IGEM:MIT/2005/Natalie Discussion: Yeast

Redesign Yeast Chromosome Check out: http://db.yeastgenome.org/cgi-bin/search/featureSearch to get info like:
 * SGD = database for yeast (Google it)
 * Chrom 1 = 117 ORFs, 13 essential genes
 * Chrom 3 = 182 ORFs, 16 essential genes
 * Chrom 6 = 141 ORFs, 27 essential genes
 * Chrom 1 is the shortest chromosome of the 16.
 * Yeast artificial chromosomes are available.
 * Resemble yeast chromosome. It is circular and can linearize. Has telomere, centromeres, and cloning sites.
 * This could be a way to move essential gene from chromosome and test from there.
 * 11/13 genes on Chrom1 (essential) examined for expression data
 * Seem to do okay with glucose starvation.
 * Look at kinds of genes on Chrom, and see what happens.
 * Chromatin structure is sensitive.
 * Drug marker (kanomysin resist) in the PCR product, transform into yeast, select for cells with drug marker. Haploid might not get anything --kill yeast. Diploid = spore it, 8-10 days. Technically difficult to do. Random spore analysis might work. To confirm, southern blot to detect.
 * Feasibility depends on what we choose as goal.
 * Discovery project for sure.
 * If goal for Nov. is for astounding re-engineering, project might be hard.
 * Time scale may be more like a grad-student project.
 * Might be good for learning microarrays.

Antibody signalling with Yeast Signalling
 * Antibod frag fused to protein -> exported
 * Fusion protein -> surface of cell
 * Also tethering protein
 * held together with sulfide bonds
 * Would it be possible to put antibody frag into bacteria
 * Bacteria are tiny = # proteins that can be expressed on their surface is less.
 * Surface-expressed E.coli out there that have been manipulated
 * Maltose binding protein -- change binding sites
 * Hellinga paper about Maltose.
 * Multimerization signal - need polypeptides on surface to generate signal
 * Antibody on outside would signal dimerization?
 * Know that it's possible to mix-match DNA binding proteins, modular.
 * Scaffold protein holds some components of transudction pathway, limits cross talk.
 * E.coli would be great to work with for this because fewer components to pathways.
 * Yeast vs. E.coli
 * More E.coli biobricks than Yeast (5 or 6 in registry and are all fluorescence)
 * More starting material w/ E.coli
 * Yeast is eukaryotic --can be more useful for application.
 * Bacteria could be first step.