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Redesign of yeast chromosome and potential application
Yingjin Yuan, Tianjin University
<https://www.youtube.com/watch?v=jvyiaLqbr0w&t=0s&list=PLHpV_30XFQ8RN0v_PIiPKnf8c_QHVztFM&index=17>
# Introduction
In most cases... medicine, biofuel, .. designer cells: improve existing system, create new application.
torpenoids, steroids, polyketones
What we are trying to do is optimize designed functional modules. Test-compile, and engineered chassis. So for doing so, ...
Design of synV and synX. Tianjin U as a core member of Sc2.0 is responsible for chemically build of chromsome 5 and chromosome 10. Also, for chromsome 10 we have a similar design. So what we're doing ...
# Cycle for building a designer chromosome
First we design, then we build, test and debug, then we learn and go back to design stage.
# Building chromosme 6
.. divided into.. so that's where... build this.. introduced.. that's cost.. called ...
# Team work
Built in parallel with team work. Each year about 120 students. And then several of them take.. try to ... form
# Timeline for designer chromosomes ynV and synX
Knowledge gained from BAG accelerated construction of synX. One week per round replacement. Long period was needed for debugging. For synV there was about 23.2 kb/month and for synX it was at 58.9 kb/month.
# Testing
genotype, phenotype, competitive growth assay, stability, 3d organization, near wild type phenotype, omics analysis.
# Perfect designer chromosome 5
34 variants were corrected from the initial chromosome to the perfect designer chromosome. By thi correction, you c... Science 2017, 355, eaaf4704.
Design in silico: PCRtags added; stop codons swapped; LoxPsym sites inserted; intermediated editings; segmentation.
Redesign manual: Design error correction/ stop codon swapping
Draft for perfect synV: lots of modifications listed
# Potential applications for designer yeast
Metabolic pathways, effects of DNA rearrangement, beyond the pathways. We could do beta-carotene synthesis, CrtE, CrtYB, CrtI, this is based on unpublished data.
# Summary
in vitro SCRAMBLE technique
Thank you.
# Q&A
Q: For entropic reasons, usually Cre causes deletion, so you get to just one Lox site. Do you really get diversity, or do you mostly get deletions?
A: ... one case... there are in fact.. up to.. regions of.. so, ...
Q: To answer that, in our previous study, we showed that the frequency of deletion is roughly equivalent... deletions don't have as big an effect. You preserve a lot more ...
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