User:Kensei Kishimoto/sandbox

Hello! My name is Kensei Kishimoto. I am learning how to edit Wikipedia page

Potential articles to expand on:


 * 1) Transactivation domain
 * 2) Pdr1 Transcription factor PDR1. No article exists yet.
 * 3) Read (biology)
 * 4) TRIF
 * 5) Transaminase
 * 6) Retinoic acid receptor

Read seems a little lite on things to add. The other ones are all good. Retinoic Acid receptor should be combined with Retinoid receptor, and another student is also looking at that one. - Dr. Tienson-Tseng

Sources: for Pdr1p

http://www.jbc.org/content/282/7/5063.full.pdf  An article on Pdr1p encoded by gene PDR1. They study PDR network using ChIP, RNA microarray, and WT and PDR1 knockout in response to Fluphenazine. They say that PDR is about drug efflux, meaning they get drug outside of their cells quickly so that cells don't die. PDR1p responsible for early PDR response. PDRE (pleiotropic drug response element) is a regulator but not sufficient for DNA binding.

Transcription factor that is encoded by a gene PDR1. http://uswest.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL013C;r=VII:469092-472298;t=YGL013C

Short description and amino acid sequence of the protein: http://www.yeastract.com/view.php?existing=protein&proteinname=Pdr1p

http://www.jbc.org/content/279/27/27855.full.pdf

http://www.jbc.org/content/262/35/16871.full.pdf : One of the early papers that describe Pdr1p being responsive for drug resistance


 * 1) Most of the studies I have been looking at are not super new. They are from like 2010. So I am hoping to get more recent publications. And possibly literature with more high-throughput analysis. Find if this gene is also present in the human and how much translational value researching Pdr1p in the yeast system has on chemotherapy or therapeutics for humans.


 * 1) Specific names of genes that it transcribes


 * 1) more about kinetics of its actions, maybe someone has done nascent RNA seq on yeasts.


 * #####I am hoping to add more stuff here later.
 * #####Potentially using diagrams or something from the publications to describe the interactions of Pdr1p and its pathways. Maybe also how it interacts with other pathways like calcium response pathways.

= Pdr1p (Pleiotropic Drug Response 1p) =

Pdr1p is a Transcription factor from Saccharomyces cerevisiae and is a key regulator of general drug response genes so that the yeast can survive under toxic chemicals. It binds to DNA at sequences that contain certain motifs called pleiotropic drug response element or PDRE for short. Pdr1p is encoded by a gene in yeast called PDR1 on chromosome VII. It is a zinc finger protein that regulates the expressions of ATP-binding cassette transporter to export toxic substances out of the cell.

Transcriptional Role

 * Pdr1p is a part of bigger PDR network and has about 50 genes that it can target
 * Pdr1p is known to bind to PDRE of 5'-TCCGYGGR-3', which is located around promoter sequences of its target genes.
 * Pdr1p seems to be bound to PDRE sites on DNA at basal level and also after simulation with toxins, which shows that Pdr1p-DNA interaction isn't dependent on toxic stimulation.
 * For cells treated with Fluphenazine, Pdr1p was the only transcription factor that is ncessary for PDR response genes induction. But at basal level, Pdr1p can be partially compensated by Pdr3p, a functional homolog of Pdr1p.
 * Loss of function studies of both PDR1 and PDR3, which codes for Pdr3p, revealed that Pdr1p mutant shows lower tolerance against Cycloheximide and Oligomycin, showing again that Pdr1p confers stronger drug response phenotype than Pdr3p. However, Pdr3p is crucial for PDR responses since cells containing loss of function PDR1 and PDR3 weren't able to grow in the presence of those two toxins. For the cells to exhibit Cycloheximide resistance, Pdr3p regulates Pdr5p, which is a type of ATP-binding cassette transporter.

Interaction with other transcription factors
Pdr1p can form a heterodimer and homdimer with Pdr3p. Pdr1p and Pdr3p also interacts with other transcription factors and their associated networks such as Yap1p, which controls oxidative stress response, and Rpn4p, which regulates proteasome activities, depending on the kinds of toxins cells face

Importance
As mentioned above, in yeast Pdr1p is regulator of pleiotropic drug resistance responses. Drugs or toxic chemicals are useful in killing pathogenic bacteria or tumor cells, and studying how they mechanistically develop tolerance to a wide range of drugs can improve therapeutics.

Related Topics

 * Multiple drug resistance