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Alicia-Bonanno

Page history last edited by abonanno 13 years, 2 months ago

 

 

 

DICER

 

 

Table of Contents

  • Overview
  • Structure
  • Mechanism
  • Diseases
  • Therapeutic targets

 


The Dicer Protein 

Dicer is an RNase III enzyme that cleaves double stranded RNA.  Double stranded RNA is involved in triggering the innate gene silencing mechanism of RNA interference.  This is important for defense against viruses, regulation of development, and genome maintenance(Zhihua et al 2009).  The two classes of RNA that are responsible for this are micro RNAs and small-interfering RNAs(Zhihua et. al. 2009).  Both of these are produced by Dicer.  The cut RNA is then used by RISC to procede with gene silencing.  Without the Dicer protein, the ability to silence genes is significantly reduced (Berstein et. al. 2001). 


 Structure 

 

Dicer has a distinct structure that causes it to make the microRNAs into a specific length of about 23 nucleotides.  To begin with, the Dicer protein is made up of three domains, two RNAse III domains, which cleave the RNA, and a PAZ domain(MacRae et al. 2006).  This Paz domain, is located far enough away from the RNAseIII domains such that it is the same length as the cut RNA(MacRae et al. 2006).  This gives a good insight as to how the specific length comes about.  The PAZ domain binds the RNA and the RNaseIII domains cleave the RNA to form the specific length of the microRNAs that are later bound to RISC proteins(MacRae et al. 2006).  It seems strange that the negatively charged backbone of the dsRNA and the highly negative sidechains of Dicer would interact, but in each binding site, there are Magnesium cations which make a favorable interaction between the protein and the RNA to make cuts at the active sites(Gan 2006).

 

                                                                            

Fig.1 Shows how the distance of the domains creates the 25 NT distance         Fig.2  The magnesium cations can be seen in purple, where

                                                                                                                                  the domains are able to bind to the dsRNA 

 As shown, by the figures, Dicer is not only able to cut the double stranded RNA, but it also acts as a ruler and cuts a specific length which is very important to the mechanism of silencing genes, which is discussed below.


Mechanism of Dicer

  

As stated above, the structure of Dicer has given many insights into the mechanism of how dicer cleaves the dsRNA into specific 21-25 nucleotide sections.  The video below shows how the Dicer molecule finds and cuts the dsRNA to then be found by the RISC protein to continue with the silencing of genes.  The PAZ domain of the molecule is also known as the handle which finds the 3' end of the dsRNA (MacRae et al. 2006).  The "connector helix" separates the PAZ and RNAse III domains to cause the exact cutting of the dsRNA (MacRae et al. 2006).  The active sites of the RNAse III molecules as stated above, favorably bind to the RNA via magnesium molecules.  There is a lysine molecule in the active site that seems to be conserved over many species(Zhihua et al. 2006).  This is a key clue to the mechanism since it may help in the phosphodiester bond cleavage of the dsRNA by the Dicer protein(Zhihua et al. 2006).  The Dicer molecule cleaves in a specific way such that it causes a 2 nucleotide overhang on the 3' ends(Bernstein et al. 2006).  This is important, so that the RISC protein can appropriately find the microRNA so that it can continue on in the gene silencing mechanism.

 

 (www.dnatube.com)

 

 

Dicer plays a huge role in the ability for a cell to recognize a virus or some foreign RNA present in the cell.  A virus or foreign RNA when created with two sides, one being a mirror image of the other, is able to fold into a loop, where the RNA molecule binds with itself.  This causes Dicer to come in and slice the foreign RNA and become silenced since the microRNA is not translated.  In this way, Dicer is very important to the process of RNAi.


Disease Associated with Dicer Difficiency

 

 

     Lately, the Dicer protein and other aspects of the gene silencing mechanism are being looked at as ways to treat and the causes of diseases due to malfunction of the proteins involved.  One experiment that had been recently done, was on a dicer knock out mice.  It seemed to lead to progressive dilated cardiomyopathy, heart failure and postnatal fatility (Chen et al. 2007).  After studying these knock out mice, they studied the Dicer protein levels in humans with failing hearts and dilated cardiomyopathy and found a decreased level of the protein present (Chen et al. 2007).  This shows that the Dicer protein and microRNAs play a large role in cardiac function and without it, heart disease may be more probable (Chen et al. 2007).

 

 

Fig. 2. Figure 3:  The -/- means the Dicer knockout mouse heart and +/+ is the normal mouse heart.

 

 

  • Fragile X syndrome 

     Fragile X syndrome is also associated with the Dicer protein.  Fragile X syndrome is an inherted disease that causes mental impairment.  The specific gene associated with the Fragile X syndrome is known as Fragile X Mental Retardation Protein(FMRP) (Plante 2006).  This protein will bind to the microRNAs that are produced by Dicer causing a malformation in the transfer of the microRNAs to the RISC protein (Plante 2006).  This causes possible gene silencing which can contribute to the disease (Plante 2006).

 

 

 

 


Possible Therapeutic Target 

 

 

The entire process of gene silencing has become a possibility for a new frontier as a therapeutic target.  The silencing process occurs when there is a specific RNA that is doubled stranded and unfamiliar.  The therapeutic process would involve introducing a gene that has the ability to produce mirror imaged RNA that will cause the activation of the gene silencing mechanism.  Just like the flower, that had caused them to discover the process of RNAi, the mechanism would be tricked into stopping all processing of one gene. This could possibly give a way to silence the genes of cancer, which would be an incredible discovery to help with treatments. 

 illustration

 


References

 

1.Bernstein, Emily, Amy A. Caudy, Scott M. Hammond, Gregory J. Hannon, "Role for a bidentate ribonuclease in the initiation step of RNA interference," Nature. 409. 331-366 (18 January 2001). http://www.nature.com.nuncio.cofc.edu/nature/journal/v409/n6818/full/409363a0.html

2.Du, Zhihua, John K. Lee, Richard Tjhen, Robert M. Stroud, and Thomas L. James “Structural and biochemical insights into the dicing mechanism of mouse Dicer: A conserved lysine is critical for dsRNA cleavage.” Proc Natl Acad Sci U S A. 2008 February 19; 105(7): 2391–2396.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2268147&tool=pmcentrez&rendertype=abstract

3.  MacRae, Ian J., Kaihong Zhou, Fei Li,Adrian Repic,Angela N. Brooks,W. Zacheus Cande,Paul D. Adams,Jennifer A. Doudna "Structural Basis for Double-Stranded RNA Processing by Dicer" Science 13 January 2006: Vol. 311. no. 5758, pp. 195 - 198. http://www.sciencemag.org.nuncio.cofc.edu/cgi/content/full/311/5758/195

4.Chen, Jian-fu, Elizabeth P. Murchison, Ruhang Tang, Thomas E. Callis, Mariko Tatsuguchi, Zhongliang Deng, Mauricio Rojas, Scott E. Hammond, Micheal D. Schneider, Craig H. Selzman, Gerhard Meissner, Cam Patterson, Gregory J. Hannon, and Da-Zhi Wang,"Targeted deletion of Dicer in the heart leads to dilated cardiomyopathy and heart failure" http://www.pnas.org/content/105/6/2111.long

5. Plante, Isabelle, Laetitia Davidoc, Dominique L. Ouellet, Lise-Andree Gobeil, Sandra Tremblay, Edouard W. Khandjian, and Patrick Provost, "Dicer-Derived MicroRNAs Are Utilized by the Fragile X Mental Retardation Protein for Assembly on Target RNAs" Journal of Biomedicine Vol 2006 (2006). http://www.hindawi.com/GetArticle.aspx?doi=10.1155/JBB/2006/64347

 

http://www.topnews.in/health/safety-adhd-treatment-kids-fragile-x-syndrome-confirmed-21111

http://nobelprize.org/nobel_prizes/medicine/laureates/2006/adv.html

http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=115200

http://ccr.cancer.gov/news/frontiers/march2007/print_all.asp

http://www.inoculatedmind.com/2007/10/monday-madness-your-brain-on-id/

http://www.sciencedaily.com/releases/2006/01/060114151229.htm

http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=60450 

http://www.autismkey.com/fragile_x.htm 

http://www.pbs.org/wgbh/nova/sciencenow/3210/02.html

http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?sunid=69065

http://pfam.sanger.ac.uk/family?acc=PF02170

 

Comments (1)

Christopher Korey said

at 8:51 am on Apr 7, 2009

Looks good. As you convert the outline to text, Remember to be concise about each subsection and provide link outs to other pages or papers that provide more in depth detail if that is required. If someone wants more information give them a way to find it not necessarily put it on the page. For example you may want to briefly describe Dilated Cardiomyopathy and then provide links out to sites that provide a more indepth description. Try to divide the sections by inserting a horizontal bar. Remember to reference just like any other paper, images as well. Also, try to make the links with text in your page rather than putting the whole URL--it looks cleaner.

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