Block III Lecture 7 Nucleocytoplasmic transport February 16, 2005

1. Block III Lecture 7 Nucleocytoplasmic transport February 16, 2005 Maria L. Zapp, Ph.D. Program in Molecular Medicine and The UMass Center for AIDS Research

2. Regulation of gene expression at the level of nucleocytoplasmic transport Prokaryotes Eukaryotes Compartmentalization and the need for nuclear transport One distinct characteristic of eukaryotic cells is the existence of nuclear and cytoplasmic compartments separated by a nuclear envelope (NE). The NE is a double membrane that is continuous with the ER and is perforated by nuclear pore complexes (NPCs). Adapted from Lewin, 1988

3. Problem: Cellular mRNAs, tRNAs, and rRNAs are transcribed in the nucleus and must be exported to the cytoplasm for protein translation. Conversely, nuclear proteins such as histones, pre-mRNA splicing and transcription factors are synthesized in the cytoplasm and must be imported into the nucleus to perform their functions. Solution: Cellular RNAs and proteins are transported bidirectionally across the NE through the NPCs. This cellular process is known as “nuclear-cytoplasmic or nucleocytoplasmic transport”. Nucleocytoplasmic transport has two distinct components: nuclear import and nuclear export

4. Nuclear Envelope (NE) : Nuclear pore complexes, nuclear lamina, and lipid membranes Nuclear pore complexes (NPCs) Nuclear lamina

5. Possible pathways for molecular movement into the nucleus: NPC 1. Direct passage through the nuclear pores 2. Synthesis on the outer nuclear membrane (ONM) or contiguous ER followed by passage through the inner nuclear membrane (INM) 3. Synthesis in the nucleoplasm 4. Passage by diffusion through the ONM and INM 5. Passage by active transport through the ONM and the INM 6. Passage in vesicles that form from the ONM and subsequently fuse with the INM 7. Passage in vesicles formed from both nuclear membranes 8. Passage through holes in the NM (i.e. at mitosis) Adapted from Maul, G. 1777

6. Micropipette filled with tracer substance * * * * * * Tracer substances: Nucleus Tritiated ( 3H-labeled) dextrans of 3 different sizes Radii= 12.0 ( ) 23.3 ( ) 35.5 ( ) Cytoplasm Å Å Å * * Longitudinal cross-section What is the permeability of the nuclear envelope? Microinjection assay using X. laevis oocytes Representative 100 mM sections Minus tracer Plus tracer Oocyte Experiment : Inject a radiolabeled tracer * into the cytoplasm of oocytes. Incubate for various times. Quench oocytes by placing at -190oC. Prepare 100mm sections (- 50oC). Determine the intracellular concentrations of tracer by ultra-low temperature autoradiography. Count the grain densities.

7. Time course of nuclear permeation, expressed as the average nuclear:cytoplasmic grain density, X n/c as a function of diffusion time after injection, td (min). Vertical bars = s. e. mean. 3H dextrans Radii= 12.0 ( ) 23.3 ( ) 35.5 ( ) Å Å Å * * * Å 35.5 * * * Å 12.0 Å 23.3 * * * Schematic representation of the data Time (minutes) Paine, et al., 1975. Nature 254: 109-114.

8. Conclusion: The NE is a molecular sieve that restricts molecular movement between the nucleus and the cytoplasm. Summary 1. These data demonstrate that the NE is less permeable to larger dextrans (>23.3 Å) than smaller dextrans (<12.0 Å). 2. The permeability of the NE plays a major role in limiting the rate of nuclear entry. 3. These classical studies suggested that the NE is a diffusion- restrictive barrier. The data are consistent with nuclear entry kinetics expected for passage through an envelope with pores.

9. Schematic representation of the Nuclear Pore Complex (NPC) Protein constituents of the NPC are known as nucleoporins or “NUPs”.

10. Selectivity at the nuclear pore Part I: Nuclear-cytoplasmic transport of proteins Key observations: Large proteins can enter the nucleus and remain there. Cytoplasmic proteins do not enter the nucleus, and remain localized in the cytoplasm. Some proteins re-equilibrate between the nucleus and the cytoplasm. Approach and Results: Nucleoplasmin is a pentameric nuclear protein that contains a protease-resistant “core” domain and a protease-sensitive “tail” domain. Nucleoplasmin injected into the cytoplasm of frog oocytes enters the nucleus. When the tail domain is removed by digestion, the residual core domain remains a pentamer and is UNABLE to enter the nucleus. The detached tail domains rapidly accumulate in the nucleus, suggesting the tail domain contains a signal for nuclear accumulation. Conclusion: Nuclear proteins contain nuclear-targeting signals

11. Nuclear protein transport occurs through the NPCs and requires ATP Key observations: Direct visualization of intracellular migration of nucleoplasmin- coated colloidal-gold particles through oocyte NPCs using EM. Particle movement is altered dramatically by ATP depletion and low temperature. Additional EM work visualized an RNA-coated gold particle moving through the NPC to the cytoplasm. Significance: These oocyte-based approaches help demonstrate that cellular proteins and RNA are transported bidirectionally through the NPC. Conclusions: 1. The steady-state distribution of cellular proteins between the nucleus and the cytoplasm is governed by an intrinsic property of the polypeptides. 2. Nuclear proteins contain specific Nuclear Localization Signals (NLS) that promote nuclear uptake. 3. Nuclear protein uptake occurs via NPCs. Bonner, et al., 1975. J.Cell Biol. 64: 431-437. Dingwall, et al., 1982. Cell 30: 449-458. Feldherr, et al., 1984. J. Cell Biol. 99:2216-2222.

12. The NLS of a protein selectively promotes its import into the nucleus Approaches to identify sequences which mediate nuclear localization of proteins i. Deletion analysis of SV40 virus large T-antigen Construction and characterization of viral protein mutants defective in nuclear import. The first NLS was identified in SV40 large T-antigen and consists of numerous charged amino acid residues. The SV40 T-antigen sequence is the “prototype”of classical NLSs. Immunofluorescence (IF) micrographs showing the intracellular distribution of the SV40 virus T-antigen containing or lacking a short peptide that serves as an NLS. (Left panel) The wild type T-antigen protein contains the lysine-rich sequence indicated and it is imported to its site of action in the nucleus, as shown by IF staining with an antibody against the T-antigen. (Right panel) An SV40 T- antigen protein with a mutant NLS peptide (Lys--> Thr ) remains in the cytosol. Lanford and Butel, 1984. Cell 37:801-813. Kalderon, et al., 1984. Cell 39: 499-509.

13. 1 AA 852 AA Yeast MATa2 E. colib-galactosidase Reporter protein Yeast Cell Nucleus Cytoplasm ii. Construction and analysis of chimeric fusion proteins Mata2 = A yeast protein involved in mating. The protein is nuclear localized. b-galactosidase (b-gal) = A bacterial enzyme involved in metabolism. The protein is localized in the cytoplasm of yeast cells. Generate a yeast expression vector : Sequences that encode Mat a2 were cloned in frame with sequences that encode b-gal. Transform plasmid into yeast cells and analyze the intracellular distribution of the fusion protein. Analysis of Protein Localization yMATa2 yMATa2-b-galactosidase b-galactosidase Richardson, et al., 1984. Cell 44: 77-85. Hall, et al., 1984. Cell 36: 1057-1065. Goldfarb, et al., 1986. Nature 322:641-644.

14. Summary: 1. The addition of an NLS can facilitate nuclear entry of a protein that is too large to enter by diffusion. 2. Nuclear proteins contain specific amino acid sequences that selectively promote nuclear localization. 3. Additional NLS peptide competition studies in frog oocytes indicated that nuclear protein localization or “nuclear import” is a saturable process. The saturation kinetics and competition effects observed suggested nuclear protein import is a carrier-mediated process. 4. Nuclear import of proteins is a receptor-mediated process. The NLS may interact with a component of the nuclear transport machinery. 5. Large proteins may interact with cellular “receptors” for nuclear import. Specific interactions would result in a selective distribution of proteins between the nucleus and the cytoplasm.

15. Development of novel assays for nuclear protein import To determine whether the protein of interest contained an NLS. To identify the molecular steps required for nuclear protein import. To identify cellular factors that mediate nuclear protein import. i. Mammalian cell microinjection assay Inject a fluorescently-labeled protein into the cytoplasm of a mammalian cell, then determine its intracellular localization using fluorescence microscopy. Cytoplasm Nucleus + NLS Protein MT-NLS protein DNLS Protein Injection substrates: D NLS Protein (lacks an NLS) + NLS Protein (contains an NLS) MT-NLS protein (contains a mutant NLS)

16. GST-NLS-EGFP hRIP hRIP GST-DNLS-EGFP ii. Mammalian cell transient transfection assay Glutathione-S-Transferase (GST) is an enzyme from S. japonicum. GST =26 kDa. Green Fluorescent Protein (EGFP) is a light-converting protein from A. victoria. GST= 27kDa. Enhanced GFP (EGFP) is a variant of wild type GFP protein, which has been optimized for brighter fluorescence and high expression in mammalian cells. Construct plasmids for transient expression of a GST- EGFP fusion protein that contains an NLS (GFP-NLS-EGFP) or lacks an NLS (GST-DNLS-EGFP) in mammalian tissue culture cells. Introduce DNA into cells using standard methods (i. e. CaPO4-mediated DNAprecipitation, cationic liposomes, DEAE-dextran or Electroporation). Analyze the intracellular distribution of the protein using indirect fluorescence microscopy. hRIP= Control or “Marker” protein. hRIP is an endogenous protein that is localized at the nuclear periphery.

17. iii. in vitro reconstituted nuclei. Assemble an assay mix containing isolated intact nuclei from mammalian cells, frog egg extract, and a fluorescently labeled protein. Results: Isolated mammalian cell nuclei import nuclear proteins efficiently when incubated in this mix, but exclude non-nuclear proteins. Nuclear import of the protein substrate displays the same characteristics for an active protein import system: a requirement for an NLS, ATP, an intact NE, and temperature dependence. Summary 1. These three assay systems provided evidence that nuclear protein import occurs in two distinct steps: rapid binding or “docking” at the NE, followed by trans- location through the NPC. 2. The binding and translocation steps can be uncoupled by incubating cells at low temperature or by treating them with inhibitors of ATP production. Translocation through the NPC is energy-dependent. 3. The NPC contains multiple docking sites that guide the movement of NLS- containing proteins from the cytoplasm to the nucleoplasmic face of the NPC. 4. Docking of the NLS-containing protein to the NPC, as well as its subsequent movement through the NPC requires cellular transport factors. Newmeyer, et al., 1986. EMBO J. 5:501-510 ; J. Cell Biol. 103: 2091-2103. Richardson, et al., 1988. Cell 52: 655-664. Adams, et al., 1990. J. Cell Biol.111: 807-816. Adams and Gerace, 1991. Cell 66: 837-847. Moore and Blobel, 1993. Nature 365: 661-663; PNAS 91: 10212-10216. Melchior, et al., 1993. J. Cell Biol. 123:1649-1659. Rexach and Blobel, 1995. Cell 83: 638-692.

18. -ATP +ATP Plus Buffer Plus Lysate Cellular factors which selectively interact with the NLS: Identification of nuclear protein import receptors i. Development of an in vitro reconstitution assay for protein import using digitonin- permeabilized mammalian cell nuclei. This unique assay system offers several technical advantages for identifying mediators of protein import : Fluorescently labeled (FITC) or epitope- tagged import substrate can be introduced into cells and nuclear uptake monitored microscopically. Cells are depleted of their soluble cytoplasmic components; thus re-import requires re-addition of a cytosolic fraction(s). RESULTS: Cytosolic fractions were added to digitonin- permeabilized cells to restore nuclear import of an FITC-labeled or epitope-tagged NLS- containing protein. Fractions demonstrated to support protein import into nuclei were subfractionated to identify components of the protein import machinery. Ultimately, cytosolic fractions were replaced with purified recombinant factors for functional analysis. ii. Chemical crosslinking of cellular proteins that bind to an NLS-containing protein. Adams, et al., 1990. J. Cell Biol. 111:807-816.

19. Molecular events in nucleocytoplasmic transport Overview Nucleocytoplasmic transport is largely mediated by a superfamily of transport “receptors” that interact directly with the NPC. These transport receptors are related, albeit often distantly, to the cellular protein importin-b(Imp b), and share an N-terminal GTPase binding motif. Based on the direction these transport receptors carry their cargo, they are called “importins” or “exportins.” These transport receptors are sometimes referred to as “karyopherins”, a more historical nomenclature. Transport receptors bind their cargo on one side of the NE, translocate to the other side, release the cargo, and return to their original cellular compartment to mediate the next round of transport. Specifically, importins bind cargo in the cytoplasm and release it in the nucleus; conversely, exportins bind their cargo in the nucleus and release it in the cytoplasm. In the simplest case, the cargo is recognized directly by its cognate transport receptor. In others, cargo recognition is more complicated and requires additional “adapter” molecules. In the most complex cases, the same receptor binds one cargo for nuclear import and a different cargo for nuclear export.

20. Ran GTP Ran GTP a NE b b a a K b K Cargo bearing an NLS K Importin a b a Importin b The nuclear protein import cycle Key adapter molecules : 1. Importin-a (Imp a) or the “NLS receptor” mediates NLS recognition. 2. Importin-b (Imp b) mediates interactions with the NPC to drive translocation of cargo. 3. A nuclear GTPase system- Ran, RCC, a Ran GAP, binding proteins 1 and 2, NTF-2 1. Imp a directly binds to the NLS of the cargo, then interacts with Imp b. 2. Imp b docks the trimeric complex to the NPC and mediates translocation. 3. Translocation is terminated by direct binding of Ran-GTP to Imp b, which releases the complex from the NPC, and dissociates Imp a from Imp b. 4. Imp a and b are recycled to the cytoplasm separately. Imp b / Ran-GTP complexes leave the nucleus directly. Imp a requires a specialized exportin (CAS 1), thus helping to explain how NLS-containing proteins remain in the nucleus. 5. Proteins with an M9-like NLS bind directly to Transportin, and do not require an adapter or a-like protein. Ran also regulates these interactions. nucleus cytoplasm

21. GAP/ Rna1 Ran GDP Ran GTP Ran GTPase system: Regulation of cargo loading onto transport receptors Ran is a small nuclear GTPase that switches between a GDP- and a GTP-bound form. This switch can only be accomplished by the aid of regulators of Ran’s nucleotide bound state. These regulatory proteins are localized on opposite sides of the NE: the Ran GTPase-nucleotide Exchange Factor (GEF) is nuclear, whereas the Ran GTPase Activating Protein (GAP) is cytoplasmic. Ran binding proteins are also cytoplasmic. The intrinsic GTPase activity of Ran is activated by the concerted action of the GAP and RanBP1. Because both proteins are in the cytoplasm, Ran is in the GDP-bound form in this compartment. Conversion of Ran-GDP to Ran-GTP requires the GEF. Because the GEF is bound to chromatin, nuclear Ran is in the GTP-bound form. The overall result of this nuclear GTPase cycle is a Ran-GTP gradient across the NE with a high concentration of Ran-GTP in the nucleus, and a low concentration in the cytoplasm. GTP GDP Ran GTP Ran GDP GEF/Rcc1 nucleus NE cytoplasm RanBP1 The nucleotide state of Ran determines compartment identity

22. Summary The existence of a Ran-GTP gradient provides a plausible explanation as to how functional asymmetry can be imposed on the transport cycle. Importins bind their cargo in the cytoplasm, and release them upon binding Ran-GTP in the nucleus. Importins then return to the cytoplasm as Ran-GTP complexes minus cargo. Ran-GTP must then be removed from the Importins to allow binding of another cargo molecule. Exportins bind their cargo in the nucleus forming a trimeric complex with Ran-GTP. This cargo-exportin-Ran-GTP complex is then transferred to the cytoplasm, where it disassembles following GTP hydrolysis. The cargo free, Ran-GTP free exportin can then re-enter the nucleus and bind another cargo molecule. The release of the one cargo molecule requires energy in the form of one molecule of GTP hydrolyzed per transport cycle.

23. Selectivity across the nuclear pore Part II. Nucleocytoplasmic transport of RNA RNA Cargo: 1. Messenger RNA (mRNA) transcripts must exit the nucleus to engage the protein translation machinery. 2. Ribosomal (rRNA) and transfer (tRNA) RNAs must exit the nucleus to participate in protein translation. 3. Small nuclear RNAs required for pre-mRNA splicing must exit the nucleus to undergo maturation to small ribonucleoprotein particles (snRNPs) within the cytoplasm. 4. Certain viral RNAs must exit the nucleus for viral replication. Advances in the nuclear protein import field contributed significantly to our current understanding of nucleocytoplasmic RNA transport. Identification of cellular factors that mediate nuclear protein import (soluble importins, insoluble NPC components). Establishment of novel assay systems to directly analyze the movement of biomolecules between the nucleus and the cytoplasm.

24. Microinjection assay for RNA export in Xenopus oocytes 32P-labeled RNA transcript injected into the nucleus Nucleus Incubate at 16oC Longitudinal cross-sectional view of nuclear-specific microinjection Manually dissect into nuclear (N ) and cytoplasmic (C ) fractions. C N Isolate RNA in fractions and analyze RNA species using PAGE and autoradiography. T N C N C RNA of interest Control RNA t0 t0 t0 t2hr t2hr Time (t): T= total RNA injected N= nuclear RNA fraction C = cytoplasmic RNA fraction

25. Microinjection / RNA titration assay in Xenopus oocytes. Purpose: To determine whether different classes of RNAs use the same or different export pathways. Approach: Test whether export of a specific class of RNA is affected by the presence of increasing amounts of an RNA competitor. Results Cold rRNA competitor (pmol) No RNA Competitor 0. 5 2. 5 5.0 N C N C TN C N C N C 32P-rRNA T= total input RNA C=cytoplasmic RNA N= nuclear RNA t = time (min) TN C N C N C N C N C 32P-U1snRNA TN C N C N C N C N C 32P-mRNA t0 t45 t45 t45 t45 Time (minutes): Summary 1. Similar to nuclear protein import, cellular RNA export is a saturable, carrier-mediated, energy dependent process. 2. Competition studies using this assay system indicate that specific factors are required for export of an individual class of cellular RNAs, and that such factors may be limiting. Conversely, nuclear export of the different classes of cellular RNAs may require common or shared factors which are not limiting.

26. Yeast cell WT strain at 37oC WT strain at 25oC nucleus cytoplasm Mutant strain at 25oC Mutant strain at 37oC Genetic analysis of nuclear RNA export in budding yeast Yeast genetic approaches facilitated the identification and functional characterization of cellular factors that mediate nuclear RNA export. Approaches: i. Development of temperature sensitive (ts ) mutant strains ii. Synthetic lethality screens for transport-defective strains. Example approach i. Incubate yeast cells with a chemical mutagen, and screen for mutants defective in mRNA export at the non-permissive temperature (37oC) using fluorescent RNA in situ hybridization (FISH). FISH analysis of poly A(+) RNA localization in wild type or temperature sensitive (ts) yeast cells poly A (+) RNA visualized using a FITC-conjugated oligo probe complementary to the poly A tail (i.e. FITC-oligo dT (52)) 25oC permissivetemperature 37oC non-permissive temperature Result Strains defective in mRNA export accumulate poly A(+) RNA in the nucleus at 37oC, but not at 25oC. Cole, et al., 2002.MethodsEnzymol. 351:568-587.

27. Retrovirus Lifecycle

28. 9kb 4kb class HIV-1 Rev-mediated nuclear export as a model system to study RNA export The Rev protein facilitates the cytoplasmic accumulation of unspliced or incompletely spliced HIV RNAs, which encode the viral structural proteins. In the absence of Rev, these RNAs are retained in the nucleus. Thus, Rev function is essential for viral replication. Northern blot of cytoplasmic HIV RNAs mock WT HIV Rev mutant HIV 2kb class

29. ARM Domain Effector Domain RRRRWR LE LPP RLTLD 1aa 116 aa NLS / RNA binding Nuclear Export Signal (NES) Oligomerization Functional domains of the HIV-1 Rev protein LE = Amino acids 78 and 79 of Rev. Note: The mutant Rev M10 protein contains amino acid substitutions in these residues i. in vitro binding assays demonstrated that Rev contains an arginine-rich motif (ARM) which binds, in a sequence-specific manner, to a cis-acting RNA sequence known as the Rev Responsive Element (RRE). The RRE is located in the second intron of unspliced (i.e. gag-pol) or incompletely spliced (i.e. env) viral RNAs. ii. Genetic analysis in mammalian cells identified a second functional domain, a leucine-rich “Effector” domain. Point mutations within its coding sequences abolish Rev function (L78, 79E to D78, A79). This particular Rev mutant, Rev M10, is a trans-dominant negative inhibitor of Rev function. These key observations suggested the Rev Effector domain interacts with a cellular cofactor (s).

30. Rev Model of HIV-1 Rev-Mediated RNA Export Nucleus Rev RRE AAAAA cytoplasm AAAAA Rev RRE AAAAA Rev RRE Rev Responsive Element Putative host factor Rev’s Mechanism of Action: Rev binds directly to the RRE within incompletely spliced viral RNAs (i.egag-pol and env ). The Rev effector domain interacts with cellular factors which mediate RNA export. Rev M10 does not support viral replication and does not promote the cytoplasmic accumulation of RRE-containing viral RNAs. The inability of Rev M10 to exit the nucleus was shown to correlate with its inability to support Rev function. Thus, the Rev effector domain contains a “Nuclear Export Signal” (NES).

31. RNA in situ hybridization assay for studying Rev-mediated RNA export Approach: Mammalian cells are transiently transfected with a plasmid that expresses an RRE-containing HIV RNA (gag-pol) in the absence or presence of a Rev expression plasmid (Rev). The intracellular distribution of these RNAs is analyzed by fluorescent RNA in situ hybridization(FISH) using a Cy3-conjugated oligo probe that is complementary to the RRE RNA. Note: Cy3 is an orange fluorescing cyanine dye that produces an intense red signal easy detected using a rhodamine filter (660nm). Rev RevM10 No DNA HIV gag-pol HIV gag-pol HIV gag-pol + probe + probe + probe + probe Additional experimental approaches that have been developed for analyzing Rev function: 1. HIV-1 or chimeric HIV-based genetic analysis. 2. Transfection assays using an Rev-dependent reporter construct. 3. Oocyte microinjection using recombinant Rev protein or peptides. 4. Yeast-based colorimetric assays using a Rev-dependent reporter construct. Sanchez-Velar et al., 2004. Genes & Devel. 18: 23-34; Meyers and Malim, 1994. Gene s & Devel. 8:1538-1547; Hope, et al., 1990. J. Virol. 91 :1231-1238.

32. Summary RNA export can be viewed as a protein process associated with an RNA cargo. HIV-1 Rev-mediated and certain classes of cellular RNAs require NES- containing proteins as RNA transport cofactors. HIV-1 Rev-mediated and cellular RNA pathways share one or more dedicated components. Several cellular proteins contain leucine-rich NESs: TFIIIA, IkB, PKI Unique NES in the hnRNP A1 protein, the M9 domain, acts as an NLS and an NES.

33. Rev-mediated export Cellular RNA export in Xenopus oocytes: Rev NES injection/ titration experiments Leptomycin B (LMB) Member of the importin-b family of transport receptors Identification of a cellular factor that interacts with the NES: Discovery of the nuclear export receptor CRM 1 Evidence : 1. Leptomycin B (LMB), a lipophilic antibiotic, was shown to block Rev or Rev- dependent RNA export in HeLa cells. 2. LMB had been previously shown to be toxic to fission yeast. The molecular target of LMB is the CRM1 gene; mutants resistant to LMB map to that gene. 3. Immunoprecipitation studies revealed that human CRM1, a member of the importin-b protein family, interacts directly with NUP 214/CAN. Collective data from mammalian cell-based assays, oocyte microinjection studies, and genetic screens in yeast demonstrated CRM1 is the nuclear export receptor (NER) for Rev. Additional studies showed CRM1 is the NER for cellular and viral proteins that contain a leucine-rich NES; nuclear export of these proteins is inhibited by LMB.

34. Cis-Acting Export Signals on Proteins and RNA Dreyfuss, et al., 2002. Nat. Rev. Mol. Cell. Biol. 3:195-205 Maniatis and Reed, 2002. Nature 416: 499-506.

35. TAP / p15 heterodimer CTE Constitutive Transport Element Constitutive Transport Element (CTE)-mediated nuclear RNA export CTE The CTE is a cis-acting RNA element located in the 3’UTR of Mason-Pfizer Monkey Virus RNA (MPMV) TAP p15 AAAAA Nucleus cytoplasm CTE p15 AAAAA CTE TAP p15 AAAAA Mechanism of Action: TAP/ p15 binds directly to the CTE to promote nuclear export of MPMV RNAs. TAP /p15 function requires an interaction with components of the cellular export machinery. Hammarskjold, M.L. (2001). Curr. Top. Microbiol. Immunol. 259: 77-93.

36. mRNA transport factors are recruited to the mRNA during splicing Nascent pre-mRNAs are packaged into hnRNPs. During spliceosome assembly, exons are packaged by non-hnRNP spliceosome components such as SR proteins. After splicing, hnRNP particles remain associated with the introns, which are retained in the nucleus. Partial or mutant pre-mRNAs unable to enter the splicing pathway are also retained in packaged hnRNPs. In contrast, the spliced mRNP is targeted for export by factors recruited during splicing, in particular the export factor Aly/REF. The spliced mRNA is exported by a conserved machinery composed of non-hnRNP factors such as TAP/p15, hGle1, hGle 2, and hDbp5. Pre-mRNA splicing coupled export model Adapted from Reed , R. and Magni, K. (2001). Nat Cell Biol. 3 :E201-4.

37. Adapted from Conti, E. and Izaurralde, E. (2001). Curr. Opin. Cell. Biol. 13: 310-320.

38. Nucleocytoplasmic Transport : Regulation Eukaryotic cells control many biological processes by regulating the movement of macromolecules in and out of the nucleus. Similar to other steps in gene expression, nucleocytoplasmic transport may be subject to positive or negative regulation. 1. To regulate a given response 2. To communicate cytoplasmic and nuclear events allowing cells to respond to environmental changes or cell cycle position 3. To generate a more robust molecular switch or affect its nature (i.e on / off) Two important issues concerning regulated nuclear translocation 1. Steady-State Localization of a Cellular Protein. The steady-state distribution of a protein is determined by its relative rate of nuclear import and export. Changes in the rate of import or export can lead to a shift in the steady-state localization of the protein. Since both import and export can be regulated, it is essential to experimentally observe import in the absence of export (or vice versa ) to determine which rate is subject to regulation.

39. 2. Protein Shuttling Shuttling proteins move continuously between the nucleus and the cytoplasm. The steady-state localization of a shuttling protein reflects a dynamic process of nuclear entry and exit. To date, two classes of shuttling proteins have been identified: “Carrier proteins” - Proteins associated with hnRNP particles, presumably are exported to the cytoplasm bound to RNA and then re-imported into the nucleus for another round of transport. HIV-1 Rev is an example. “Non-Carrier proteins”- Proteins that use shuttling as a way of regulating their activity. These proteins would be localized in the cytoplasm at steady-state because their nuclear export is more efficient than nuclear import. Their nuclear export is blocked under conditions in which their activities are required in the nucleus. Thus, protein shuttling as a mode of regulation may be important for coordinating nuclear and cytoplasmic events. Additionally, it offers a simple, reversible, and rapid mechanism for regulating nuclear activity.

40. How do you determine whether a protein shuttles between the nucleus and the cytoplasm: A heterokaryon assay Schematic representation of approaches for detecting nucleoplasmic shuttling of proteins. (A) Migration of fluorescently labeled (FITC) or epitope-tagged nuclear proteins in interspecies heterokaryons. (B) Antigen-mediated nuclear accumulation of antibodies injected into the cytosol. In both types of experiments, cyclohexamide (CX) was used to distinguish the migration of pre-existing proteins from the contribution of newly synthesized proteins. Nuclear protein export in this assay is sensitive to LMB treatment.

41. Possible steps in nuclear translocation that could be targets for regulation 1. The binding of the cargo to an import or export receptor. 2. The activity of the soluble transport machinery. 3. The NPC can be modified to affect its transport properties. 4. The cargo-receptor complex can be tethered to an insoluble component, thereby preventing it from binding to the NPC. Regulation of Cargo-Receptor Complex Formation i. Phosphorylation: Regulate the affinity of a cargo for its transport receptor, thus regulating the sub-cellular localization of the cargo. ii. Intermolecular Association: Regulate cargo interactions with accessory adapter proteins. Note: These modes of regulation are not mutually exclusive because they can be used sequentially to regulate nuclear localization. These mechanisms can enhance or decrease the affinity of a cargo for its receptor (i.e. have a positive or negative effect).

42. P P NLS Nuclear Factor of Activated T-Cells (NF-AT): A Cellular Factor Whose Function is Regulated at the Level of Nucleocytoplasmic Transport Mode of Regulation: Phosphorylation and molecular associations affect its sub-cellular localization by modulating its rate of nuclear import and export. NF-AT Stimulation of T-cell receptors leads to activation of signal transduction pathways which induce cytokines and cell surface molecule gene express- ion. T-cell receptor stimulation also causes an elevation in cytosolic Ca2+ levels, which activates the phosphatase Calcineurin . Active calcineurin leads to dephosphorylation of NF-AT. P N C NLS NES Dephosphorylation of NF-AT results in formation of a dephosphorylated NF-AT/ calcineurin complex. Once formed, the complex translocates into the nucleus and facilitates transcription of genes required for T-cell specific activation. Phosphorylation of NF-AT inhibits its nuclear import rate by inducing an intra-molecular conformational change that makes the NLS inaccessible for receptor binding. Calcineurin maintains NF-AT in its unphosphorylated form, leading to a decrease in its rate of nuclear export. Direct binding and masking of the NF-AT NES by calcineurin inhibits its association with export receptors, leading to nuclear accumulation of NF-AT. This model provides a simple explanation for the observation that NF-AT/calcineurin is imported to the nucleus as a complex. Kaffman and O’Shea (1999.Annu. Rev.Cell.Dev. Biol. 15: 291-339.

43. Transport of small nuclear RNAs (snRNAs) between the nucleus and the cytoplasm Regulation by localization snRNAs (U1, U2, etc.) are transcribed in the nucleus and exported to the cytoplasm in a CRM1-dependent fashion. In the cytoplasm, they associate with SM proteins to form small nuclear ribonucleoprotein particles (snRNPs). The assembled snRNPs are then imported back into the nucleus, the site of their function.

44. Regulation of nuclear import of transcription factors A B A. The transcription factor NF-B is maintained as an inactive complex with IB, which masks its NLS in the cytoplasm. In response to appropriate extracellular signals, IB is phosphorylated and degraded by proteolysis, allowing the import of NF-B to the nucleus. B. In contrast, the yeast transcription factor SW15 is maintained in the cytoplasm by phosphorylation in the vicinity of its NLS. Regulated dephosphorylation exposes the NLS and allows SW15 to be transported into the nucleus at the appropriate stage of the cell cycle.