

Thank you, that's a good approach!!

Let's see if I can find that sequence... Hopefully, it's been
annotated.

[Patrik]

On Feb 23, 11:15 pm, rwst <r...@ark.in-berlin.de> wrote:
> Taking resveratrol as example you would first look up the pathway,
> e.g. in Metacyc or from a paper:http://metacyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-84
>
> The last 3 steps for example are catalyzed by stilbene synthase and
> resveratrol synthase.

Not quite. The last step, from 4-coumaroyl-CoA to trans-resveratrol is
catalyzed by a *single* enzyme, which is alternatively named
resveratrol synthase (in Arachis hypogaea), or stilbene synthase (in
Rheum tataricum and Vitis vinifera).

In fact, link to the Vitis enzyme is already right there on this page:
if you click on where it says "stilbene synthase (Vv)", that will take
you to this page with all the info:

http://metacyc.org/META/NEW-IMAGE?type=ENZYME-IN-PATHWAY&object=CPLX-6931

Make sure to read the Summary towards the bottom of that page, and
follow some of the reference at the bottom - that will give you a good
summary of what is known about this enzyme, and where to find teh
sequences.

[Cathal Garvey]

Here's a pretty good paper on resveratrol engineering; they used a
shortcut in the pathway using L-tyrosine rather than L-phenylalanine,
which meant most cells are only three enzymes away from
trans-resveratrol synthesis.

Well, since they fused two of the enzymes (finding that it improved
yields significantly), you could say they only need two genes to make
resveratrol in any given species.

One of those species, crucially, is yeast; probably the most sensible
way to make and delivery trans-resveratrol, as it's alcohol soluble.
Alcoholic delivery may help it to get across the sublingual/buccal route
to the bloodstream (i.e., through the tissue of the mouth), which
appears to be the main way functional resveratrol reaches the blood.
More or less immediately on arriving in the digestive tract, it's
apparently conjugated to one or two compounds that seem to entirely
inhibit proper absorption.

For that reason, when I take resveratrol I usually break open a knotweed
capsule into a small amount of red wine or port, and hold it under my
tongue for a minute.