Wishing for T-DNA clarity with ALADIN finding.

Kentaro Tamura and co-workers recently published a paper in PLoS One that should be of interest to all Arabidopsis researchers, even though it might fill them with a little concern!

Kentaro works with Ikuko Hara-Nishimura at Kyoto University with a research focus on the biology of the plant nucleus, having published a number of studies regarding the function of proteins that control nuclear size, shape and movement. Therefore they were in the process of studying the ALADIN protein (which is a putative component of the plant nuclear pore complex) when they made a surprising finding. They were analyzing a T-DNA insertion mutant that removes expression of the ALADIN gene but, during the course of their investigation, realised that mutant phenotypes that they were observing (small stature, low photosynthetic activity) were in fact due to a downregulation of the adjacent PLASTID-SPECIFIC 50S RIBOSOMAL PROTEIN 5 (PSRP5) gene. They performed necessary complementation experiments to indeed show that the T-DNA was altering expression of the gene adjacent to the one in which is was inserted.

PSRP5This might not be a surprise to those researchers who have been previously thwarted in their attempts to compliment a T-DNA insertion mutant. However it certainly is a timely reminder that analysis of a mutant phenotype might require a greater depth of analysis than intially though.

Can a researcher always be confident about the phenotype that they are observing, especially when it shows a novel or unexpected effect?

What is the genetic distance for which a T-DNA insertion might be able to effect the local chromatin environment?

If ever it was needed, this certainly shows the need for providing complementation data in your study, especially if the phenotype is in any way surprising.

In some manner this paper is a reminder of the recent controversy surrounding a T-DNA insertion within the AUXIN BINDING PROTEIN1 (ABP1) gene. In this case the previously considered lethal abp1-1 T-DNA mutant was in fact due to a deletion in the adjacent BELAYA SMERT (BSM) gene, which was recently confirmed by Dai et al (2015) in Nature Plants. In the Tamura case there is no evidence of an adjacent deletion but rather for a gene silencing effect, by an as yet uninvestigated mechanism.

Ultimately both cases are an excellent reminder for researchers to make sure they fully interrogate any mutant phenotype that they are working with. This is especially true if it seems too good to be true, as in fact it might very well be!!


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