Nuclear Transport/Ribo Biogenesis

Nuclear Import & Export/Ribosome Biogenesis
David M. Bedwell, Ph.D.
Office: BBRB432
Phone: 934-6593
E-mail: [email protected]
General Reading:
 Alberts et al., Molecular Biology of the Cell (5th Ed.) Chapter 12, pp. 695-712
Other References (if your interested):
 Komeili and O’Shea. New Perspectives on Nuclear Transport. Ann. Rev.
Genet. 35: 341-364 (2002).
 Strambio-De-Castillia et al. The Nuclear Pore Complex: Bridging Nuclear
Transport and Gene Regulation. Nat. Rev. Mol. Cell Biol. 11: 490-501 (2010).
 Tschochner and Hurt. Pre-Ribosomes on the Road From the Nucleolus to the
Cytoplasm. Trends Cell Biol. 13: 255-363 (2003).
 Other reviews and papers indicated in the slides.
Lecture Overview
 Overview of cellular compartmentalization.
 Features of nuclear pores.
 Mechanism of nuclear Import.
 Mechanism of nuclear export.
 Ribosome assembly and export.
Overview of Cellular Compartmentalization
The Cellular Compartmentalization Problem
Protein Trafficking Mechanisms
There are two basic pathways of biosynthetic protein traffic:
 Default localization
 Signal-mediated localization
 gated transport
 transmembrane transport
 vesicular transport
Intracellular Protein
Transport Mechanisms
Endoplasmic Reticulum
Golgi Apparatus
Late Endosome
Early Endosome
Cell Surface
Three-Dimensional Model of the Nucleus
Scanning EM of the Nucleus
Blue pseudo-coloring highlights the nuclear pore complexes, while green pseudocoloring highlights the nuclear envelope together with the attached ribosomes.
Kiseleva, Nature Cell Biol. 6: 497 (2004)
Types of Traffic That Pass Through Nuclear Pores
RNA Polymerases
40S ribosomal subunits
60S ribosomal subunits
DNA Polymerases
Ribosomal Proteins
Transcription factors
Volume of Traffic Through Nuclear Pores
 A single HeLa cell contains 10 million ribosomes, ~4000 nuclear
pores, and divides every 24 hrs. This means a total of:
 400,000 ribosomal proteins must be imported each minute
(~100 r-proteins/pore).
 12,000 ribosomal subunits must be exported each minute (~3
ribosomal subunits/pore).
 If synthesizing DNA, need ~1 million new histone molecules every 3
minutes, so need to transport 100 histones/pore each minute.
 Several hundred other proteins, RNAs, and RNPs move in and out
of a single nuclear pore each minute.
Features of Nuclear Pores
Nuclear Pore Complex
 8 fold rotational symmetry.
 Size exclusion ranges from 9 nm (“closed”)
to 26 nm (“open”).
Nuclear Pores Embedded in the Nuclear Membranes
The nuclear pore contains spoke and ring assemblies that are
integrated into the two membranes of the nuclear envelope.
Nuclear Pore Complex (NPC) Composition
A single nuclear pore contains ~ 1000 proteins (total) and 60-100 different proteins.
These nuclear pore complex (NPC) proteins are called nucleoporins.
Many nucleoporins are glycoproteins that carry O-linked N-Acetylglucosamine (GlcNAc) residues.
Nuclear pore fibrils and other nucleoporins within the NPC channel contain
phenylalanine and glycine (FG) repeats that facilitate binding of the nuclear import
receptors to the nuclear pore complex during its translocation through the nuclear
pore. These interactions allow transported molecules to pass bi-directionally through
the 15nm long pore.
A relative size perspective: The NPC has a MW of 125 million Daltons. By
comparison, a mammalian ribosome has a molecular weight of ~ 4 million Daltons.
Nuclear Pore Complex Structure
 Each nuclear pore complex (NPC) is a cylindrical structure comprised of eight spokes surrounding a
central tube that connects the nucleoplasm and cytoplasm.
 The outer and inner nuclear membranes (ONM and INM, respectively) of the nuclear envelope join to
form grommets in which the NPC sits.
 The NPC is anchored to the nuclear envelope by a transmembrane ring structure that connects to the
core scaffold and comprises inner ring and outer ring elements.
 Linker nucleoporins (Nups) help anchor the Phe-Gly (FG) Nups such that they line and fill the central
Strambio-De-Castillia et al., Nat. Rev. Mol. Cell Biol. 11: 490-501 (2010)
The Nuclear Pore Complex
Functions as a “Virtual Gate”
 The outer and inner nuclear membranes (ONM
and INM, respectively) of the nuclear envelope
join to form a ring-shaped pore where the
nuclear pore complex (NPC) resides.
 At the NPC, the nucleus and cytoplasm are
connected by a channel, which is filled with
flexible, filamentous Phe-Gly nucleoporins (FG
 Spurious macromolecules are physically
excluded from entering the densely packed FG
Nup meshwork.
 Nuclear transport factor (NTF)-bound cargo can
enter the channel from either its cytoplasmic or
nucleoplasmic side and hop between binding
sites on the FG Nups until they return to the
original compartment or reach the opposite side
of the NPC.
Strambio-De-Castillia et al., Nat. Rev. Mol. Cell Biol. 11: 490-501 (2010)
Two Models For Natively Disordered FG-Repeat
Domains in the Transport Channel of the Nuclear Pore
Left: FG-repeat network may form a hydrogel, crosslinked by hydrophobic interactions
between the phenylalanines.
Right: FG repeats could form a network of unlinked polymers whose thermally
activated undulations create a zone of "entropic exclusion”.
Elbaum, Science 314: 766-767 (2006)
FG Repeats Can Form an Elastic
Hydrogel in Aqueous Solution
Left: An aqueous solution with 26 mg/ml wild-type FG-repeat domain from Nsp1p (400 µM) was
filled into a silicon tubing, where it completed gelling. The formed gel was pushed out of the
tubing by gentle pressure, placed onto a patterned support (1 square = 1.4 mm2), and
photographed. Note that the pattern shows clearly through this transparent gel. Inset illustrates
how interactions between the hydrophobic clusters (shown in red) cross-link the repeat domains
into a hydrogel.
The FG repeats can form a free-standing gel, and they measure elasticity comparable to 0.4%
Right: The FS mutated repeat domain remained liquid after identical treatment.
Frey et al., Science 314: 815-817 (2006)
Hydrogel Model of Nuclear Pore Function
Selective phase model for the passage of a nuclear transport receptor (NTR) through
the permeability barrier of nuclear pore complexes.
 Inter-repeat contacts between the hydrophobic clusters ( ) of FG-repeat-domains create
a sieve-like barrier which restricts the passage of inert objects larger than the mesh-size.
 NTRs can overcome this size-limit, because they possess binding sites ( ) for the
hydrophobic clusters. They compete with inter-repeat contacts, thereby open adjacent
meshes and dissolve within the barrier. Since the involved interactions are of low affinity,
the NTR can leave the barrier on the other side.
Frey et al., Science 314: 815-817 (2006); Burke, Science 314: 766-767 (2006)
Mechanism of Nuclear Import
Selective (Signal-Mediated) Nuclear Entry
Nuclear pores don't close completely - time required for proteins that lack a
nuclear targeting signal to diffuse through the nuclear pore in living cells has been
-2 minutes
-30 min
-does not enter nucleus
Remarkably, even 20 nm gold particles coated with molecules having nuclear import or
export signals can pass readily through the nuclear pore.
Outcomes of Nuclear Pore Function
** * *
* *
* *
** * * *
Nuclear Exclusion
* *N***
* * **
Nuclear Localization
** * *
** *
* ** *
Characteristics of Nuclear Transport
 Active transport through the nuclear pore complex (NPC) has the
following features:
 Energy dependent
 Temperature dependent
 Signal dependent
 Saturable
 These are features of a carrier-mediated process.
Nuclear Localization Signals
 Two types of Nuclear Localization Signal (NLS):
 Short basic sequences of 4-8 residues
[PPKKKRKV is the NLS of SV40 large T antigen]
 Bipartite signals with two stretches of basic amino acids
separated by ten less-conserved amino acids.
[KRPAATKKAGQAKKKK is the NLS of nucleoplasmin]
 Both types of NLS are rich in the basic amino acids arginine and lysine
and usually contain proline.
Location of Nuclear Localization Signals
Proteins don’t unfold during nuclear import. An NLS can be located
anywhere in a protein, as long as they lie on the surface of the folded
protein molecule where they can be recognized by an NLS receptor.
Methods Used to Identify NLSs
 Microinjection studies- can be used to study nuclear targeting
signals either in their natural context, when fused to passenger
proteins, or when stuck to gold particles.
 Deletion and gene fusion studies- Deletions can be used to identify
regions necessary for nuclear import, while the fusion of these
sequences to a passenger protein tests whether these sequences are
sufficient for nuclear import.
 Mutational analysis- Determine specific amino acid sequence
necessary for nuclear localization.
Micro-injection Studies
to Identify the Location
of an NLS
Use of Electron Microscopy to Identify NLSs
Electron micrograph showing nuclear entry of
colloidal gold particles coated with
nucleoplasmin following microinjection.
Use of Immunofluorescence to Identify NLSs
The 8 amino acid SV40 NLS can target a cytosolic protein to the
nucleus when introduced either genetically or by crosslinking.
Pyruvate Kinase
Pyruvate Kinase
plus SV40 NLS
Mutational analysis of the SV40 Large T antigen
(90 kDa protein required for viral DNA replication)
Cytosolic Receptors Mediate Nuclear Protein Import
Mechanism of Nuclear Import
 Importin-, a component of the nuclear localization signal (NLS)
receptor complex binds to the NLS of a protein to be imported.
 Importin-, the other subunit of the NLS receptor complex,
mediates docking with the outer surface of the nuclear pore in a
rapid, energy-independent fashion.
 Translocation of the trimeric complex occurs along FG-repeat
proteins within the nuclear pore in an energy-dependent manner.
Importin- interacts with the FG-containing components of the pore
 Once the complex enters the nucleoplasm, Ran-GTP binds,
releasing the cargo molecule from the complex.
 Following the dissociation of the imported protein from the
complex, the receptor components (with bound Ran-GTP) are then
re-exported to the cytoplasm for another cycle.
Mechanism of Nuclear Import (cont)
 Three important accessory proteins assist Ran function:
 A cytosolic Ran Binding Protein (BP) dissociates Ran-GTP from
the receptor.
 The cytosolic Ran GTPase-Activating Protein (Ran-GAP)
triggers GTP hydrolysis, converting Ran-GTP to Ran-GDP.
 The Ran Guanine nucleotide Exchange Factor (Ran-GEF),
which promotes exchange of GDP to GTP, is nuclear.
 The nuclear location of the Ran-GEF maintains nuclear Ran in the
GTP-bound form, providing directionality to nuclear transport.
 Once cytosolic Ran-GTP is hydrolyzed to Ran-GDP by Ran-GAP, the
Ran-GDP is then re-imported into the nucleus for another cycle.
Role of Ran in Nuclear Protein Import
Regulated Nuclear Import
In some cases, pre-synthesized transcription factors and cell cycle
regulators are maintained in the cytoplasm and only translocate into the
nucleus at specific times or in response to specific signals.
Mechanisms used to achieve regulated entry include:
A conformational change upon ligand binding.
Covalent modification (e.g., phosphorylation of NLS).
Attachment to a cytoplasmic structure to block import.
Binding of regulatory subunits that mask the NLS.
Ligand-Induced Activation of an NLS
Regulation by Covalent Modification
Regulation by Covalent Modification (cont)
 NFAT (Nuclear Factor of Activated T cells) is a transcription factor
that contains a nuclear localization sequence, but it is buried in the
protein interior.
 Whether NLS or NES is masked depends on the phosphorylation
state of specific serine residues in the regulatory
domain. Phosphorylation of these serine residues exposes an
NES, whereas dephosphorylation exposes an NLS.
 In resting cells, the NLS of the cytoplasmic NFAT is masked
due to phosphorylation on these serine residues.
 In stimulated cells, an increase of intracellular calcium ions
activates calcineurin, which then dephosphorylates the masking
residues. Consequently, the NLS is exposed and NFAT can be
carried into the nucleus by the importin / complex.
 Inside the nucleus, NFAT may be re-phosphorylated by a protein
kinase, exposing its NES so it can be exported by the exportin
Induced Activation of Nuclear Entry by the Level
of Cytosolic Calcium
Nuclear entry of the transcription factor NFAT is
induced when the level of cytosolic calcium increases.
Regulation by Cytosolic Retention
NLS Masking by a Regulatory Subunit
Glucocorticoid Receptor
Why aren’t nuclear localization
signals removed following import?
The Lamina Controls Nuclear Integrity
 At the onset of mitosis, phosphorylation
of nuclear lamins leads to the
dissassembly of the lamina and the
subsequent breakdown of the nuclear
 Prior to nuclear re-assembly,
dephophorylation of the lamins occurs.
Lamin B, which remains associated
with a specific receptor on nuclear
membrane vesicles, is then rejoined by
lamins A and C. This is followed by the
reassembly of the lamina and the
membrane in a GTP-dependent
 Mutations in the gene encoding lamin A
have been shown to be associated with
at least six different diseases that are
collectively called the laminopathies.
Repeated Nuclear Entry
 Nuclear proteins are capable of repeated entry into the
nucleus because nuclear localization signals are not
removed when the protein enters the nucleus.
 This is important, because when the cell undergoes mitosis,
the nuclear membranes break down and nuclear proteins
freely mix with cytosolic proteins.
 Once mitosis is completed and the nuclear membranes reform the nuclear proteins are imported again. This process
can occur repeatedly.
Nuclear Membranes Break Down During Mitosis
Mechanism of Nuclear Export
Features of Nuclear Export
Nuclear export occurs by a mechanism analogous to nuclear import:
 Protein to be exported contains a leucine-rich Nuclear Export
Signal (NES).
 A substrate to be exported is bound by an export receptor (such
as Crm1) and Ran-GTP mediates its export from the nucleus.
 Once in the cytosol, Ran-BP dissociates the exported substrate
and its receptor.
 Ran-GAP converts Ran-GTP to Ran-GDP.
 Ran-GDP and the export receptor are then re-imported into the
nucleus for another cycle of export.
CRM1-Mediated Nuclear Protein Export
(a) The CRM1 transport cycle.
 In the nucleus, Ran-GTP
stimulates binding of CRM1 to
NES substrates.
 After passage through the
NPC, the CRM1/RanGTP/NES substrate complex
is disassembled at the
cytoplasmic filaments by the
concerted action of Ran-BP1
and Ran-GAP.
 The NES substrate is released
to the cytoplasm and empty
CRM1 is recycled back to the
(b) Model of CRM1 export
complex disassembly.
Kutay and Güttinger, Trends Cell Biol. 15: 121-124 (2005)
 CRM1 is released into the
cytoplasm and, for recycling
into the nucleus, binds to a
series of different, cargoindependent CRM1-binding
Example of Nuclear Protein Export
If you inject Protein Kinase A (PKA) and PKA Inhibitor (PKI)(†) into a cell nucleus, the
PKI binds to PKA and transports PKA out of the nucleus by an active mechanism.
Many proteins and RNAs undergo export from the nucleus. Nuclear Export Signals
(NES) mediate the export of protein and RNA species.
PKI contains a Nuclear Export Signal (NES) [LALKLAGLDI]
PKI transport of
PKA out of the
nucleus is both
temperature and
indicating an
active process.
Nuclear Export of Various RNA Species
 mRNAs, snRNAs and ribosomes are transported in or out of the
nucleus as ribonucleoprotein complexes (RNPs).
 Like protein transport, RNA transport is signal-dependent, carrier
mediated, and occurs through the nuclear pore complex.
 In general, nuclear export is mediated by adaptor proteins and
export receptors (exportins).
 Adaptor proteins bind the export signal and present it to the
exportin, which facilitates transport of the complex through
the nuclear pore complex.
 However, different classes of RNAs utilize different adaptors
and receptors. Not all require Ran-GTP.
Nuclear Export of mRNA
 mRNA export occurs only following the attachment of the m7G cap at
the 5´ end, splicing, poly(A) addition, and the attachment of various
proteins during these steps.
 Export requires the function of adaptor proteins that couple the mRNA
to the exportin complex.
 Nuclear mRNA export is mediated by the mammalian Tap-Nxt exportin
complex (corresponds to Mex67-Mtr1 in yeast).
 Ran-GTP is not involved in mRNA export (unlike the export of most
other RNAs).
 Certain viral RNAs contain a constitutive transport element (CTE) that
eliminates the need for an adaptor protein.
Factors involved in Nuclear Export of mRNA
 Recruitment of UAP56 to mRNA molecules, either by splicing or possibly via one of the other
indicated mechanisms, likely represents the key initial step in inducing nuclear mRNA export.
 UAP56 then recruits Aly, which in turn binds the Tap-Nxt nuclear RNA export factor.
 In contrast, the Mason-Pfizer Monkey Virus (MPMV) CTE RNA can bind the Tap-Nxt heterodimer
directly, thus obviating the need for upstream factors.
 UAP56, Tap and Nxt are all essential for bulk mRNA nuclear export, but Aly is not, thus implying that
a second, unknown factor may also mediate recruitment of the Tap-Nxt heterodimer by mRNA-bound
UAP56 molecules.
Cullen, J. Cell Sci 116: 587 (2003)
Nucleocytoplasmic Trafficking of snRNAs
 Like mRNAs, the m7G cap at the 5´ end of snRNAs is bound
by a monomethyl cap-binding complex (CBC), which is
important for its nuclear export.
 Transport of the assembled snRNP particle back into the
nucleus requires a two-component signal composed of the
Sm proteins and a trimethyl G cap on the RNA (a cytosolic
methylase hypermethylates the m7G cap to m3G).
 Export is mediated by the Crm1 export receptor and RanGTP.
Nuclear Export of tRNAs
 tRNA export mediated by exportin-t (and Ran-GTP).
 All processing and modification must occur before the tRNA
molecule can be transported from the nucleus.
 Mutations that alter tertiary base pairs often effect both
processing and transport, indicating that the mature conformation
of the molecule is critical for each of these processes.
Rev-Mediated HIV-1 Genomic RNA Export from the Nucleus
For cellular RNAs, the presence of introns prohibits
nuclear export. Similarly, unspliced HIV-1 RNA is not
exported in the absence of the Rev protein.
Rev-Response Element (signal in the HIV-1 RNA)
Rev-Mediated HIV-1 Genomic RNA Export from the Nucleus
The HIV-1 Rev protein functions as an export adaptor that mediates the Crm1dependent export of unspliced HIV RNA through its leucine-rich NES [LPPLERLTL].
Nuclear export
mediated by the
Crm1 export
receptor and
Rev (adaptor protein )
Rev-Response Element (signal in the HIV-1 RNA)
Summary of Non-mRNA Export from the Nucleus
Adaptor for
RNA Export
Cullen, J. Cell Sci 116: 587 (2003)
Ribosome Assembly and Export
Pre-RNA processing in Yeast
Structure of the pre-rRNA
35S containing the mature
rRNA, 18S, 5.8S and 25S.
Schematic representation
of the rRNA processing
Fromont-Racine et al., Gene 313: 17-42 (2003)
Simplified Scheme For Assembly, Maturation and
Export of Pre-40S and Pre-60S Ribosomal Subunits
 35S pre-rRNA synthesized by RNA polymerase 1, 5S rRNA made by RNA polymerase 3.
 snoRNAs, ribosomal proteins and non-ribosomal factors form the 90S pre-ribosomal particle.
 Cleavage of the 35S pre-rRNA splits the 90S precursor into 40S and 60S pre-ribosomes.
 After export into the cytoplasm via the nuclear pores, additional maturation steps occur and the final
non-ribosomal factors dissociate from mature 60S and 40S ribosomal subunits.
Tschochner and Hurt, Trends Biochem. Sci. 13: 255-263 (2003)
The Ribosome Synthesis Pathway
 Nucleolar processing/assembly events are
highlighted in yellow.
 The major role of U3 in processing 90S preribosomes (part of a larger processome) is
 Note that assembly of the small ribosomal
subunit probably starts while the pre-rRNA
35S is still being transcribed. The early
dichotomy of the 40S and 60S processing
machinery is symbolized by the relative
higher content of mature 40S ribosomal
proteins in the 90S pre-ribosomes.
 Synthesis of 60S ribosomes comprise early,
middle and late steps based on protein and
RNA composition.
 Late steps include maturation of 40S and
60S ribosomes within the cytoplasm.
 A number of factors know to control the
synthesis of 40S and 60S ribosomes are
depicted respectively in the left and right
margins. The Rpl3-Rrb1 association is an
example of regulatory protein-protein
Fromont-Racine et al., Gene 313: 17-42 (2003)
Post-Transcriptional Modifications during Ribosome Biogenesis
Two Major Types of rRNA Modifications:
 2’O methylation modifications are carried
out by box C/D snoRNPs.
 Pseudouridylation modifications of prerRNAs are guided by box H/ACA snoRNPs
(basically, this is an isomerization of
 These modifications primarily occur early in
the biogenesis process in the 90S preribosomal particle.
 Schemes of the interactions established
between the pre-rRNA and a box H/ACA
snoRNP (left) or a box C/D snoRNP (right).
 The modifications are carried out by
snoRNPs, which contain proteins and
“guide RNAs” that target the site of
modification via base-pairing.
 Dissociation of guide snoRNAs probably
require helicase activities.
Henras et al., Cell. Mol. Life Sci. 65 2334 – 2359 (2008)
Export of Pre-60S and Pre-40S Ribosomal
Subunits Prior to Final Maturation
 Schemes of export-competent pre60S (A) and pre- 40S (B) particles
with associated factors relevant to
nuclear export.
 The red protuberances on the
adaptors Ltv1p and Nmd3p
represent the nuclear export
signals mediating interaction with
 Arrows between export receptors
and the hydrophobic mesh of the
NPCs refer to the reported ability
of these factors to interact directly
with the FG repeats of some
Henras et al., Cell. Mol. Life Sci. 65 2334 – 2359 (2008)
Late Cytoplasmic Steps of Ribosome Assembly
 For the large ribosomal subunit, two GTPases
seem to play an important role. GTP hydrolysis
of Efl1 accelerates nucleolar recycling of the
anti-associating factor Tif6 whereas that of the
putative Kre35/Lsg1 helps to recycle another
exported nucle(ol)ar factor.
 Tif6 release is thought to be mediated by
 Besides its role in pre-60S export, Nmd3 seems
to play a role in recycling of mature free 60S
subunits together with Lsg1.
 Cleavage of the 20S pre-rRNA into mature 18S
occurs in the cytoplasm. While the endonuclease
in charge of this reaction is still unknown, Rio1
and Rio2 are thought to play a role in this
process. Hcr1 is believed to influence the
cleavage reaction and to play a role in
translation initiation.
Fromont-Racine et al., Gene 313: 17-42 (2003)
Proposed Pathway of 60S Maturation in the Cytoplasm
The stalk is made up of P0,
P1 and P2 (corresponds to
L10, L7/12 in bacteria).
 Maturation is initiated by the ATPase Drg1.
Drg1 facilitates the replacement of Rlp24 by
Rpl24, which then recruits Rei1. Rei1
enables the release of the export receptor
Arx1, located near the polypeptide exit tunnel.
 In parallel, Yvh1 enables replacement of Mrt4
with P0 to construct the ribosome stalk. Prior
assembly of the ribosomal stalk is required for
the release of Tif6.
 Note that the stalk contains the GTPase
Activating Center, or GAC. It normally
recruits GTPases during translation.
Interestingly, the GTPase Efl1 is
required for the release of Tif6. Because
Efl1 resembles the translation elongation
factor eEF2 (EF-G in bacteria),
assembly of the stalk may be required to
recruit Efl1. Thus, this step in 60S
biogenesis appears to mimic
translocation, with Efl1 providing a
mechanism to functionally check the
nascent subunit.
 Finally, The release of Tif6 activates Lsg1 to
release the export adaptor Nmd3.
Lo et al., Mol. Cell 39, 196–208 (2010)

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