Mitochondria research areas

MIT 20.109 Spring 2008 Research Proposal

Red WF Team (Evan Hefner and Stephanie Yaung)

preliminary site -- ongoing updates within the next two weeks

Overview

Development of mitochondrial cultures

Background Information

Areas of interest regarding mitochondria research and regenerative medicine:

• Mitochondria "cell" cultures -- Self-sustaining mitochondria may require cytoskeletal-like scaffolds and modified plasmids with necessary proteins encoded by nuclear and not mitochondrial DNA
• Mitochondrial diseases -- accelerated aging can arise from deletions accumulated in mitochondrial DNA
• Future applications: mitochondrial model for toxicity tests

Statement of Research Problem and Goals

Create mitochondrial cultures as an enabling technology for critical research (e.g., toxicology)

Details and Methods

• isolating mitochondria
• consequences of damaged mitochondria (mtDNA deletions, accelerated aging, early death)
• cytosol-like materials; mimic environment around the mitochondria
• mitochondrial genome, what's made inside and what's from outside (from nuclear DNA)
• mitochondrial function, interaction with other elements of the eukaryotic cell

Predicted Outcomes

• successful creation of mitochondrial model

Resources Needed

• mitochondria isolation kits
• matrix with cytosol-like material properties

References

• Mitochondria: dynamic organelles in disease, aging, and development. http://www.ncbi.nlm.nih.gov/pubmed/16814712
• Mitochondria isolation kit (such as from Thermo Fisher Scientific)

http://www.piercenet.com/Products/Browse.cfm?fldID=45F252F7-2410-40C9-81CD-57B19AA095DB

 Assay to isolate intact mitochondria, six samples at a time.
 Two methods: 1) reagent-based cell lysis  2) optimized Dounce homogenization (gives 
 two-fold more mitochondria recovery)   In both approaches, differential centrifugation
 separates mitochondrial from cytosolic fractions using bench-top microcentrifuge.

• Vermulst M, Wanagat J, Kujoth GC, Bielas JH, Rabinovitch PS, Prolla TA, Loeb LA. (2008) DNA deletions and clonal mutations drive premature aging in mitochondrial mutator mice. Nature Genetics 40 , 392-394.

 Mutant polymerase gamma (PolgA) that contains a proofreading-deficient subunit causes 
 an increase in mitochondrial DNA (mtDNA) mutations by hindering homology-directed DNA 
 repair mechanisms.  mtDNA mutations play a role in aging that may vary among different 
 tissues, where deletions accumulate the most in the brain and heart.  With defective 
 PolgA, there are more mtDNA mutations, the deletions accumulate at an accelerated rate,
 and the mice have a shortened lifespan.

• Mitochondria: more than just a powerhouse. http://www.ncbi.nlm.nih.gov/pubmed/16860735
• Characterization of the human heart mitochondrial proteome. http://www.ncbi.nlm.nih.gov/pubmed/12592411
• Vimentin supports mitochondrial morphology and organization. http://www.ncbi.nlm.nih.gov/pubmed/17983357
• Protein transport into mitochondria. http://www.ncbi.nlm.nih.gov/pubmed/10744987
• Mitochondrial toxicity of antiviral drugs. http://www.ncbi.nlm.nih.gov/pubmed/7585087
• Direct analysis of mitochondrial toxicity of antiretroviral drugs. http://www.ncbi.nlm.nih.gov/pubmed/11546944

 Antiretroviral drugs, particularly nucleoside reverse transcriptase inhibitors (NRTI), 
 are highly toxic to mitochondria.   The in vitro assay used in this study consisted of 
 pancreatic and hepatic human cell lines and tested the toxicity of didanosine (ddI) alone 
 or in combination with hydroxyurea (HU).  Results expressed as mitochondrial toxicity index
 (MTI), ranging from 0 to 100: the negative control was 0, and 100 indicating maximal 
 toxicity. The group found dose-dependent pancreatic toxicity of ddI while HU alone was not
 toxic but increased ddI toxicity when added in combination.

• ROS-Generating Mitochondrial DNA Mutations Can Regulate Tumor Cell Metastasis. http://www.sciencemag.org/cgi/content/short/320/5876/661

New Research Idea

The goal of this project is to create nuclear genes whose resulting proteins will be transported into the mitochondria. This will consist of several phases:

• Identify the N-terminal tags that allow proteins to be transported into the mitochondria (one of our references might already have this information)
• In order to test how well they work, fuse GFP to these sequences, then extract the mitochondria and compare the fluorescence in the mitochondria versus the rest of the cell (testing in yeast)
• Once it has been confirmed that these sequences will get stuff transported to the right place, possibly mutate the sequences to see if the targeting can be improved
• Next, engineer this system into mouse embryonic stem cells.

Goal for the New Research Idea

Nuclear DNA is much better protected against damage than is mitochondrial DNA. In order to safeguard the mitochondria, it would be desirable to encode their proteins in the nucleus with the proper tags for transport into the mitochondria. This would result in cells that are better able to withstand DNA damaging agents.