Gene Loss in WolbachiaHow does an obligately intracellular

symbiont differ from a free-living bacterium?

http://microbewiki.kenyon.edu/index.php/Wolbachia_pipientis

Goals

• To demonstrate the power and utility of Bioinformatics to students in my genetics, microbiology and cell biology classes

• To help students (and myself) learn to use these tools on real data.

• To see if there is a common set of genes shared with other obligately intracellular parasites/endosymbionts (eg. Buchneria, Rickettsia, Wigglesworthia, etc.)

Approach:reinventing the...

Phylogenomics of the Reproductive Parasite Wolbachia pipientis wMel: A Streamlined Genome

Overrun by Mobile Genetic Elements

Wu et al PLoS Biology | http://biology.plosjournals.org March 2004 | Volume 2 | Issue 3 | Page 0327

wMel Genome FeaturesGenome size 1,267,782Predicted CDS 1,270Average gene length 852Percent coding 85.4%Assigned function 719 (56.6%)Conserved hypothetical 123 (9.7%)Unknown function 91 (7.2%) – (in 2004)Hypothetical 337 (26.5%)Transfer RNA 34Ribosomal RNA 1 each of 5S, 16S, 23SStructural RNAs 2Prophage 3GC content 35.2%DOI: 10.1371/journal.pbio.0020069.t001

There is more than one kind of wheel out there!

Approaches/Ideas

• Use published work as a guide to validate what we are doing

• Phylogenetic Profiler to compare the genomes of various endosymbionts

• BLAST searches using genes with unknown function

• Protein database tools to look for functional domains in genes with unknown function

Foreseeable Problems

http://www.google.com/imgres?um=1&hl=en&client=firefox-a&sa=N&rls=org.mozilla:en-US:official&biw=1366&bih=638&tbm=isch&tbnid=OsGCgNryFKx3HM:&imgrefurl=http://findingrest.blogspot.com/2010/09/hurdles.html&docid=Woa9Uw2lzY8m_M&imgurl=http://1.bp.blogspot.com/_mP2bjjd5WTY/TI8KB-hIaiI/AAAAAAAABvg/Cvy68ClXkhE/s1600/Hurdles_Runner.gif&w=451&h=443&ei=a6xaT7n9LoLF0AGyrcDSDw&zoom=1&iact=hc&vpx=772&vpy=83&dur=161&hovh=222&hovw=227&tx=127&ty=109&sig=107588080868887692847&page=2&tbnh=143&tbnw=146&start=21&ndsp=26&ved=1t:429,r:10,s:21

http://www.google.com/imgres?um=1&hl=en&client=firefox-a&sa=N&rls=org.mozilla:en-US:official&biw=1366&bih=638&tbm=isch&tbnid=HaiOsuItJz1XCM:&imgrefurl=http://cheezburger.com/View/2557933568&docid=5eg0fWJkWfnrCM&imgurl=http://images.cheezburger.com/completestore/2009/8/22/128954160337786990.jpg&w=500&h=558&ei=a6xaT7n9LoLF0AGyrcDSDw&zoom=1&iact=hc&vpx=371&vpy=75&dur=5142&hovh=237&hovw=212&tx=113&ty=179&sig=107588080868887692847&page=2&tbnh=143&tbnw=128&start=21&ndsp=26&ved=1t:429,r:7,s:21

http://www.google.com/imgres?start=202&um=1&hl=en&client=firefox-a&sa=N&rls=org.mozilla:en-US:official&biw=1366&bih=638&addh=36&tbm=isch&tbnid=HQa1l76Ctw2gHM:&imgrefurl=http://www.freerepublic.com/focus/fchat/2358682/posts&docid=kWMWLfJzEZtlpM&imgurl=http://i23.photobucket.com/albums/b399/littleceeg/obamahurdle.jpg&w=500&h=338&ei=La1aTvfGO3J0AGEmumcDw&zoom=1&iact=hc&vpx=695&vpy=136&dur=593&hovh=184&hovw=273&tx=161&ty=118&sig=107588080868887692847&page=9&tbnh=140&tbnw=195&ndsp=25&ved=1t:429,r:3,s:202

Little Steps at First!

The Biggest Hurdle?

The Laws of Physics“A tenured, associate professor at rest

tends to stay at rest unless a force can overcome his inertia.”*

Thanks for the push ASM!* anonymous