Lecture 38: Protein Trafficking and Nuclear Transport (good but look at c summary) Flashcards

Monday 20th January 2025

1
Q

All eukaryotic cells have a basic set of membrane-enclosed organelles – compartmentation!

A

All eukaryotic cells have a basic set of membrane-enclosed organelles – compartmentation!

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2
Q

Nucleus…

A

site of DNA and RNA synthesis

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3
Q

Cytoplasm…

A

cytosol + organelles

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4
Q

Cytosol…

A

50% cell volume, site of protein synthesis and many metabolic pathways

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5
Q

Endoplasmic reticulum…

A

50-60% cell membrane, start point of secretory pathway

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6
Q

Golgi apparatus…

A

10% cell membrane, important for sorting and modifying proteins and lipids passing through it.

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7
Q

Lysosomes…

A

1% cell volume, multiple “suicide” bags for digestion of materials

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8
Q

Mitochondria/Chloroplasts (plants)…

A

25% cell volume, generate ATP

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9
Q

Peroxisomes…

A

1% cell volume, multiple sites for oxidative reactions

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10
Q

Plant vacuoles…

A

90% cell volume, for turgor or protein storage/ degradation

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11
Q

In 1999, what did Günter Blobel win a Nobel prize for?

A

He won the Nobel prize for the discovery that proteins have intrinsic signals that govern their transport and localisation in the cell.

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12
Q

In 2013, what did Jim Rothman, Randy Schekman, and Thomas Südhof win a Nobel prize for?

A

They won a Nobel prize for their discoveries of machinery regulating vesicle traffic, a major transport system in our cells.

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13
Q

What are the different modes of protein transport?

A

Gated transport

Protein translocation

Vesicular transport

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14
Q

What is gated transport?

A

import into and export out of the nucleus.

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15
Q

What is protein translocation?

A

protein import into ER

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16
Q

What is Vesicular transport?

A

secretion along the organelles of the secretory pathway

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17
Q

what so proteins that don’t reside in the cytosol need in order for them to reach their location?

A

They need sorting signals.

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18
Q

Are sorting signals part of a protein’s sequence?

A

Yes

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19
Q

What can sorting signals be?

A
  • Short peptides at the N- or C-termini, which can be removed after use or kept on if needed again (e.g. for nuclear transport).
  • 3-dimensional domains (secondary/tertiary structure) e.g. for transport to lysosomes
  • Other molecules attached to the protein (post-translational modifications) such as sugars and lipids.
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20
Q

What happens to sorting signals?

A
  • They’re recognised by specific receptors within the cell
  • This in turn triggers the transfer of the protein to the correct destination
  • Every organelle uses different receptors and different sorting processes
  • If any of this processes goes wrong, the cell is in big trouble (there’s several diseases associated with the mis-sorting of proteins).
  • Can be removed after use or kept on if needed again
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21
Q

How do proteins and other macromolecules (e.g. ribosomes) move between the cytoplasm and nucleus (in and out)?

A

Via large aqueous nuclear pore complexes (NPC).

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22
Q

How many nuclear pore complexes does a mammalian nuclear pore complex (NPC) contain?

A

A mammalian nuclear envelope contains 3000-4000 nuclear pore complexes (NPCs)

23
Q

Describe the structure of a nuclear pore complex

A
  • Eightfold radial symmetry, embedded in the nuclear envelope.
  • Composed of ~30 nucleoporins (Nups) forming distinct regions:
  • Cytoplasmic & Nuclear Rings – Anchor NPC; cytoplasmic filaments aid cargo recognition.
  • Central Transport Channel – FG-nucleoporins create a selective sieve.
  • Nuclear Basket – Extends into nucleoplasm, regulates cargo.
  • Membrane-Embedded Scaffold – Anchors NPC to the nuclear envelope.
24
Q

How large are ribosomes?

25
Q

How large are nucleoporins?

A

Each NPC is 125,000 kDa (30 times bigger than a ribosome) and is made up of many copies (16 or multiples of 16) of ~30 different nucleoporins

26
Q

‘Small molecules diffuse extremely fast (almost free flow) through Nuclear Pore Complexes’. Is this true?

27
Q

What would a small molecule be classed as?

A

5 kDa or less)

28
Q

How quickly do proteins of 20-40 kDa diffuse?

A

They diffuse a lot more slowly

29
Q

Can proteins larger than 40kDa diffuse freely through a nuclear pore complex?

A

No, and instead, they move through active transport.

30
Q

What do proteins that are larger than 40kDa carry?

A

They carry nuclear localisation or export signals.

31
Q

What is the diffusion barrier caused by?

A

The diffusion barrier is caused by unstructured (disordered) regions of channel nucleoporins rich phenylalanine-glycine (FG) repeats forming a tangled network (mesh, or matrix), blocking the passive diffusion of large molecules (e.g. ribosomes).

32
Q

Describe nuclear localisation signals (NLS)

A
  • NLS are rich in lysine and Arginine (+ charged), and can be in any position of the passenger (= cargo) protein, so long as they are exposed to the surface of the protein
  • So long as they are exposed to the surface of the protein
  • Nuclear Localisation Signals are recognised by a family of cytosolic nuclear import receptors (importins or karyopherins) – each member being responsible for a set of cargo molecules (or sometimes a cargo adaptor
33
Q

How do FG repeats facilitate active transport through the Nuclear Pore Complex (NPC) ?

A
  • Nucleoporins with FG repeats form the mesh
  • Import receptors have low affinity binding sites for the FG repeats
  • FG repeats in cytosolic fibrils help recruit the receptors and bind the cargo
  • This complex then travels through the pore mesh through transient interactions
  • The receptor disengages from the cargo protein on the other side
34
Q

Gated transport – ACTIVE nuclear import
ACTIVE how?

A
  • Moving certain proteins inside the nucleus creates different protein pools in the nucleoplasm compared to the cytoplasm
  • This type of nuclear transport creates order in the cell
  • ORDER = energy required to maintain it
  • The energy for this type of transport comes from GTP via the GTPase-Ran
35
Q

What does the energy for the active transport come from?

A

The energy for this type of transport comes from GTP via the GTPase-Ran

36
Q

The GTPase Ran..

A
  • GTPase ‘switch’:
  • Hydrolyses GTP to GDP (binds both)
  • Conformation is different depending if bound to GTP or GDP
  • different conformation = different activity
37
Q

In the nucleus: RanGTP binds importins, causing them to release cargo.

A

In the nucleus: RanGTP binds importins, causing them to release cargo.

38
Q

‘Ran-GTPase provides both the free energy and the directionality for nuclear transport’. Is this true?

39
Q

What is the net import of cargo driven by?

A

Net import of cargo is driven by two conformational states of the GTPase Ran, that depend on whether Ran binds GDP or GTP

40
Q

Ran-GDP…

A

Ran-GDP has conformation (A) and is in this state only in the cytosol

41
Q

Ran-GTP…

A

Ran-GTP has conformation (B) and is in this state only in the nucleus

42
Q

What is Ran-GTPase regulated by?

A

Ran-GTPase is regulated by GAP and GEF

43
Q

What is GAP?

A

GTPase activating protein (promotes hydrolysis of GTP to GDP)

44
Q

What is GEF?

A

guanine nucleotide exchange factor (exchanges GDP with GTP)

45
Q

Nuclear import (ACTIVE TRANSPORT): summary

A
  • GTPase activating protein
    GAP ensures that Ran-GDP is generated, and in this state, Ran falls off the importin
  • Facilitated transport via low affinity binding or IMPORTIN to FG repeats
  • Guanine Nucleotide Exchange factor
    GEF ensures that Ran-GTP is generated, and this prefers to bind to importin, displacing the imported protein
46
Q

Unlike other signal peptides for protein sorting, the NLS is not cleaved after import because:

A
  • it is often needed again. This is because many nuclear proteins constantly cycle to the cytosol, so they must be repeatedly imported-
  • re-import must also happen after every mitosis when the nucleus reforms
  • the NLS may be internal and part of a functional domain

-

47
Q

Is it true that nuclear export is like nuclear import, but in reverse?

48
Q

What are Nuclear export signals (NES) ‘seen’ by?

A

Nuclear export signals (NES) are “seen” by soluble nuclear export receptors - exportins.

49
Q

Exportins…

A
  • Exportins (related to importins) bind the NES and the FG-nucleoporins in the channel and filaments, to move the cargo to the cytosol.
  • and use Ran in reverse (RanGDP releases cargo in the cytosol)
50
Q

How can we visualise subcellular organelles in vivo?

A

We can visualise subcellular organelles in vivo using dyes or Fluorescent Proteins such as GFP.

51
Q

Is nucleo-cytoplasmic trafficking reversible?

52
Q

What are other roles of NPCs?

A
  • NPCs also control genome regulation and ageing:
  • Nup98 activates genes in the context of acute myeloid leukemia
  • Some Nups have a very long half-life (several years!), so they deteriorate with age and affect cellular health
53
Q

SUMMARY

A
  • Proteins need signals to travel to their correct intracellular destination
  • Sorting signals are found within the protein and need to be exposed e.g. nuclear proteins require NLS
  • Cytoplasm – nucleoplasm traffic:
  • Occurs through the nuclear pore complexes (NPCs)
  • Uses receptors called importins (into the nucleus) or exportins (out of the nucleus)
  • Directionality of movement is provided by the Ran GTPase switch
  • Asymmetric distribution of Ran GTP (nucleus) and Ran GDP (cytosol) depends on the Ran GAP (cytosol) and Ran GEF (nucleus)
  • Asymmetric distribution of Ran GAP and Ran GEF depends on their preferential association with the cytosolic cytoskeleton and nuclear chromatin, respectively