Question

Cell Biology Tutorial: Signaling Pathways and Gene Expression

Answer 1

[This is a tutorial, not a question. Please save all comments or questions until the end. I will be handing out warnings and possibly suspensions for annoying or irrelevant spam comments.]

Answer 2

There are four types of signal transduction pathways:

1. receptor-associated kinases: a single transmembrane domain activated by a receptor. These kinases phosphorylate other signal-transducing proteins such as GTP switch proteins or transcription factors
2. cystolic kinases: activate GTP-binding G-alpha proteins, which activate kinases and signaling molecules
3. protein subunit dissociation: the binding activates the disassembly of a multiprotein complex which releases a transcription factor
4. protein cleavage: irreversible, cleavage of the inhibitor/receptor releases the transcription factor

Answer 3

\({\bf{transcription~factors}}\) may bind to multiple sites on DNA but only in the open chromatin conformation in the presence of master transcription factors and other cell-specific proteins bound adjacent to the binding sites

Answer 4

\({\bf{receptor~serine~kinases}}\)

The TGF-β receptor family phosphorylates a set of transcription factors known as Smads, which are normally located in the cytosol but move to the nucleus to regulate transcription. The TGF-β family includes signaling molecules that control/regulate development.

Three isoforms: TGF-β1, TGF-β2, TGF-β3, primary function is to reduce proliferation of malignant cells.

BMP7: a member of the TGF-β family involved in bone formation

Answer 5

\({\bf{TGF-β~family}}\)

TGF-β has a N-terminal prodomain that is cleaved off in the Golgi complex. Monomeric form: three dilsulfide linkages + a cysteine to link the monomers into dimers in the ER. The prodomain is noncaovalentl y bonded to the growth factor domain, preventing binding of the TGF-β complex to the cell surface receptors.

The complex can be released from the ECM to activate cell signaling, through a complex mechanism involving the prodomains of TGF-β1 and TGF-β3 with a three amino aicd motif RGD, binding to integrins, which pull the prodomain away from the complex, allowing it to bind to cell-surface receptors.

Answer 6

\({\bf{TGF-β~receptors}}\)

RI, RII, RIII.

RIII is most abundant, is a proteoglycan, binds TGF-beta near the surface, facilitates binding to the RII.

RI and RII are dimeric with serine/threonine kinases in their cytosolic domains. RII is active even when not bound. Binding of TGF-β to RII generates a new molecular surface to "dock" to RI, copying RI and RII.

RII phosphorylates serine and threonine, activating RI.

Answer 7

\({\bf{Smad~transcription~factors}}\)

Three types, R-Smad (Smad 2 and 3) and I-Smads (Smad 7), co-smads (Smad 4) (regulatory and inhibitory).

R-Smad: contains MH1 (N-terminal) and MH2 domain separated by linker. contains NLS (nuclear localization signal). Normally the NLS is masked and cannot bind to importin, MH1 and MH2 domains cannot bind to DNA.

The two domains are separated when the serine residues are phosphorylated, exposing the NLS.

Serines in Smad3 bind to phosphoserine binding sites in MH2, forming complex with phosphorylated Smad3 + co-smad.

R-smad is modified by phosphorylated linker domains, acetylated MH! domains, monoubuqitinylation of MH2, dephosphorylation of C-terminal.

Answer 8

\({\bf{negative~feedback~loops}}\)

SnoN and Ski proteins (oncoproteins) down-modulate the TGF-β receptor pathway. They bind to the co-Smad/R-Smad complex and prevent Smad from binding to DNA regulatory regions. They block transcription activation by de-acetylating histones, reducing signaling effects.