bims-nucpor 2023-06-11 papers

bims-nucpor

Biomed News

on Nuclear pore complex and nucleoporins in stress, aging and disease

Issue of 2023–06–11
seven papers selected by
Sara Mingu, Johannes Gutenberg University

Cul3 substrate adaptor SPOP targets Nup153 for degradation.
Regulation of FLC nuclear import by coordinated action of the NUP62-subcomplex and importin β SAD2.
A new Karyopherin-β2 binding PY-NLS epitope of HNRNPH2 linked to neurodevelopmental disorders.
Analysis of Bub3 and Nup75 in the Drosophila male germline lineage.
Exploring the relationship between abnormally high expression of NUP205 and the clinicopathological characteristics, immune microenvironment, and prognostic value of lower-grade glioma.
Toxoplasma Gondii Importin α Shows Weak Auto-Inhibition.
Identification and functional characterization of a bipartite nuclear localization signal in ANKRD11.

bioRxiv. 2023 May 30. pii: 2023.05.13.540659. [Epub ahead of print]

Cul3 substrate adaptor SPOP targets Nup153 for degradation.

Joseph Y Ong, Jorge Z Torres.

SPOP is a Cul3 substrate adaptor responsible for degradation of many proteins related to cell growth and proliferation. Because mutation or misregulation of SPOP drives cancer progression, understanding the suite of SPOP substrates is important to understanding regulation of cell proliferation. Here, we identify Nup153, a component of the nuclear basket of the nuclear pore complex, as a novel substrate of SPOP. SPOP and Nup153 bind to each other and colocalize at the nuclear envelope and some nuclear foci in cells. The binding interaction between SPOP and Nup153 is complex and multivalent. Nup153 is ubiquitylated and degraded upon expression of SPOP WT but not its substrate binding-deficient mutant SPOP F102C . Depletion of SPOP via RNAi leads to Nup153 stabilization. Upon loss of SPOP, the nuclear envelope localization of spindle assembly checkpoint protein Mad1, which is tethered to the nuclear envelope by Nup153, is stronger. Altogether, our results demonstrate SPOP regulates Nup153 levels and expands our understanding of the role of SPOP in protein and cellular homeostasis.

DOI: https://doi.org/10.1101/2023.05.13.540659
J Integr Plant Biol. 2023 Jun 06.

Regulation of FLC nuclear import by coordinated action of the NUP62-subcomplex and importin β SAD2.

Gang Chen, Danyun Xu, Qing Liu, Zhichuang Yue, Biao Dai, Shujuan Pan, Yongqiang Chen, Xinhua Feng, Honghong Hu.

  FLC is a central transcriptional repressor that controls flowering time. However, how FLC is imported into the nucleus is unknown. Here, we report that Arabidopsis NUP62, NUP58, and NUP54 composed NUP62-subcomplex modulates FLC nuclear import during floral transition in an importin α-independent manner, via direct interaction. NUP62 recruits FLC to the cytoplasmic filaments and imports it into the nucleus through the NUP62-subcomplex composed central channel. Importin β SAD2, a carrier protein, is critical for FLC nuclear import and flower transition, which facilitates FLC import into the nucleus mainly through the NUP62-subcomplex. Proteomics, RNA-seq, and cell biological analyses indicate that the NUP62-subcomplex mainly mediates the nuclear import of cargos with unconventional nuclear localization sequences (NLSs), such as FLC. Our findings illustrate the mechanisms of the NUP62-subcomplex and SAD2 on FLC nuclear import process and floral transition, and provide insights into the role of NUP62-subcomplex and SAD2 in protein nucleocytoplasmic transport in plants. This article is protected by copyright. All rights reserved.

Keywords:  FLC; flowering time; importin; nuclear import; nucleoporin

DOI:  https://doi.org/10.1111/jipb.13540
Structure. 2023 May 25. pii: S0969-2126(23)00165-X. [Epub ahead of print]

A new Karyopherin-β2 binding PY-NLS epitope of HNRNPH2 linked to neurodevelopmental disorders.

Abner Gonzalez, Hong Joo Kim, Brian D Freibaum, Ho Yee Joyce Fung, Chad A Brautigam, J Paul Taylor, Yuh Min Chook.

  The HNRNPH2 proline-tyrosine nuclear localization signal (PY-NLS) is mutated in HNRNPH2-related X-linked neurodevelopmental disorder, causing the normally nuclear HNRNPH2 to accumulate in the cytoplasm. We solved the cryoelectron microscopy (cryo-EM) structure of Karyopherin-β2/Transportin-1 bound to the HNRNPH2 PY-NLS to understand importin-NLS recognition and disruption in disease. HNRNPH2 206RPGPY210 is a typical R-X2-4-P-Y motif comprising PY-NLS epitopes 2 and 3, followed by an additional Karyopherin-β2-binding epitope, we term epitope 4, at residues 211DRP213; no density is present for PY-NLS epitope 1. Disease variant mutations at epitopes 2-4 impair Karyopherin-β2 binding and cause aberrant cytoplasmic accumulation in cells, emphasizing the role of nuclear import defect in disease. Sequence/structure analysis suggests that strong PY-NLS epitopes 4 are rare and thus far limited to close paralogs of HNRNPH2, HNRNPH1, and HNRNPF. Epitope 4-binidng hotspot Karyopherin-β2 W373 corresponds to close paralog Karyopherin-β2b/Transportin-2 W370, a pathological variant site in neurodevelopmental abnormalities, suggesting that Karyopherin-β2b/Transportin-2-HNRNPH2/H1/F interactions may be compromised in the abnormalities.

Keywords:  HNRNPH1; HNRNPH2; Karyopherin; Neurodevelopmental disorder; Nuclear Import; PY-NLS; Transportin-1; Transportin-2; hnRNP; importin

DOI:  https://doi.org/10.1016/j.str.2023.05.010
Cells Dev. 2023 Jun 05. pii: S2667-2901(23)00039-6. [Epub ahead of print] 203863

Analysis of Bub3 and Nup75 in the Drosophila male germline lineage.

Kerem Yildirim, Patrick van Nierop Y Sanchez, Ingrid Lohmann.

  Extensive communication at the stem cell-niche interface and asymmetric stem cell division is key for the homeostasis of the Drosophila male germline stem cell system. To improve our understanding of these processes, we analysed the function of the mitotic checkpoint complex (MCC) component Bub3 and the nucleoporin Nup75, a component of the nuclear pore complex realizing the transport of signalling effector molecules to the nucleus, in the Drosophila testis. By lineage-specific interference, we found that the two genes control germline development and maintenance. Bub3 is continuously required in the germline, as its loss results in the beginning in an over-proliferation of early germ cells and later on in loss of the germline. The absence of the germline lineage in such testes has dramatic cell non-autonomous consequences, as cells co-expressing markers of hub and somatic cyst cell fates accumulate and populate in extreme cases the whole testis. Our analysis of Nups showed that some of them are critical for lineage maintenance, as their depletion results in the loss of the affected lineage. In contrast, Nup75 plays a role in controlling proliferation of early germ cells but not differentiating spermatogonia and seems to be involved in keeping hub cells quiescent. In sum, our analysis shows that Bub3 and Nup75 are required for male germline development and maintenance.

Keywords:  Bub3; Drosophila; Hub cells; Loss of germline; Mitotic checkpoint; Niche expansion; Nucleoporin; Nup62; Nup75; Stem cell development; Stem cell maintenance; Stem cell niche; Testis

DOI:  https://doi.org/10.1016/j.cdev.2023.203863
Front Oncol. 2023 ;13 1007198

Exploring the relationship between abnormally high expression of NUP205 and the clinicopathological characteristics, immune microenvironment, and prognostic value of lower-grade glioma.

Wenjia Liang, Chenchen Hu, Qingyun Zhu, Xingbo Cheng, Shanjun Gao, Zhendong Liu, Hongbo Wang, Pengxu Li, Yanzheng Gao, Rongjun Qian.

  Nuclear pore complex (NPC) is a major transport pivot for nucleocytoplasmic molecule exchange. Nucleoporin 205 (NUP205)-a main component of NPC-plays a key regulatory role in tumor cell proliferation; however, few reports document its effect on the pathological progression of lower-grade glioma (LGG). Therefore, we conducted an integrated analysis using 906 samples from multiple public databases to explore the effects of NUP205 on the prognosis, clinicopathological characteristics, regulatory mechanism, and tumor immune microenvironment (TIME) formation in LGG. First, multiple methods consistently showed that the mRNA and protein expression levels of NUP205 were higher in LGG tumor tissue than in normal brain tissue. This increased expression was mainly noted in the higher WHO Grade, IDH-wild type, and 1p19q non-codeleted type. Second, various survival analysis methods showed that the highly expressed NUP205 was an independent risk indicator that led to reduced survival time of patients with LGG. Third, GSEA analysis showed that NUP205 regulated the pathological progress of LGG via the cell cycle, notch signaling pathway, and aminoacyl-tRNA biosynthesis. Ultimately, immune correlation analysis suggested that high NUP205 expression was positively correlated with the infiltration of multiple immune cells, particularly M2 macrophages, and was positively correlated with eight immune checkpoints, particularly PD-L1. Collectively, this study documented the pathogenicity of NUP205 in LGG for the first time, expanding our understanding of its molecular function. Furthermore, this study highlighted the potential value of NUP205 as a target of anti-LGG immunotherapy.

Keywords:  NUP205; immunotherapeutic target; lower-grade glioma; pathogenic gene; prognosis

DOI:  https://doi.org/10.3389/fonc.2023.1007198
Protein J. 2023 Jun 07.

Toxoplasma Gondii Importin α Shows Weak Auto-Inhibition.

Manasi Bhambid, Vishakha Dey, Sujata Walunj, Swati Patankar.

  Importin α is a nuclear transporter that binds to nuclear localization signals (NLSs), consisting of 7-20 positively charged amino acids found within cargo proteins. In addition to cargo binding, intramolecular interactions also occur within the importin α protein due to binding between the importin β-binding (IBB) domain and the NLS-binding sites, a phenomenon called auto-inhibition. The interactions causing auto-inhibition are driven by a stretch of basic residues, similar to an NLS, in the IBB domain. Consistent with this, importin α proteins that do not have some of these basic residues lack auto-inhibition; a naturally occurring example of such a protein is found in the apicomplexan parasite Plasmodium falciparum. In this report, we show that importin α from another apicomplexan parasite, Toxoplasma gondii, harbors basic residues (KKR) in the IBB domain and exhibits auto-inhibition. This protein has a long, unstructured hinge motif (between the IBB domain and the NLS-binding sites) that does not contribute to auto-inhibition. However, the IBB domain may have a higher propensity to form an α-helical structure, positioning the wild-type KKR motif in an orientation that results in weaker interactions with the NLS-binding site than a KRR mutant. We conclude that the importin α protein from T. gondii shows auto-inhibition, exhibiting a different phenotype from that of P. falciparum importin α. However, our data indicate that T. gondii importin α may have a low strength of auto-inhibition. We hypothesize that low levels of auto-inhibition may confer an advantage to these important human pathogens.

Keywords:  Auto-inhibition; Hinge; IBB domain; Importin α; Nuclear import pathway; Toxoplasma gondii

DOI:  https://doi.org/10.1007/s10930-023-10128-2
Biochem Biophys Res Commun. 2023 May 15. pii: S0006-291X(23)00609-5. [Epub ahead of print]670 117-123

Identification and functional characterization of a bipartite nuclear localization signal in ANKRD11.

Min Chen, Xue Yang, Haiyang Liu, Jun Wan.

  ANKRD11 gene encodes for the large nuclear protein essential for multiple system development including the nervous system. However, the molecular basis for the proper nuclear localization of ANKRD11 has not yet been elucidated. In this study, we have identified a functional bipartite nuclear localization signal (bNLS) between residues 53 and 87 of ANKRD11. Using biochemical approaches, we discovered two major binding sites in this bipartite NLS for Importin α1. Through site-directed mutagenesis and functional analysis, we further found that this bipartite NLS is sufficient for nuclear import of overexpressing GFP in HeLa cells and necessary for nuclear localization of ANKRD11. Importantly, our study provides a possible pathogenic mechanism for certain clinical variants located within the bipartite nuclear localization signal of ANKRD11.

Keywords:  ANKRD11; Bipartite nuclear localization signal (bNLS); Nuclear import

DOI:  https://doi.org/10.1016/j.bbrc.2023.05.046