One Cell, Three Genomes Laboratory

Background

In high school you probably learned that the nucleus, chloroplast, and mitochondrian came into existence through endosymbiotic events— i.e., that one cell engulfed two others and now the three cells rely on each other for survival as a single plant cell. This lab is designed to let you test this hypothesis.

Chloroplasts are only found in eukaryotic algae, leaves and other green plant organs. They are the photosynthetic organelles in plants that harvest light energy and convert it to chemical energy for growth and other vital functions. The chloroplasts do not produce energy for (ATPs) the cell, however. Through the process of photosynthesis, they produce the raw materials that the mitochondria use in the process of cellular respiration.

Mitochondria, on the other hand, are found in almost all eukaryotic cells. Not only are they much more efficient at generating ATP that are the fermentation pathways in the cytosol, by uncoupling or coupling electron transport from oxidative phosphorylation, they are the primary regulator of heat productionin cells.

Nuclear DNA refers to the DNA that has become trapped within the nucleus of eukaryotic cells. This is one of the defining features separating prokaryotic organisms from eukaryotic organisms.

Tools

Biology Workbench (http://workbench.sdsc.edu -- the San Diego one).
      Note: Select to search ONLY the organelle database

Potential Investigations

• Has any organelle (chloroplast or mitochondrial) DNA "jumped" to the nuclear DNA in evolutionary history?
• If both mitochondria and chloroplasts evolved from prokaryotic cells, have they retained any of the features of the prokaryotic cells from which they evolved?
• Can you find any primitive eukaryotic cells that are devoid of these organelles— either chloroplasts or mitochondria? Where do they branch off from a tree of all eukaryotes?
• Is it feasible to consider that a bacterium was once "ingested" by a primative eukaryotic cell such that the bacterium became symbiotic?
• Do the genes located in the organelle genomes change at the same rate as the nuclear DNA (i.e. do they all use the same molecular clock)?
• Has there been horizontal gene transfer between mitochondria and chloroplasts?
• Relate your investigation of transfer of genes between organelles over evolutionary time with published models of protein trafficking between organelles over the course of the lifetime of a single live cell.

Goals

• Identify definable questions that can be approached using phylogenetics
• Find the data & use the tools provided to explore these questions
• Design and execute experiments to approach these larger questions
• Using your analyses, the data & tools provided explore these questions
• Share your insights with the group
• Evaluate the effectiveness of this exercise and this session.

Data

Data for Workbench Practice
Rearranging the Branches on a New Tree of Life - A New York Times article describing the role of molecular data in figuring out the phylogenetic relationships between groups of organisms. Here is a very small dataset to look at the relationship between plants animals and fungi. [enolase dataset]

Phylogenetic Profiling (Rubisco)

Phylogenetic profiling involves generating and comparing multiple phylogenies to look for similarities and differences across species and molecules. http://www.doe-mbi.ucla.edu/People/Yeates/Gallery/phylo_profile.html

The following datasets are available:

Description of sequences
Rubisco large subunit
Rubisco small subunit

Developing phylogenies from 3-genomes

Barkman TJ, Chenery G, McNeal JR, Lyons-Weiler J, Ellisens WJ, Moore G, Wolfe AD, dePamphilis CW.
Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny.
Proc Natl Acad Sci U S A. 2000 Nov 21;97(24):13166-71.
PMID: 11069280      PubMed Abstract

Sequences studied for the paper:
http://depcla4.bio.psu.edu/basals/taxon.list.suppmaterial2.html

Support materials for the paper:
http://depcla4.bio.psu.edu/basals

The Barkman dataset:
Sequences in Fasta format

Chaw SM, Parkinson CL, Cheng Y, Vincent TM, Palmer JD.
Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers.
Proc Natl Acad Sci U S A. 2000 Apr 11;97(8):4086-91.
PMID: 10760277     PubMed Abstrat

Chaw dataset:
Sequences in Fasta format

Popset:
http://www.ncbi.nlm.nih.gov:80/cgi-bin/Entrez/PopSet/wwwddv.cgi?gi=7546769

Deep Green Challenges

A tradition in the computer science, information technology, and mathematical communities is to issue "challenges." Such challenges pose problems to fellow scientists, and provide an entertaining way to advance the discipline. Because the concept of challenges has not been widely applied in the life sciences, we hope that introducing them will promote additional interactions among the biological and analytical communities. http://www.life.umd.edu/labs/delwiche/deepgreen/DGchallenges.html

Origins of plastids

Collect a set of sequences to test a hypothesis about chloroplast and mitochondria evolution. We have lots of references to get you started.

Additional Resources

Peeters_2000.pdf (1.5 mb)

Pellegrini_1999.pdf (105 kb)

Marcotte_2000.pdf (556 kb)

Grey_1999.pdf (177 kb)

Delwiche_1999.pdf (544 kb)

Delwiche_1995.pdf (2.46 mb)