probio quality control

polysome

a body of many ribosomes working on an mRNA

ribosomal profiling

using antibodies to pull down certain ribosomes in a polysome and sequencing their mRNA

translotome

whole set of translated mRNAs

The Frydman ribosomal profiling lab

• pulled down Rpl16 full translotome - captures all ribosomes

• pulled down SRP (signal recognition particle) - captures secretion/membrane proteins

• Pulled down Ssb - captures proteins that need folding assistance

These proteins are binded to ribosome while translating

What are the crossovers between SRP and SSB bound proteins?

They are not all crossover, some are different location bound. thats why the heat map is different.

Characteristics of SSB-bound proteins

longer on avg

high beta sheets

increased chance of aggregation

• thats why ssb works to protect vulnerable intermediates

Stress that induce HSP

heat

osmotic stress

ethanol

mistranslation

Hsp104

disaggregates proteins for hsp70/40

induced thermotolerance

yeast exposed to some heat are resistant to lots of heat, hsp104 induced at 37 degrees

starving of cells

starving cells are stressed and also contain more refolding chaperones

RpOH

prokaryote sigma32 stress factor that induces heat shock genes, replacing usual sigma70

leaves DnaK at high heat cus DnaK is pulled to misfolds

oxidative stress

superoxide and hyddrogen peroxide that are super damaging to proteins

inactivated by Superoxide dismutases and Catalases and

glutathione peroxidases

mother-specific retention

mother cell keeps aggregates when daughter cell buds

passive retention

aggregates dont flow to daughter

active retention

associated with cytoskeleton

retrograde transport

daughters transport aggregates to mother

Sir2

sirtuin: cell survival, aging, apoptosis, modifies chaperonin

cct

chaperonin - folds actin

polarisome

determiens cell polarity

actin cables

transport and retention of aggregates

Hsp104

links aggregates to cables or moves them

IPOD

insoluble protein deposit - huge deposit that states in mother cell (of aggregates)

Describe symmetry in cell division

cell division is morphologically symmetric but the aggregation transport is not

stem cell splitting is asymmetric bc it makes diff cells

aging may be from stem cell splitting

aggresome

mammallian cytoprotective aggregate group for overwhelmed systems

perinuclear

contains ubiquitins, proteases, hsps

protein degredation inhibited

when do proteins need to be destroyed?

high stress and cell cycle progression

Ubiquitin - proteasome system for degredation

Cytoplasmic and nuclear proteins

Retrograde transport ER proteins

Lysosome system (in yeast, vacuole)

Membrane proteins (may be autophagy or cyto-vacuole transport)

ER Proteins through autophagy and cyto-vacuole transport

E1

activates ub (Ub gly - cys E1)

E2

conjugates Ub (carries) (ub gly - cys e2)

E3

Attaches Ub Gly to lys of protein

E4

polymerizes Ub additional Ubs attach their glys to the lys of the prev Ubs

DUB

deubiquitinating enzymes

Dfiferent Lys(K) residues: K29, K63, K11, K6, K48

K29: degrade via UFD pathway (K9s at UF)

K63: receptor internalization, autophagy, DNA repair (K3 need to fix herself)

K11: degredation of mitotic substrates, chaperone function, autophagy (Yk11 going to give you cancer)

K6: synthesized by BRCA1/BARD1/RAD6 (Barca scored 6 goals)

K48: required to formal singal for targeting proteins for degredation (K-8 is required)

Ubiquitin routes

endocytosis, gene expression, proteasome proteolysis, dna damage, kinase activation, trafficking, translation

UB systems in proks and archaea

proks and archaea contain proteasomes

ub in cyanobacteria

Archaea: SAMPS: Small archael modifier proteins are similar to Ub