cell signalling II (intracellular signalling and the central dogma) Flashcards
cell signalling II models:
- model 1: second messenger activates a protein kinase
- model 2: activated cell membrane receptor directly activates a transcription factor
- model 3: pathways involved in regulated proteolysis
- model 4: intracellular receptors
- model 5: non-coding RNA affecting transcription
–> all slower pathways that involved gene transcription and altered protein synthesis
- model 1: second messenger activates a protein kinase
-cAMP –> PKA
-Ca2+ –> CaM kinase
-Ras –> MAP kinase
-DAG + Ca2+ –> PKC
-PI 3 Kinase AKT pathway - model 2: activated cell membrane receptor directly activates a transcription factor
-JAK –> STAT
-Smad - model 3: pathways involved in regulated proteolysis
-Wnt-Beta catenin pathway
-NFkB - model 4: intracellular receptors
-steroid hormones
-thyroid hormones - model 5: non-coding RNA affecting transcription
-miRNA
-lncRNA
how can intracellular signalling cascades effect transcription
-affect transcription factors
-affect co-activators and co-repressors
-affect histone remodelling
transcription factor (direct or indirect)
binds DNA sequence directly to affect transcription
co-activator / co-repressor (direct or indirect)- what does it bind?
binds a transcription factor to affect transcription- doesn’t bind DNA directly
model 1: second messenger activates a protein kinase
enzyme –> 2nd messenger –> protein kinase –> signalling cascade –> goes into nucleus to regulate transcription
shut it off by deactivating or breaking down 2nd messenger
model 1: second messenger activates a protein kinase
cAMP
Gs GPCR stimulates an increase in cytosolic cAMP which activates a cAMP-dependent protein kinase (PKA)
PKA is multimeric protein; cAMP causes the dissociation of catalytic and regulatory subunits
release catalytic subunits –> can phosphorylate target proteins
i.e. transcription factors, phosphodiesterase (lower cAMP, negative feedback), other enzymes
model 1: second messenger activates a protein kinase
cAMP –> PKA then what’s next
- activated PKA (the catalytic subunits) enters nucleus and activates CREB
- CREB (with CBP= complex) binds CRE on the DNA
= gene transcription
*CBP (creb binding protein) is co-activator
model 1: second messenger activates a protein kinase
CaM kinase
Ca2+/calmodulin-dependent kinases
activate the CaM kinase by calcium and calmodulin
phosphorylate transcription regulators to increase or decrease transcription (i.e. phosphorylate CREB to increase transcription of genes with a CRE)
model 1: second messenger activates a protein kinase
calcium calmodulin pathway
- signal molecule bind Gq GPCR which then activates phospholipase C
phospholipase C takes PIP2 and gets DAG and IP3
IP3 opens calcium channel in the endoplasmic reticulum and releases calcium
calcium and calmodulin activate CaM kinase
which then activates CREB and bind CRE to transcribe genes
model 1: second messenger activates a protein kinase
PKC
protein kinase C via Gq GPCR
phosphorylates target to activate or inhibit
- Gq GPCR activates phospholipase C which gets PIP2 to make IP3 and DAG
IP3 gets Ca2+ from ER
DAG binds PKC
the Ca2+ also binds the PKC to then cause transcriptional effects
PKC needs both the DAG and Ca2+
model 1: second messenger activates a protein kinase
Ras
Ras is a protein activated by receptor tyrosine kinase
Ras triggers activation of phosphorylation of MAP kinase;
Raf–> Mek –> Erk
-use ATP
-MAP kinase (ERK) can enter the nucleus and phosphorylate transcription factors
-needed for immediate early genes
model 1: second messenger activates a protein kinase
PI 3 Kinase AKT pathway
growth factors
AKT activated many things i.e. CREB, mTOR complex 1
- growth factor binds receptor tyrosine kinase
- phosphorylates and activates PI 3 Kinase
- PI3 kinase turn PIP2 into PIP3 –> AKT –> TOR
- TOR does 2 things
5.TOR stimulates transcription regulatory proteins - TOR inhibits 4E-BP which allows it not to inhibit eIF4E (transcription factor) (“Double inhibit”)
- results in increased production of ribosomes
model 2: activated cell membrane receptor directly activates a transcription factor
receptor –> transcription factor –> nucleus to modify gene transcription
model 2: activated cell membrane receptor directly activates a transcription factor
JAK STAT
JAK is a cytosolic tyrosine kinase
-JAK is activated by a cytokine ligand binding to its cell membrane receptor
JAK phosphorylates and activates transcription factors called STATS
-STAT = signal transducers and activators of transcription
-once activated, STAT travel to the nucleus and regulate gene transcription
- cytokine binds 2 JAK receptors which autophosphorylate then STAT is activated at bottom of receptor
- STAT forms dimer and goes into nucleus for target gene transcription
model 2: activated cell membrane receptor directly activates a transcription factor
Smad
initiated by activation of receptor serine/threonine kinases
-activated by TGF-beta and BMP ligands
-once activated, the receptor will bind and phosphorylate Smad (transcription factor)
- TGFB binds receptor
- serine/threonine kinase on receptor phosphorylate
- Smad then goes to receptor and gets phosphorylated
- sad is activated, dissociates from receptor and forms complex with co-smad
- complex goes into nucleus and associated with other transcription factors to regulate transcription
model 3: pathways involved in regulated proteolysis
activation of receptor triggers destruction of an inhibitory protein of a transcription factor
transcription factor goes to nucleus and modifies gene transcription
model 3: pathways involved in regulated proteolysis
Wnt-Beta catenin pathway
without wnt: beta-catenin is phosphorylated and targeted via ubiquitylation for destruction by a beta catenin degradation complex (APC in complex)
–> ubiquitylation targets beta catenin for destruction by proteosome
-wnt responsive genes are kept silent by an inhibitory complex of transcription regulatory proteins
if wnt is there then it disrupts the bet catenin degradation complex
-this leaves beta catenin unphosphorylated and it can go to the nucleus
-binding of beta catenin to DNA displaces the co-repressor and functions as a co-activator
model 3: pathways involved in regulated proteolysis
NFkB
in response to acute inflammatory ligand (IL-1 and TNFalpha) a cell surface receptor is activated
–> activated receptor triggers the ubiquitylation and phosphorylation to release and destroy inhibitory protein complex (IkB) that’s bound to NFkB
-NFkB travels to nucleus and initiates transcription of NFkB responsive genes
model 4: intracellular receptors
what ligand dont need cell surface receptors?
how do they get into the cells?
-small, hydrophobic ligands dont need cell surface receptors since they can easily diffuse across the plasma membrane
-ligands: steroid hormones, thyroid hormones, retinoids, vitamin D
-their receptors are located inside the cell
-receptors are all structurally similar and are part of a nuclear receptor superfamily
-ligand diffuses into the cell and binds to its receptor to alter the ability of the receptor to control transcription of specific genes
-the receptor is BOTH the intracellular receptor AND a transcription factor
-a co-regulator is often recruited as well
–>hormone ligand binds to intracellular receptor that, when activated directly modifies transcription (receptor may be in cytosol or already in nucleus)
model 4: intracellular receptors
steroid hormones
-steroid hormone diffuses into the cytosplasm and binds to the receptor in the cytosol
-this displaces an inhibitory protein (hsp) bound to the inactive receptor
-receptor will dimerize and travel to the cell nucleus
-inside the nucleus the receptor will bind to a DNA sequence specific to the steroid hormone (hormone response element)
-coactivator will also bind and transcription will be initiated
-thyroid hormone receptor is located in the nucleus, already bound to DNA
–> binding of thyroid hormone can increase or decrease transcription of genes depending on the gene itself
–> thyroid hormone receptors commonly form heterodimers with other nuclear receptors
a) positively regulated genes will have increased transcription when thyroid hormone binds to its receptor
b) negatively regulated genes will have decreased transcription when thyroid hormone binds to its receptor
model 5: non-coding RNA affecting transcription
miRNA
miRNA
-mature miRNA is ~21-30 nucleotides in length
-modulate translation of target messenger RNAs (mRNAs)
-post-transcriptional silencing of gene expression by miRNA is a fundamental mechanism of gene regulation present in all eukaryotes
-each miRNA can modulate activity of multiple protein-coding genes
miRNA process:
-transcription of miRNA forms a primary transcript (pri-miRNA)
-further processing by a # of enzymes (ie. dicer) produces smaller and smaller miRNA segments –> get active miRNA
-miRNA associated with proteins to form a RNA induced silencing complex (RISC)
-base pairing of miRNA (within RISC) can either: induce mRNA cleavage/ destruction or repress translation
-imperfect match of RISC complex + miRNA with target mRNA= translational repression
-perfect match of RISC complex + miRNA with target mRNA= mRNA cleavage
–>net effect is that miRNAs within a RISC complex act to silence mRNA post-transcription
model 5: non-coding RNA affecting transcription
lncRNA
lncRNA
->200 nucleotides in length
-can bind chromatin to interfere or promote transcription
-also involved in X chromosome inactivation
lncRNA can function in many ways to modify transcription by:
a) promote gene transcription
b) suppress gene transcription
c) promote chromatin modification directly (methylation, acetylation)
d) stabilize protein complexes that modify chromatin structure
