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Nuclear export signal

A nuclear export signal (NES) is a short, typically leucine-rich amino acid sequence, usually 8–15 residues long, that serves as a targeting motif to direct the export of proteins and certain ribonucleoprotein complexes from the nucleus to the cytoplasm via nuclear pore complexes.^[1] These signals are recognized by specific nuclear export receptors, known as exportins, which facilitate the selective and energy-dependent transport across the nuclear envelope, ensuring proper spatiotemporal regulation of cellular processes.^[2] The consensus sequence of classical NESs, often classified as CRM1-dependent or leucine-rich NESs (LR-NESs), follows patterns such as Φ-X₂₋₃-Φ-X₂₋₃-Φ-X-Φ (where Φ represents hydrophobic residues like leucine, valine, isoleucine, phenylalanine, or methionine, and X is any amino acid), though structural variations exist that allow flexibility in binding.^[3] Exportins, particularly CRM1 (also called exportin 1), bind NES-containing cargoes in the nucleus in complex with Ran-GTP, a GTP-bound form of the Ran GTPase that is enriched in the nucleus due to its asymmetric distribution across the nuclear envelope; this interaction promotes translocation through the pore, followed by cargo release in the cytoplasm upon GTP hydrolysis to Ran-GDP.^[2] Non-classical NESs, which may lack the strict leucine-rich motif, are recognized by other exportins like exportin-t for tRNAs or exportin-5 for microRNAs. Classical NESs, often via adaptor proteins bearing the signal, also facilitate export of ribonucleoprotein complexes such as ribosomal subunits.^[1] NES-mediated export plays a critical role in cellular homeostasis by controlling the localization of transcription factors, signaling proteins, and viral components, thereby influencing gene expression, signal transduction, and pathogenesis.^[3] Dysregulation of NES function, such as through mutations or overexpression of CRM1, has been implicated in diseases including cancers, where altered nuclear-cytoplasmic shuttling of tumor suppressors like p53 disrupts normal cellular responses.^[4] Databases like NESdb catalog over 400 experimentally validated NESs from CRM1 cargoes (as of 2021), aiding in the prediction and analysis of these signals through sequence and structural studies.^[5]

Introduction

Definition and Overview

A nuclear export signal (NES) is a short peptide sequence, typically 8–15 amino acids in length, embedded within cargo proteins that mediates their active transport from the nucleus to the cytoplasm via nuclear pore complexes (NPCs).^[3] These signals enable the selective shuttling of proteins and associated RNA cargoes across the nuclear envelope, ensuring balanced nucleocytoplasmic distribution that is vital for cellular homeostasis and function.^[3] NESs function in opposition to nuclear localization signals (NLSs), which direct protein import into the nucleus; while both signals exploit the bidirectional permeability of NPCs, NESs drive outward trafficking to regulate gene expression, signal transduction, and stress responses.^[3] The concept of NES was first established in 1995 through independent studies identifying functional export motifs in the HIV-1 Rev protein^[6] and the cAMP-dependent protein kinase inhibitor (PKIα).^[7] At their core, NESs feature a pattern of spaced hydrophobic residues, often leucines, that facilitate recognition and binding by export receptors such as CRM1 (also known as exportin 1).^[8]^[4]

Biological Importance

Nuclear export signals (NES) play a pivotal role in gene regulation by facilitating the export of transcription factors from the nucleus, thereby deactivating their transcriptional activity and preventing prolonged gene expression in response to stimuli. This shuttling mechanism allows for precise control over transcription, as NES-mediated export ensures that factors return to the cytoplasm after their nuclear function, maintaining balanced gene expression levels. Similarly, NES enable the export of mRNA-binding proteins, which influences post-transcriptional processes such as mRNA stability and translation efficiency in the cytoplasm.^[9]^[10] In signaling pathways, NES are essential for the rapid nucleocytoplasmic shuttling of proteins like kinases and repressors, enabling cells to respond dynamically to external cues such as stress or hormones. This export process terminates nuclear signaling events, preventing aberrant activation and ensuring signal transduction fidelity. For instance, NES-dependent export silences pathways like those involving STAT proteins after stimulation, restoring cellular equilibrium.^[9]^[11]^[10] NES contribute significantly to RNA export by being present in adaptor proteins that mediate the formation and translocation of ribonucleoprotein complexes, including those for mRNA and rRNA. These signals interact with export receptors like CRM1 to facilitate the directed movement of RNAs from the nucleus to the cytoplasm, ensuring proper gene expression and ribosome biogenesis. Dysregulation of NES function can lead to nuclear accumulation of proteins, disrupting cellular homeostasis and impairing processes such as proliferation, differentiation, and apoptosis.^[12]^[13]^[14] The presence of NES across eukaryotic organisms underscores their evolutionary conservation, reflecting a fundamental mechanism for nuclear-cytoplasmic compartmentalization that has been preserved to support essential cellular functions. This conservation highlights the indispensable role of NES in maintaining compartmentalized processes from yeast to humans. Viruses, such as HIV, exploit conserved NES pathways, like that of the Rev protein, to export their RNAs and hijack host machinery.^[15]^[16]^[17]^[18]

Structure and Motifs

Classical Leucine-Rich NES

The classical leucine-rich nuclear export signal (NES) is characterized by a consensus sequence consisting of a hydrophobic core pattern Φ-X_{2-3}-Φ-X_{2-3}-Φ-X-Φ, where Φ represents leucine (L), isoleucine (I), valine (V), methionine (M), or phenylalanine (F), and X denotes any amino acid residue.^[19] This motif is typically approximately 10 residues in length and serves as the primary recognition element for the exportin CRM1 (also known as XPO1).^[17] The key structural features of this NES involve four conserved hydrophobic residues positioned at specific intervals relative to spacer regions: typically at positions 1, 4, 7, and 10 within the 10-residue span.^[20] These positions form a critical scaffold that enables interaction with the hydrophobic groove on CRM1. In the unbound state, classical NES sequences are frequently located within intrinsically disordered regions of proteins, providing the necessary flexibility for recognition and binding.^[3] Upon engagement with CRM1, the NES adopts an α-helical conformation, which stabilizes the cargo-exportin complex.^[21] Experimental validation of the classical NES has been established through mutagenesis studies, where substitution of the key hydrophobic leucines (or equivalent residues) with alanines abolishes nuclear export activity, as demonstrated in reporter assays using proteins like the protein kinase A inhibitor (PKI).^[22] The seminal identification of this motif in PKI highlighted its role in rapid nuclear extrusion.^[22] In the Eukaryotic Linear Motif (ELM) resource, this pattern is designated as the TRG_NES_CRM1_1 motif.^[23]

Non-Classical NES

Non-classical nuclear export signals (NES) are protein sequence motifs that facilitate nuclear export through CRM1-dependent mechanisms with non-canonical motifs or via alternative exportin-mediated pathways, often lacking the hydrophobic leucine-rich consensus and instead relying on charged, phosphorylated, or structural features tailored to specific exportins and cargoes such as those involved in RNA processing. These signals are typically shorter or more variable than classical NES, incorporating elements like phospho-serines or dsRNA-binding domains to enable recognition by alternative receptors including exportin-5 (and its yeast homolog Msn5) or exportin-t.^[24]^[25] A prominent example is the NES in the transcription factor Pho4, which mediates phosphate-dependent export in response to environmental cues. This 35-residue motif (residues 100–134) within Pho4's intrinsically disordered region is enriched in small polar and hydrophobic residues, adopting an extended zig-zagging conformation with three 90° turns upon binding. Phosphorylation at key serines (pS114 and pS128) by kinases like PKA is essential, aligning these sites 30 Å apart to engage specific pockets on the exportin Msn5, forming a high-affinity interface (K_D ≈ 25 nM) spanning 1256.9 Å² across Msn5's concave HEAT repeat surface (h8–h18). A 2025 cryo-EM structure at 3.0–3.2 Å resolution reveals this dynamic assembly with RanGTP, highlighting Msn5's solenoid flexibility and the motif's deviation from leucine-rich patterns.^[24]^[26] Another key instance involves the phosphorylated adaptor for RNA export (PHAX), which directs small nuclear RNAs (snRNAs) via a variant NES that integrates serine phosphorylation for complex stability. PHAX's NES (residues 117–136) features a helical structure binding CRM1's cleft, but deviates from classical motifs with a conserved glutamine (Q127) at the Φ0 position instead of a hydrophobic residue, potentially reducing basal affinity and requiring regulatory inputs. Phosphorylation at up to five serine/threonine sites (e.g., in the ST2 region, residues 64–76) by CK2 enhances electrostatic interactions with RanGTP's basic surface, promoting synergistic assembly of the PHAX-CBC-snRNA subcomplex with CRM1-RanGTP. A 2025 cryo-EM structure at 2.45 Å resolution elucidates this quaternary complex, showing PHAX bridging capped RNA and exportin components while folding dependently on all partners to reinforce cap recognition and export specificity.^[27]^[28] In cases like tRNA export, non-classical signals often manifest as structural determinants rather than linear sequences; exportin-t recognizes mature tRNA conformations directly, independent of CRM1, while associated proteins such as eukaryotic elongation factor 1A (eEF1A) rely on exportin-5 binding via aminoacylated tRNA adaptors involving eEF1A's GTP- and tRNA-binding domains. Similarly, exportin-5 exports double-stranded RNA-binding proteins (dsRBPs) like PKR and ILF2 through their dsRNA-binding domains acting as structural export signals, enhanced by RanGTP without a discernible linear NES. These mechanisms underscore how non-classical NES prioritize cargo-specific recognition, often bypassing CRM1 for dedicated pathways in RNA biogenesis.^[29]^[25]

Export Mechanism

Cargo Recognition by Exportins

Cargo recognition by exportins begins with the specific interaction between the nuclear export signal (NES) on cargo proteins and the exportin receptor, primarily CRM1 (also known as XPO1), which facilitates the export of classical NES-bearing cargoes. CRM1 binds to the hydrophobic residues within the NES through a central hydrophobic groove formed by its HEAT-repeat structure, enabling selective recognition of leucine-rich motifs.^[30] In the binding interface, the key leucine residues of the NES insert into a series of hydrophobic pockets (typically four) along the CRM1 groove, with the peptide adopting a predominantly extended conformation that can include helical elements for optimal fit. This interaction is characterized by moderate affinity in the absence of cofactors, but it is significantly enhanced by the binding of Ran-GTP to a distinct site on CRM1, which allosterically stabilizes the NES association and promotes complex assembly.^[21]^[31] The resulting export complex forms a quaternary structure comprising the NES-linked cargo, CRM1, and Ran-GTP, with a stoichiometry of 1:1:1, ensuring efficient packaging for translocation. Crystal structures from pre-2020 studies, such as those resolved for various NES peptides bound to CRM1-RanGTP, have elucidated this architecture, revealing how the NES leucines anchor into the groove while the cargo remains flexibly tethered.^[31]^[21] CRM1 specifically recognizes NES sequences approximately 10 residues long, characterized by spaced hydrophobic elements, whereas non-classical NES cargoes, such as precursor microRNAs (pre-miRNAs), are handled by dedicated exportins like exportin-5 (XPO5), which binds structured dsRNA hairpins rather than linear motifs. Recent cryo-EM structures from 2025, including those of CRM1 complexes with viral or snRNP cargoes, further confirm the helical conformation of certain NES peptides within the binding groove, highlighting conformational adaptability in cargo recognition.^[32]^[33]^[34]

Ran-GTP Dependent Transport

The Ran cycle provides the energy and directionality for nuclear export by establishing a steep concentration gradient of Ran-GTP, which is high in the nucleus due to the chromatin-bound guanine nucleotide exchange factor RCC1 and low in the cytoplasm owing to the GTPase-activating protein RanGAP. This gradient promotes the assembly of the export complex—consisting of the exportin, NES-bearing cargo, and Ran-GTP—within the nucleus, where Ran-GTP binding induces a conformational change in the exportin that stabilizes cargo association.^[35]^[36] In the cytoplasm, RanGAP stimulates GTP hydrolysis on Ran, converting it to Ran-GDP and triggering dissociation of the trimeric complex, thereby releasing the cargo.^[37] This hydrolysis step is essential for complex disassembly and ensures the unidirectional flow of transport cycles.^[35] The translocation of the export complex through the nuclear pore complex (NPC) occurs via transient, multivalent interactions between hydrophobic patches on the exportin surface and phenylalanine-glycine (FG) repeats of FG-nucleoporins lining the NPC channel. These interactions facilitate rapid, energy-dependent passage across the permeability barrier, with the process being bidirectional in principle but strongly biased toward export due to the Ran-GTP gradient, which favors complex stability in the nucleus and disassembly in the cytoplasm.^[36] Recent three-dimensional MINFLUX microscopy studies have revealed that import and export pathways overlap within the NPC, with NES-dependent export complexes traversing shared central regions of the pore scaffold, underscoring the NPC's efficient multiplexing of traffic directions.^[38]^[39] Upon reaching the cytoplasmic face of the NPC, the hydrolysis of Ran-GTP to Ran-GDP by RanGAP, often in concert with Ran-binding protein 1 (RanBP1), fully dissociates the exportin from both Ran and the cargo, enabling cargo release into the cytoplasm. The exportin and Ran-GDP are then recycled back to the nucleus via distinct mechanisms, including nuclear import of Ran-GDP by nuclear transport factor 2 (NTF2), which sustains the Ran gradient and allows multiple rounds of export.^[37]^[40] The primary exportin mediating NES-dependent transport is CRM1 (also known as XPO1).^[41] The NES contributes to export directionality by enhancing the bias toward net outward movement, as the affinity of NES for exportins correlates with the stability of the nuclear ternary complex under the Ran-GTP gradient. Transport efficiency through individual NPCs is regulated by this NES affinity, with rates typically on the order of several molecules per second per NPC for NES-bearing complexes, reflecting the balance between binding kinetics and NPC saturation.^[42]^[38]

Regulation

Masking and Exposure

The activity of nuclear export signals (NES) is often regulated through physical masking, where the NES sequence is concealed within the three-dimensional structure of the protein or by interactions with binding partners, thereby preventing recognition by exportins such as CRM1. One common masking mechanism involves burial of the NES within folded protein domains, which sterically hinders access to the export machinery; for instance, in the tumor suppressor p53, the leucine-rich NES located in the tetramerization domain is masked in the tetrameric form, retaining p53 in the nucleus until conditions favor disassembly. Another mechanism entails binding to nuclear retention factors that occlude the NES; in the transcription factor STAT1, association with DNA masks the NES, inhibiting export and promoting transcriptional activity at target sites. These strategies ensure that NES-dependent export occurs only under appropriate cellular contexts.^[43]^[44] Exposure of masked NES typically arises from triggers such as proteolysis, which cleaves inhibitory domains to reveal the signal, conformational rearrangements that reposition the NES for accessibility, or dissociation of binding partners that previously shielded it. For example, in the Nrf2 transcription factor, heterodimerization with small Maf proteins masks the NES in the zipper motif, but stimulus-induced dissociation unmasks it, facilitating rapid nuclear exit. In p53, a shift from tetrameric to monomeric conformation exposes the NES, enabling CRM1-mediated export. Such unmasking events are tightly coupled to cellular signals, allowing precise spatiotemporal control of protein localization.^[45]^[43] This masking and exposure dynamic critically prevents premature nuclear export, maintaining proteins in the nucleus for their functions until specific cues demand relocation; in signaling pathways, stimulus-induced unmasking enables swift cytoplasmic redeployment, amplifying responses like stress adaptation or immune activation. For instance, in NF-κB signaling, interactions with the inhibitor IκB contribute to regulated NES accessibility within the complex, ensuring export only post-nuclear activity to terminate transcription. These mechanisms underscore the role of structural control in NES regulation, complementary to other forms like phosphorylation.^[46]^[47] Experimental validation of masking and exposure often employs fluorescence microscopy to monitor nucleocytoplasmic shuttling in live cells, where disruption of masking interactions—via mutations or binding partner knockdown—results in altered localization patterns that confirm NES functionality. For example, tagging proteins with fluorescent reporters like GFP allows real-time tracking of export kinetics upon induced unmasking, revealing how conformational changes or dissociations accelerate shuttling rates by 2- to 5-fold in responsive systems. Heterokaryon fusion assays complement this by quantifying redistribution between nuclei, but microscopy provides direct visualization of dynamic exposure events.^[48]^[49]

Post-Translational Modifications

Post-translational modifications (PTMs) play a crucial role in regulating the activity and accessibility of nuclear export signals (NESs), thereby controlling the nucleocytoplasmic shuttling of proteins. Among these, phosphorylation of serine or threonine residues adjacent to the NES core often inhibits binding to the export receptor CRM1 (also known as exportin 1), preventing nuclear export and promoting nuclear retention. For instance, in hypoxia-inducible factor-1α (HIF-1α), mitogen-activated protein kinase (MAPK) phosphorylates serine residues 641 and 643 within the NES-containing MAPK target domain, which disrupts the interaction between the NES and CRM1, leading to HIF-1α nuclear accumulation and enhanced transcriptional activity under hypoxic conditions.^[50] Conversely, dephosphorylation by nuclear phosphatases can reverse this inhibition; in the case of extracellular signal-regulated kinases (ERKs, members of the MAPK family), dephosphorylation facilitates binding to NES-containing MEK1/2, enabling CRM1-dependent nuclear export and cytoplasmic reactivation.^[51] Specific kinases, such as cyclin-dependent kinases (CDKs), target phosphorylation sites flanking NES motifs to modulate export dynamics. CDK phosphorylation of sites within an NLS-NES module in cell-cycle regulators like Mcm3 promotes net nuclear export during G1 phase, as demonstrated by phosphomimetic mutations that enhance export and impair replication initiation when mislocalized.^[52] This reversibility is maintained by phosphatases, which remove phosphate groups to restore NES functionality and allow dynamic regulation of protein localization in response to cellular signals. Beyond phosphorylation, other PTMs fine-tune NES function by altering charge, conformation, or receptor affinity. Sumoylation, the covalent attachment of small ubiquitin-like modifier (SUMO) proteins, can enhance NES-mediated export; in p53, SUMOylation at lysine residues promotes its interaction with CRM1, facilitating nuclear export and cytoplasmic relocation to modulate stress responses.^[53] In contrast, cysteine oxidation inhibits NES recognition by CRM1; in the yeast transcription factor Yap1p, oxidative modification of flanking cysteine residues masks the NES, blocking CRM1 binding and causing nuclear accumulation under oxidative stress conditions.^[54] These modifications generally alter electrostatic interactions or induce conformational changes that either occlude or expose the hydrophobic NES core for receptor binding. A notable example of phosphorylation-dependent NES activation occurs in non-classical motifs, where phosphate groups directly coordinate with exportins. In the yeast phosphate-sensing transcription factor Pho4, phosphorylation at serines 114 and 128 within a 35-residue NES enables high-affinity binding to the exportin Msn5 (K_D ≈ 25 nM), as revealed by a 2025 cryogenic-electron microscopy structure showing phospho-serine coordination with conserved arginine and histidine residues in Msn5's binding pocket; dephosphorylation weakens this interaction (K_D ≈ 2.4 µM), retaining Pho4 in the nucleus to activate phosphate-responsive genes.^[24] Thus, PTMs provide a versatile mechanism for signal-responsive control of NES accessibility, distinct from non-covalent masking strategies.

Examples

In Viral Proteins

Nuclear export signals (NES) in viral proteins enable viruses to exploit the host cell's CRM1-dependent export machinery, facilitating the relocation of viral components from the nucleus to the cytoplasm to support replication and evade host defenses. A prominent example is the HIV-1 Rev protein, which contains a classical leucine-rich NES (residues 73-83) that binds directly to the exportin CRM1, allowing the export of unspliced and partially spliced viral mRNAs bound to the Rev response element (RRE). This NES-mediated process is essential for the cytoplasmic translation of structural proteins like Gag and Env, bypassing the host's splicing-dependent mRNA export restrictions. Although Rev's RNA-binding domain is arginine-rich, its NES functions as a standard hydrophobic leucine-based motif, distinct from arginine-rich variants in other contexts. In adenoviruses, the E1B-55K protein harbors a CRM1-dependent NES that promotes the nuclear export of the E1B-p53 complex, thereby inhibiting p53's transcriptional activity and facilitating viral oncogenesis. This export mechanism relocalizes p53 to cytoplasmic aggresomes for degradation, suppressing host antiviral responses during infection. Similarly, in influenza A virus, the NS2 (nuclear export protein, NEP) contains a conserved N-terminal NES (residues 12-21) that recruits CRM1 and acts as an adaptor to bridge the matrix protein M1-associated viral ribonucleoproteins (vRNPs), enabling their coordinated nuclear export and relocation to the cytoplasm for virion assembly. Viruses often incorporate multiple NES motifs within polyproteins to ensure synchronized export of viral complexes, as seen in retroviruses like Rous sarcoma virus, where the Gag polyprotein's p10 domain NES facilitates the nuclear egress of Gag and associated genomic RNA, coordinating particle assembly. This strategy allows viruses to hijack and overload the host CRM1 pathway, evading regulatory checkpoints such as phosphorylation-dependent masking of cellular NES. In foamy viruses, a similar N-terminal NES in the Gag polyprotein is required for efficient nuclear export and subsequent viral propagation. These NES elements are critical for viral gene expression and infectivity; for instance, mutations in the HIV-1 Rev NES disrupt mRNA export, severely impairing late-stage virus production and abolishing replication in cell culture. Likewise, alterations in the influenza NS2 NES or RSV Gag p10 NES lead to nuclear retention of vRNPs or polyproteins, resulting in defective virion assembly and loss of infectivity. Recent post-2020 studies have shown that the SARS-CoV-2 accessory protein ORF6 binds the Rae1-Nup98 complex at the nuclear pore, disrupting nucleocytoplasmic transport pathways, including CRM1-mediated nuclear export, thereby inhibiting host mRNA export and interferon signaling to promote viral replication.^[55] This interference, more potent in SARS-CoV-2 than in SARS-CoV-1, underscores ORF6's contribution to pathogenesis through targeted subversion of nucleocytoplasmic transport.

In Cellular Proteins

Nuclear export signals (NES) are integral to the function of numerous cellular proteins, enabling their shuttling from the nucleus to the cytoplasm to regulate diverse processes such as signaling, metabolism, and stress responses. Bioinformatic predictions suggest that over 1,000 human proteins contain potential NES motifs, with experimental validation confirming their presence in hundreds of cases across functional categories including transcription factors, kinases, and metabolic enzymes.^[8] For instance, signal transducer and activator of transcription (STAT) family members, such as STAT1 and STAT3, utilize NES to terminate nuclear signaling after cytokine stimulation, facilitating dephosphorylation and recycling in the cytoplasm to prevent prolonged transcriptional activity.^[56] Similarly, metabolic regulators like the pyruvate kinase M2 isoform incorporate NES to modulate nuclear-cytoplasmic distribution in response to glycolytic demands.^[3] A seminal example of NES in cellular proteins is the protein kinase inhibitor (PKI), the first non-viral NES identified, which contains a classical leucine-rich motif that binds CRM1 to actively export the complex of PKI with protein kinase A (PKA) catalytic subunit from the nucleus. This export mechanism inhibits PKA activity in the cytoplasm, preventing ectopic nuclear signaling and maintaining spatial control over cAMP-dependent pathways.^[57] The NES in PKI, spanning residues 24-37 (LALKLAGLDI), exemplifies how such signals ensure rapid, energy-dependent translocation, as demonstrated by microinjection assays showing net extrusion within minutes. Survivin, an inhibitor of apoptosis protein (IAP) family member, relies on its NES (residues 80-88, LPPLP) for dynamic nucleocytoplasmic shuttling that balances its dual roles in mitosis and cell survival. During interphase, CRM1-mediated export prevents nuclear accumulation of survivin, thereby suppressing its anti-apoptotic function and sensitizing cells to stress-induced death; mutation of this NES abolishes export, leading to persistent nuclear localization and loss of apoptosis regulation without affecting mitotic chromosome passenger complex assembly.^[58] In mitosis, transient nuclear retention allows survivin to localize to kinetochores, highlighting NES as a regulatory switch. Nuclear actin, a monomeric form of the cytoskeletal protein, incorporates two functional NES motifs (NES1 at residues 170-181 and NES2 at 211-222) that facilitate its export via Exportin 6, preventing excess accumulation that could disrupt chromatin dynamics.^[59] This export is crucial for recycling actin after its role in nuclear processes, such as binding to chromatin-remodeling complexes like INO80 and BAF to facilitate ATP-dependent nucleosome repositioning during transcription and DNA repair.^[60] Dysregulation of actin NES leads to nuclear retention, impairing remodeling efficiency and cellular homeostasis.^[61] Transcription factors like NF-E2-related factor 2 (Nrf2) employ an NES in their Neh5 domain (residues 175-186, LLSIPELQCLNI) to control antioxidant responses by enabling post-activation export from the nucleus.^[62] Upon oxidative stress, Nrf2 translocates to the nucleus to bind antioxidant response elements (ARE) and induce protective genes like heme oxygenase-1; subsequent NES-dependent export, insensitive to redox changes but modulated by Keap1, terminates this response to avoid overactivation. This relocation exemplifies how NES in transcription factors fine-tune temporal gene expression for adaptive cellular defense.

Biological Roles and Disease Implications

Cellular Functions

Nuclear export signals (NES) play crucial roles in various physiological processes by facilitating the relocation of regulatory proteins from the nucleus to the cytoplasm, thereby modulating their activity and availability for downstream functions. In gene expression control, NES-mediated export of circadian clock proteins such as PERIOD (PER) and BMAL1 fine-tunes transcriptional rhythms. For instance, mammalian PER1 contains a leucine-rich NES (amino acids 485–495) that promotes its cytoplasmic accumulation, preventing premature nuclear re-entry and ensuring oscillatory gene expression patterns essential for the circadian clock.^[63] Similarly, BMAL1 shuttling via its NES motifs regulates CLOCK/BMAL1 heterodimer transactivation of E-box-containing genes like Per and Cry, while also controlling heterodimer degradation through ubiquitin-proteasome pathways during active transcription phases.^[64] In the stress response, NES enables the timely relocation of heat shock factors (HSFs) to the cytoplasm post-stress, allowing recovery and preventing prolonged transcriptional activation. Heat shock factor 1 (HSF1), the master regulator of the heat shock response, undergoes CRM1-dependent nuclear export mediated by its NES following stress resolution; inhibition of this export with leptomycin B reverses HSF1 cytoplasmic sequestration by 14-3-3ε, highlighting NES's role in terminating chaperone gene transcription like Hsp70.^[65] This relocation supports the translation of stress-induced proteins in the cytoplasm, maintaining cellular proteostasis. During the cell cycle, NES ensures precise spatiotemporal localization of key regulators like survivin, which is essential for mitotic progression. Survivin's NES, recognized by CRM1, drives its nuclear export to tether the chromosomal passenger complex to mitotic structures; homodimerization antagonizes this export, balancing survivin's nuclear and cytoplasmic pools to promote proper chromosome segregation and cytokinesis.^[66] Disruption of NES function impairs survivin's relocation, leading to mitotic defects. In RNA processing, NES in export adaptors such as TAP (also known as NXF1) facilitates bulk mRNA export through nuclear pores. TAP's novel NES, distinct from classical CRM1 pathways, supports its shuttling and binding to processed mRNAs via the constitutive transport element, enabling efficient nucleocytoplasmic transport of cellular and viral transcripts without relying on splicing.^[67] NES-mediated shuttling also contributes to embryonic development by regulating signaling pathways like Wnt/β-catenin. Although β-catenin lacks a classical NES, its nuclear export is facilitated by associated factors, allowing dynamic retention and release in the nucleus; Twa1/Gid8 acts as a retention factor that stabilizes nuclear β-catenin during Wnt activation, ensuring proper transcriptional control of developmental genes in dorsal-ventral patterning.^[68] For example, the protein kinase inhibitor (PKI) exemplifies classical NES function in shuttling cAMP-dependent protein kinase, influencing developmental signaling.^[1]

Role in Pathologies

Dysregulation of nuclear export signals (NES) plays a critical role in cancer pathogenesis by enabling the cytoplasmic retention or enhanced export of oncoproteins, thereby promoting tumor survival and progression. In survivin, an inhibitor of apoptosis protein overexpressed in many cancers, the NES facilitates CRM1-mediated nuclear export, which is essential for its anti-apoptotic function and resistance to therapy-induced cell death. Mutation or inhibition of this NES leads to nuclear accumulation of survivin, sensitizing cancer cells to apoptosis, as demonstrated in studies on tumor cell lines where export blockade reduced survivin-mediated protection.^[69] A 2024 study revealed a noncanonical oncogenic mechanism involving a RAS•GTP:RanGAP1 complex that enhances XPO1-dependent nuclear export of cargo proteins, independent of canonical RAS signaling, thereby driving cytoplasmic mislocalization of tumor suppressors and accelerating tumor growth in RAS-mutant cancers.^[70] In neurodegeneration, defects in NES-mediated shuttling of fragile X mental retardation protein (FMRP) contribute to fragile X syndrome (FXS), the leading genetic cause of intellectual disability, by impairing nuclear export of specific mRNAs essential for synaptic function. FMRP contains a functional NES that enables its nucleocytoplasmic shuttling and regulation of mRNA transport; loss of FMRP due to FMR1 mutations disrupts this process, leading to aberrant dendritic mRNA localization and translational dysregulation in neurons. A missense variant in the FMRP NES has been linked to intellectual disability and behavioral issues, underscoring how NES impairment exacerbates FXS phenotypes.^[71] Recent reviews highlight that FMRP deficiency alters mRNA export pathways, contributing to synaptic deficits and neurodevelopmental abnormalities in FXS. NES in viral proteins facilitate replication by hijacking host nuclear export machinery, with implications for diseases like HIV and adenovirus infections. In HIV-1, the Rev protein's NES binds CRM1 to export unspliced viral mRNAs from the nucleus to the cytoplasm, enabling production of structural proteins and virion assembly critical for replication.^[72] Similarly, the adenovirus E4orf6 protein's NES supports CRM1-dependent export, forming complexes that promote viral mRNA cytoplasmic accumulation and efficient virus production during infection.^[73] Emerging evidence suggests potential roles for SARS-CoV-2 ORF proteins in modulating nuclear export; for instance, ORF6 disrupts bidirectional nucleocytoplasmic transport more potently than its SARS-CoV-1 counterpart, inhibiting host mRNA export and interferon signaling to favor viral replication in COVID-19.^[74] In autoimmunity, dysregulated NES-dependent export of transcription factors like NF-κB contributes to chronic inflammation by prolonging nuclear activity and excessive proinflammatory gene expression. NF-κB complexes are exported via CRM1 using NES in IκBα, which sequesters NF-κB in the cytoplasm under normal conditions; defects in this export lead to sustained nuclear NF-κB, driving cytokine overproduction in autoimmune disorders such as rheumatoid arthritis.^[75]^[76] This dysregulation amplifies immune responses, linking NES alterations to inflammatory pathologies where NF-κB hyperactivity promotes tissue damage and autoantibody production. A 2025 study identified TSPYL5 as a driver of pathological nuclear export in tumors, where it binds G3BP1 to enhance its phosphorylation and nuclear membrane translocation, thereby accelerating RanBP2-mediated SUMOylation and CRM1-dependent export of p53, sequestering it in the cytoplasm and promoting neuroblastoma progression.^[77] This mechanism highlights how NES hyperactivity in stress granule components like G3BP1 can suppress tumor suppressor functions, fostering aggressive tumor growth.

Therapeutic Targeting

CRM1 Inhibitors

CRM1 inhibitors target the nuclear export receptor CRM1 (also known as XPO1) to block the recognition and export of proteins bearing nuclear export signals (NES), thereby accumulating tumor suppressor proteins in the nucleus and promoting apoptosis in cancer cells. These agents have been particularly explored for their therapeutic potential in malignancies characterized by dysregulated nuclear transport. Leptomycin B (LMB), a natural fungal toxin derived from Streptomyces species, was the first identified CRM1 inhibitor. It covalently binds to the NES-binding groove of CRM1 at cysteine residue 528 (Cys528), irreversibly blocking the interaction with NES-bearing cargoes and halting nuclear export. Despite demonstrating potent preclinical anticancer activity at nanomolar concentrations, LMB's clinical development was halted due to severe toxicity, including gastrointestinal distress and bone marrow suppression, limiting its use to experimental settings.^[78] Selinexor (KPT-330), an orally bioavailable selective inhibitor of nuclear export (SINE), represents a more clinically viable CRM1 antagonist. Approved by the FDA in 2019 for use in combination with dexamethasone for relapsed or refractory multiple myeloma after at least four prior therapies, selinexor traps NES-bound cargoes in the nucleus by forming a slowly reversible covalent bond with Cys528 in CRM1's cargo-binding groove.^[79] In December 2020, selinexor received full approval for multiple myeloma after at least one prior therapy in combination with bortezomib and dexamethasone. In 2020, selinexor received accelerated approval for relapsed or refractory diffuse large B-cell lymphoma after at least two prior systemic therapies. This mechanism selectively impairs highly proliferative tumor cells, which often exhibit elevated CRM1 expression and nuclear export activity compared to normal cells, leading to nuclear retention of tumor suppressors like p53 and IκB, and subsequent induction of apoptosis.^[80] In clinical trials, selinexor has shown meaningful efficacy in hematologic malignancies. The phase 2b STORM trial reported an overall response rate of 26% and a median progression-free survival of 3.7 months in triple-class refractory multiple myeloma patients, with improved overall survival in responders.^[81] Common adverse effects include thrombocytopenia (73% incidence), fatigue (73%), and nausea (72%), often manageable with dose adjustments and supportive care.^[81] As of 2025, ongoing trials continue to evaluate its role in solid tumors such as endometrial cancer (e.g., phase 3 XPORT-EC-042 trial showing PFS benefits in TP53 wild-type advanced disease) and pediatric solid tumors including sarcomas, aiming to address unmet needs in advanced settings. Lower-dose and weekly schedules of selinexor have shown improved tolerability while maintaining efficacy in multiple myeloma.^[82]^[83]

Recent Developments

Recent advancements in nuclear export signal (NES) targeting have focused on developing more selective and safer inhibitors beyond traditional covalent binders, with emphasis on reversible CRM1 modulators entering clinical evaluation. The small-molecule LFS-1107 represents a promising next-generation reversible CRM1 inhibitor, demonstrating potent antiproliferative effects in extranodal NK/T cell lymphoma models through non-covalent binding and a clear dissociation profile that may reduce off-target toxicities compared to earlier agents. Building on the foundation of Selinexor, which established CRM1 inhibition as a viable anticancer strategy, LFS-1107 remains in preclinical optimization as of 2025, highlighting improved safety in hematologic malignancies.^[84] Structural biology has accelerated NES-targeted drug design through high-resolution cryo-EM studies of NES-CRM1 complexes. In 2025, cryo-EM structures revealed the atomic details of HIV-1 Rev NES interactions within the CRM1-Ran nuclear export complex, enabling rational design of allosteric inhibitors that disrupt RanGTP-dependent cargo release with sub-nanomolar affinity. These insights have informed the development of conformation-specific binders for enhanced selectivity.^[34]

Resources

Databases

NESbase version 1.0, released in 2004 by researchers at the Technical University of Denmark (DTU) and the University of Copenhagen (UCPH), serves as a foundational curated repository of experimentally validated leucine-rich nuclear export signals (NESs). The database compiles data from over 200 published articles, focusing on NESs not annotated in major protein databases like SWISS-PROT at the time, and includes 75 proteins with 80 distinct NESs confirmed through experimental methods such as mutational analysis and shuttling assays.^[85] Each entry in NESbase provides detailed information on the NES sequence, its position within the parent protein, a conservation score derived from a sequence logo analysis, the associated protein (cross-referenced to SWISS-PROT/TrEMBL accessions), organism of origin, experimental evidence, and literature references. Users can search the database by organism (e.g., Homo sapiens or Saccharomyces cerevisiae) or by motif sequence to retrieve matching entries, facilitating targeted queries for specific biological contexts. Notable examples include the NES from HIV-1 Rev protein (positions 75-84: LQLPPLERLT) and the protein kinase inhibitor (PKI) NES (positions 37-46: LALKLAGLDI), both verified for CRM1-dependent export. Maintenance of NESbase has been limited, with no updates since its 2004 release, though the resource remains accessible via the DTU Health Tech services for download in text format.^[86] NESdb, developed by the Chook Laboratory and first released in 2012, is a comprehensive database of CRM1-dependent NES-containing cargoes, updated in 2021 to include 399 experimentally validated entries from proteins and some RNAs. It catalogs NES sequences, their positions, experimental validation methods (e.g., shuttling assays, CRM1 binding), associated cargoes, organisms, and references, serving as a key resource for nuclear export research. Users can browse or search by cargo name, NES sequence, or organism; examples include NESs from p53 (positions 305-317: LRLRQALGELRL) and HIV-1 Rev. The database is accessible online and supports downloads.^[5]^[87] Complementary to these, the Eukaryotic Linear Motif (ELM) resource catalogs NES motifs under the identifier TRG_NES_CRM1_1, offering a regular expression pattern (L-x[2,3]-[LIVFM]-x[2,3]-L-x-[LI]) for classical leucine-rich NESs recognized by CRM1/exportin-1, while also integrating instances of non-classical variants through curated instances across eukaryotic proteomes. ELM is actively maintained, with updates as of 2024.^[88] These databases support annotation of NESs in newly sequenced proteins and validation of predictions from computational tools, enabling researchers to cross-reference experimental data for functional studies in nuclear transport.

Prediction Tools

Several computational tools have been developed to predict nuclear export signals (NES) in protein sequences, primarily focusing on classical leucine-rich motifs recognized by the CRM1/exportin-1 pathway. These tools employ machine learning approaches, such as neural networks and hidden Markov models, to scan sequences for patterns characterized by hydrophobic residues (especially leucines) spaced at specific intervals, typically following the consensus Φ-X_{2-3}-Φ-X_{2-3}-Φ-X-Φ (where Φ is a hydrophobic residue). Predictions help annotate potential export activity but are probabilistic and require experimental verification. NetNES, a server hosted by DTU Health Tech, uses a combination of neural networks and hidden Markov models to identify leucine-rich NES in eukaryotic proteins. The tool generates scores based on sequence hydrophobicity and residue spacing, reflecting the biophysical properties essential for CRM1 binding; higher scores indicate stronger predicted export potential. Trained on experimentally validated NES, NetNES has been widely applied since its release, demonstrating utility in analyzing viral and cellular proteins.^[89]^[90] NESmapper is a web-based predictor that enhances accuracy by using activity-based profiles derived from machine learning optimization of amino acid properties and positional weights. It maps potential NES while assigning flexibility scores to account for variability in disordered protein regions, where many NES occur, thereby reducing false positives compared to earlier methods. This approach yields improved sensitivity for classical NES, making it suitable for high-throughput screening.^[91] Machine learning models since 2020 have begun incorporating structural predictions, such as from AlphaFold, and post-translational modifications like phosphorylation to refine NES identification in research contexts, often trained on databases like NESdb. However, dedicated NES-specific tools remain limited. Tool predictions are validated through mutagenesis experiments, where key residues are altered to assess export disruption, or nuclear shuttling assays monitoring protein localization. Accuracies for classical NES typically range from 70-80% in benchmark tests against verified datasets, with tools like NESmapper and LocNES outperforming older consensus-based methods in precision and recall.^[91]^[92] A key limitation of these tools is their poor performance on non-classical NES, which deviate from leucine-rich patterns and rely on alternative pathways or structures, often resulting in high false-negative rates. All predictions necessitate experimental confirmation, as sequence-based methods cannot fully capture contextual factors like protein folding or interactions.^[93]

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NESbase 1.0 - DTU Health Tech
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Analysis and prediction of leucine-rich nuclear export signals
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Prediction of leucine-rich nuclear export signal containing proteins ...
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