ploidity evolution in raffinose, david pellman lab

Anna Selmecki

haploid and diploid are stable during controlled evolution in raffinose
triploid, tetradploid tend to have aneuploid, lead to faster evolution.

CGH detected segment chromosome anueploids

spatial sensing in cerevisiae

pheromone receptors polarizes and concentrated on one spot?
Cdc42 patch determine the point of growth

positive feedback loop

hyphae

Normally, hyphae occur in diploid a/alpha and only on solid media.

Occur more in sigma background, rare in S288c.

yeast14, august 1, afternoon

=> temperature sensitive genetic interactions
4.4x more than the 2010 version.

negative essential interactions are functionally informative (are locally important).
In other words, possitive genetic interactions are long-range. 

=> sirtuins substrates, David Paul Toczyski
nitotinamide treatment, quantitatvie mass-spec

52 substrates of sirtuins, many are TFs, growth and ribosome biogenesis

=> Ohnuki, Ohya, phenotyping in haplosufficiency in essential genes

ribosomal complex
chaperonin CCT complex

positive correlated GO terms:
netative correlated  GO terms: proteosome <--> tRNA synthesis

=> disordered proteins,  Daniel Jarosz
20 yeast proteins with prion domain (N/Q rich)
screens show many more, suggest more non-canonical prion-domains

GAR+ loves longer than gar-
bacteria elicit [GAR+] via a small molecule (unknown)

GAR+ coexist with bacteria

=> Hofmann
Ure2, Cyc8, Sfp1, Mot3 --> FLO11, HXT2

predicted prion TFs

FLO11 bistable
Holmes 2013 Cell

fermentable carbon ~ nonfermentable carbon

azide blocks electron transfer chain

FLO11 is heavily glycosylated, a glucose sink

Iodine staining of colony (glycogen)

50 nM R3a-5a small molecule inhibitor of manno-transferase?

Dan G: why cheater? Just two mode of development states?  (It is the same genome.)


=> Ben Tu's lab, mitochondria biogenesis
 yeast metabolic cycles
glucose depletion and ethenao+glycerol  induce mitochondria biogenesis

yeast14, August 1, Friday

=> Vacuole pH in replicative aging, Gotschling lab.
Vacuole acidity is reduced during aging and is asymmetric. Hughes Nature 2012

plasma membrane H+-ATPase has the opposite asymmetric pattern from vacuole acitiy between mother and daughter cells.

Pma1

Quinaccine, vacuole acidity
Vph1-mCherry

1 million of Pma1 on plasma membrane, 100K ATPase on vacuole. only 3000 free protons in cytoplasma ??

Glucose activate Pma1(ATPase), so low glucose decrease ATPase activity.

Proton diffuses very fast, so cytoplamic proton are instaneous. Yet, proton gradient are observed.

Tor1 activity affects vacuole activity.

=> Peroxisome
major ROS producers, similar to liver bile function. peroxisomes always split, but do not fuse.

older peroxisome have different membrane compositions
older peroxisomes are retained in older mother cells.

Older peroxidsomes are removed by autophagy.

Peroxidsome division is similar to mitochondria divisions. Drp1

=> translocation of cyclin C (cnc1) to mitochondrai mediate stress induced fission and programmed cell death
Randy Strich
Chen JCB 2003, AY JCS 2010, mitochondrial fission and fusion

Good: fusion, Bad: fission
H2O2 induce mitrochondria fission

Drp1 control mitochondrial fission

cyclinC does not cycle and do not control cell cyle. Instead, regulate trancription of stress genes.

July 31, Thu, yeast14

 thyimidine kinase, lost in pre-cambrian age
TkMX absent
antifolate media


50 genes with > 3 mutations in long-term mutation lines

Frank Albert
McManus genomes research 2014, translation beffering between species, but not between strains

Meiotic rejuvenation hypothesis

Micro fluidic yeast aging paper

July 30, yeast 2014

=> Hippo pathway, -- Eric Weiss
 ancient pathway, morphogensis, cytokinesis

Ace2 is turned on once in a life time in yeast daughter cells.  It leads to separation of mother and daughter cells.

super computing molecular dynamics simulation


=> Swe1 morphology checkpoint, Sepp Kohlwein,
triglycerides is fat for yeast cells.

cerulenin inhibit de novo synthesis of fat, triglyceride

Swe1 kinase -> lipolysis mediated cell cycle progression.
Swe1 --| Cdc28 --(P)--> Swe1

=> Cdk28 (Cdk1), Andreas Doncic, Jan Skoheim. 
Single-cell fluorescence signal detection

Yeast mating pathway, 

Yeast has 'memory" of past experiences

Far1 feed-forward regulation combined current and past signals to provide informed decisions.

Inherited Far1 total protein level give yeast cells an intergenerational memory which can make an more informed cell cycle reentry decision. 

growth    --(CDK)-->cell cycle
                      ||       
MAPK(t) --Far1 --> mating arrest

It seems that growth before mating must be done in haploid strains. In wild, cells can switch mating types. The argument on 'memory' must a very short memory.


=> cdk regulated expression, CDK28/CDK1 targets
Cdk --> Fkh2, Ndd1  --> G2/M genes
Hcm1 --> Fkh2, Ndd1

HCM1 targets: TUB1, SPC34, NDD1, CIN8

=> RNP granules in quiescent cells, Paul Herman's lab
ribonucleoprotein granules: Processing bodies(PBS), stress granules (translation)

Decreased P-bodies shortens CLS.

=> Linden Breeden, Quiescence
stationary phased cells have two populations: quiescent and dividing ones.

cell wall fortification improved in quiescent cells
deletion library was screened, 131 genes -> cell wall defect, and several other categories

log phase: cln3/cdk --| Whi5 --| SBF/MBF  --> Cln1/Cln2
S phase: DNA damage

In Q-cells: how G1 arrest is maintained
Xbp1 --> Cnb3/Cdk

Q: do some genes change the population fractions of dividing and quietscent cells? 

=> Cdc14 phosphatase, a hub in NaCl responsive subnetwork.

=> metabolite regulation, Sean Hackett, Joshua Rabinowitz
LC-MS, 106 metabolite
Flux balance analysis (FBA)
Flux is carried in 270 reactions
Model comparison by fitting to measured flux. a p-value is calculated.
Limiting nutrient effects

=> Calcineurin (CN) substrates in yeast, Jagoree Roy
Calcineurin has a conserved docking site.
Screen method: motif search;  hyper-phosphorylation in calcineurin-null mutant

CN signaling network evolves rapidly in the yeast species.

=> George Church, future of yeast
1. 3D/4D structure of yeast cells
2. synthesis of genomes
3. Synthesis of cells.

3D RNA fluorescence in situ sequencing, FISSEQ, Lee, Daugharthy, Science 2014

Reasons for synthetic genomes: metabolic isolation, non-canonical AA, multi-virus resistance

Cause & effect of N-terminal codon bias in bacterial genes

Mirror DNA & RNA polymerase

Synthetic biology, a lab manual.