Monday, July 14, 2014

The CBF Cold Stress Pathway

I spend a lot of time talking about what I do in a rather vague way. For this week's Molecular Monday post I thought I would take some time to go into specifics about the pathway I am investigating. Because this is my blog, I will not be citing all my sources but just explaining things in my own words. If you want to be referred to some great review articles, leave me a comment or send me a note and I'd be happy to provide references :)


Plants have lots of different stress pathways. When it comes to responding to cold stress, there are two important pathways: ABA-dependent and ABA-independent. ABA is abscisic acid, a very important plant hormone involved in a plethora of pathways. But I don't care, as I am interested in the ABA-independent pathway.

The main "man" in this pathway is CBF (C-repeat Binding Factor) and, as such, this pathway is often called the CBF cold response pathway. CBF is a transcription factor. A transcription factor is a protein that binds to specific elements in the promoters of genes to turn them on/off appropriately. It's kind of like when the Wonder Twin's have to touch their rings in order to activate their powers, the transcription factor has to bind to the promoter element to cause a reaction. Promoter elements are composed of semi-precise nucleotide sequences in the DNA. I say semi-precise because there can be a little variation in the sequence. CBF3 (the protein I am most interested in), for example, binds to the CRT/DRE element which has the general consensus sequence of RCCGAC, where R can be either A or G.

Simplistic diagram of the CBF pathway
When a plant experiences a sudden decrease in temperature, the cellular membranes become more rigid and an increase in calcium levels are noted within the cells. This calcium increase is suspected to drive kinase cascades which can then activate ABA and/or CBF pathways. For CBF to be transcribed, ICE1 must first be activated. ICE1 is another transcription factor which is kept inactive in the cells by HOS1, which interacts and mediates the ubiqutination of ICE1. Once the kinase cascades are activated, SIZ1 interacts with ICE1 and causes sumoylation which then allows ICE1 to be stable enough to interact with the MYC promoter element in the CBF gene.

Confused yet? :-D Basically, the ICE1 protein is kept suppressed by HOS1 and has to be activated by SIZ1 before it can do it's job. That job is to activate the transcription of CBF by binding to a special spot in the gene. Then our awesome transcription factor can come out and do his job!

CBF will then bind to the CRT/DRE sequences in the promoters of cold regulated (COR) genes. There are a great many different types of COR genes that have been described. In soybean, my organism of interest, we know that CBF transcript levels go up as they do in Arabidopsis (the lab rat of the plant kingdom). But the downstream COR genes are not activated. My quest is to find what's up in soybean that makes these COR genes not activate.

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