gene with unknown function

[rasing02]

If you have a gene sequence which is known to be expressed but does not have a biochemical or physiological function, then how can one determine the function and prove it, lets say in a plant system? Also consider the fact that you have to work from scratch no database (gene bank, blast,etc) is avaliable???

[CharonY]

This clearly limits the possibilities. Without the genomics info one is generally limited to reverse genetics techniques (you may want to look them up). Also I would ask myself the question under which conditions are the genes expressed and how are they controlled.

[rasing02]

Thank you, I would look it up and ask any further question if required, this is mainly going back it how it all started, when technology was not there how people found the function of unknown genes

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Reverse genetics can help in determination of a specific phenotypic change, how will it help in determining biochemical/metabolic change which is not phenotypic???

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Thanks for thr response.Reverse genetics can help in determination of a specific phenotypic change, how will it help in determining biochemical/metabolic change which is not phenotypic???

[CharonY]

How are metabolic changes not phenotypes?

Edited June 27, 2010 by CharonY

[rasing02]

I meant let say the unknown gene function is concerning fatty acid biosynthesis then overexpression of this in plant system would not show a phenotypic change? Am I thinking right ??? if not then please correct me, I am finding this difficult to understand.

If the gene is invovled in biochemical pathway which leads to production of any of the intermediate etc, then how we will see it via phenotypic change???

Would really appreciate your help.

[CharonY]

Think about what a phenotype is. Now think about a bacterium that is not able to utilize fatty acid as nutrient. Then imagine one that is auxotrophic for certain fatty acids. Now think about a bacterium that overaccumulates a certain amino acid. Now put that back into context of phenotypes.

[rasing02]

thanks a lot, now i understand this concept, so through testing what its needs in minimal medium to grow, i can find what kind of biochemical compound it lacks, right? I really appreciate your help. Thanks !

[CharonY]

This is one possibility, yes. One could also directly measure metabolites. Of course, in earlier days you were a bit stuck with single compounds, but nowadays you could screen the whole metabolome.