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I need the genetic regulatory network of TAG synthesis (Kennedy pathway) of Jatropha plant?? Or is there any way to convert metabolic pathway into genetic regulatory network?

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Please look up some literature. Look for transcription factor binding sites in the promoters of the genes involved in the pathway. If jatropha genome is not sequenced then look for homologs in the nearest species. it is not possible to obtain a gene regulatory network from a metabolic network. –  WYSIWYG Mar 7 at 10:04

1 Answer 1

Triacylglycerol synthesis in plants is probably highly conserved. The metabolic pathway is here.

The Jatropha genome sequence is also available.

Given this some effort has been made to figure out how these genes are regulated. This is a microarray study of Jatropha focusing on fatty acid and TAG biosynthesis. This gives some idea of how TAG genes respond to one another, but of course will not find the promoter sequences or the transcription factors themselves.

Having spent a summer going over fatty acid synthesis, I can only say that there has been a lot of wet lab work done on these pathways which would probably be conserved in the Jatropha plant. The literature would be quite extensive. Integrating all of that is more like a paper for publication than an answer on stackexchange. This sort of outlines the procedure... do you have a more focused question?

I'll outline one way of approaching this - there are an uncountable number of variants if you tweak it. There are other ways to get this, most notably looking for defective mutants, the method which is still used in plants quite a bit.

Anyway here is a genome based approach:

1) Identify genes in the pathway of interest. choose 10 or so genes that you think constitute your network. This is an editorial decision. Ultimately if you start looking at genes regulated by the same transcription factors as being included in your network, you will eventually take in the entire genome and the work will be impossible to accomplish.

2) find candidate promotor binding sites. look at the upstream promotor regions for all these genes. you can look at how these are conserved between similar plants by examining the same gene promotor regions aligned against each other. This doesn't work very well.

2b) Another way of finding these is to do a pull down experiment where transcription factors are bound to DNA and a DNAse digestion is done and remaining fragments identify the binding sites. All this somewhat assumes that you kind of know which transcription factors are responsible for each gene. That is probably not the case here.

3) find the transcription factors important for the plant pathway. this is not easy - one way is to try knock outs of the TF genes. I imagine this plant has 4000 + of these genes. around 1-2% may be involved.

So far these methods have been use for the ENCODE project as well as some bacterial genomes. a plant is a new scenario which will have issues of its own.

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Yes..I need the details of how to get the gentic regulatory network of TAG synthesis Pathway?? A step wise protocol please. How to get The regulatory gene network from geneome of Jatropha curcas. –  Shradha Mar 9 at 12:17
    
do you mean transcription factor binding sites or also the mechanims of regulation? still sounds like you are looking for a few hundred pages or a review article. –  shigeta Mar 9 at 13:04
    
I dont have much knowledge about systems biology and gene regulatory network. I have do the pathway modelling in two forms...frst for metabolic pathway and then for gene regultory network. I dnt know how to do it with gene regultory network? –  Shradha Mar 9 at 16:32
    
Thanks a lot shigeta :) –  Shradha Mar 10 at 5:41

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