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Статті в журналах з теми "NUBP1"

Автор: Grafiati

Опубліковано: 10 березня 2023

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1

Okuno, Takashi, Hiroko Yamabayashi, and Kentaro Kogure. "Comparison of intracellular localization of Nubp1 and Nubp2 using GFP fusion proteins." Molecular Biology Reports 37, no. 3 (March 5, 2009): 1165–68. http://dx.doi.org/10.1007/s11033-009-9477-7.

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2

Kypri, Elena, Andri Christodoulou, Giannis Maimaris, Mette Lethan, Maria Markaki, Costas Lysandrou, Carsten W. Lederer, et al. "The nucleotide-binding proteins Nubp1 and Nubp2 are negative regulators of ciliogenesis." Cellular and Molecular Life Sciences 71, no. 3 (June 27, 2013): 517–38. http://dx.doi.org/10.1007/s00018-013-1401-6.

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3

Christodoulou, A. "Motor protein KIFC5A interacts with Nubp1 and Nubp2, and is implicated in the regulation of centrosome duplication." Journal of Cell Science 119, no. 10 (May 15, 2006): 2035–47. http://dx.doi.org/10.1242/jcs.02922.

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4

Stehling, Oliver, Daili J. A. Netz, Brigitte Niggemeyer, Ralf Rösser, Richard S. Eisenstein, Helene Puccio, Antonio J. Pierik, and Roland Lill. "Human Nbp35 Is Essential for both Cytosolic Iron-Sulfur Protein Assembly and Iron Homeostasis." Molecular and Cellular Biology 28, no. 17 (June 23, 2008): 5517–28. http://dx.doi.org/10.1128/mcb.00545-08.

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ABSTRACT The maturation of cytosolic iron-sulfur (Fe/S) proteins in mammalian cells requires components of the mitochondrial iron-sulfur cluster assembly and export machineries. Little is known about the cytosolic components that may facilitate the assembly process. Here, we identified the cytosolic soluble P-loop NTPase termed huNbp35 (also known as Nubp1) as an Fe/S protein, and we defined its role in the maturation of Fe/S proteins in HeLa cells. Depletion of huNbp35 by RNA interference decreased cell growth considerably, indicating its essential function. The deficiency in huNbp35 was associated with an impaired maturation of the cytosolic Fe/S proteins glutamine phosphoribosylpyrophosphate amidotransferase and iron regulatory protein 1 (IRP1), while mitochondrial Fe/S proteins remained intact. Consequently, huNbp35 is specifically involved in the formation of extramitochondrial Fe/S proteins. The impaired maturation of IRP1 upon huNbp35 depletion had profound consequences for cellular iron metabolism, leading to decreased cellular H-ferritin, increased transferrin receptor levels, and higher transferrin uptake. These properties clearly distinguished huNbp35 from its yeast counterpart Nbp35, which is essential for cytosolic-nuclear Fe/S protein assembly but plays no role in iron regulation. huNbp35 formed a complex with its close homologue huCfd1 (also known as Nubp2) in vivo, suggesting the existence of a heteromeric P-loop NTPase complex that is required for both cytosolic Fe/S protein assembly and cellular iron homeostasis.

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5

Stehling, Oliver, Jae-Hun Jeoung, Sven A. Freibert, Viktoria D. Paul, Sebastian Bänfer, Brigitte Niggemeyer, Ralf Rösser, Holger Dobbek, and Roland Lill. "Function and crystal structure of the dimeric P-loop ATPase CFD1 coordinating an exposed [4Fe-4S] cluster for transfer to apoproteins." Proceedings of the National Academy of Sciences 115, no. 39 (September 10, 2018): E9085—E9094. http://dx.doi.org/10.1073/pnas.1807762115.

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Maturation of iron-sulfur (Fe-S) proteins in eukaryotes requires complex machineries in mitochondria and cytosol. Initially, Fe-S clusters are assembled on dedicated scaffold proteins and then are trafficked to target apoproteins. Within the cytosolic Fe-S protein assembly (CIA) machinery, the conserved P-loop nucleoside triphosphatase Nbp35 performs a scaffold function. In yeast, Nbp35 cooperates with the related Cfd1, which is evolutionary less conserved and is absent in plants. Here, we investigated the potential scaffold function of human CFD1 (NUBP2) in CFD1-depleted HeLa cells by measuring Fe-S enzyme activities or 55Fe incorporation into Fe-S target proteins. We show that CFD1, in complex with NBP35 (NUBP1), performs a crucial role in the maturation of all tested cytosolic and nuclear Fe-S proteins, including essential ones involved in protein translation and DNA maintenance. CFD1 also matures iron regulatory protein 1 and thus is critical for cellular iron homeostasis. To better understand the scaffold function of CFD1-NBP35, we resolved the crystal structure of Chaetomium thermophilum holo-Cfd1 (ctCfd1) at 2.6-Å resolution as a model Cfd1 protein. Importantly, two ctCfd1 monomers coordinate a bridging [4Fe-4S] cluster via two conserved cysteine residues. The surface-exposed topology of the cluster is ideally suited for both de novo assembly and facile transfer to Fe-S apoproteins mediated by other CIA factors. ctCfd1 specifically interacted with ATP, which presumably associates with a pocket near the Cfd1 dimer interface formed by the conserved Walker motif. In contrast, ctNbp35 preferentially bound GTP, implying differential regulation of the two fungal scaffold components during Fe-S cluster assembly and/or release.

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6

Schnatwinkel, Carsten, and Lee Niswander. "Nubp1 Is Required for Lung Branching Morphogenesis and Distal Progenitor Cell Survival in Mice." PLoS ONE 7, no. 9 (September 17, 2012): e44871. http://dx.doi.org/10.1371/journal.pone.0044871.

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7

Ververis, Antonis, Andri Christodoulou, Maria Christoforou, Christina Kamilari, Carsten W. Lederer, and Niovi Santama. "A novel family of katanin-like 2 protein isoforms (KATNAL2), interacting with nucleotide-binding proteins Nubp1 and Nubp2, are key regulators of different MT-based processes in mammalian cells." Cellular and Molecular Life Sciences 73, no. 1 (July 8, 2015): 163–84. http://dx.doi.org/10.1007/s00018-015-1980-5.

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8

Nakashima, Hiroshi, Marija J. Grahovac, Richard Mazzarella, Hiroyuki Fujiwara, John R. Kitchen, Tracy A. Threat, and Minoru S. H. Ko. "Two Novel Mouse Genes—Nubp2, Mapped to the t-Complex on Chromosome 17, and Nubp1, Mapped to Chromosome 16— Establish a New Gene Family of Nucleotide-Binding Proteins in Eukaryotes." Genomics 60, no. 2 (September 1999): 152–60. http://dx.doi.org/10.1006/geno.1999.5898.

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9

Camponeschi, Francesca, Nihar Ranjan Prusty, Sabine Annemarie Elisabeth Heider, Simone Ciofi-Baffoni, and Lucia Banci. "GLRX3 Acts as a [2Fe–2S] Cluster Chaperone in the Cytosolic Iron–Sulfur Assembly Machinery Transferring [2Fe–2S] Clusters to NUBP1." Journal of the American Chemical Society 142, no. 24 (May 20, 2020): 10794–805. http://dx.doi.org/10.1021/jacs.0c02266.

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10

Guarascio, Rosellina, Dervis Salih, Marina Yasvoina, Frances A. Edwards, Michael E. Cheetham, and Jacqueline van der Spuy. "Negative Regulator of Ubiquitin-Like Protein 1 modulates the autophagy–lysosomal pathway via p62 to facilitate the extracellular release of tau following proteasome impairment." Human Molecular Genetics 29, no. 1 (November 6, 2019): 80–96. http://dx.doi.org/10.1093/hmg/ddz255.

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Abstract Negative regulator of ubiquitin-like protein 1 (NUB1) and its longer isoform NUB1L are ubiquitin-like (UBL)/ubiquitin-associated (UBA) proteins that facilitate the targeting of proteasomal substrates, including tau, synphilin-1 and huntingtin. Previous data revealed that NUB1 also mediated a reduction in tau phosphorylation and aggregation following proteasome inhibition, suggesting a switch in NUB1 function from targeted proteasomal degradation to a role in autophagy. Here, we delineate the mechanisms of this switch and show that NUB1 interacted specifically with p62 and induced an increase in p62 levels in a manner facilitated by inhibition of the proteasome. NUB1 moreover increased autophagosomes and the recruitment of lysosomes to aggresomes following proteasome inhibition. Autophagy flux assays revealed that NUB1 affected the autophagy–lysosomal pathway primarily via the UBA domain. NUB1 localized to cytosolic inclusions with pathological forms of tau, as well as LAMP1 and p62 in the hippocampal neurons of tauopathy mice. Finally, NUB1 facilitated the extracellular release of tau following proteasome inhibition. This study thus shows that NUB1 plays a role in regulating the autophagy–lysosomal pathway when the ubiquitin proteasome system is compromised, thus contributing to the mechanisms targeting the removal of aggregation-prone proteins upon proteasomal impairment.

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11

Loeb, J. D., L. I. Davis, and G. R. Fink. "NUP2, a novel yeast nucleoporin, has functional overlap with other proteins of the nuclear pore complex." Molecular Biology of the Cell 4, no. 2 (February 1993): 209–22. http://dx.doi.org/10.1091/mbc.4.2.209.

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We have isolated a new gene, NUP2, that encodes a constituent of the yeast-nuclear pore complex (NPC). The NUP2 protein sequence shares a central repetitive domain with NSP1 and NUP1, the two previously characterized yeast nucleoporins. Like NUP1 and NSP1, NUP2 localizes to discrete spots in the nuclear envelope, as determined by indirect immunofluorescence. Although the sequence similarity among these three nucleoporins suggests that they have a similar role in the nuclear pore complex, NUP2, in contrast to NSP1 and NUP1, is not required for growth. Some combinations of mutant alleles of NUP1, NSP1, and NUP2 display "synthetic lethal" relationships that provide evidence for functional interaction between these NPC components. This genetic evidence of overlapping function suggests that the nucleoporins act in concert, perhaps participating in the same step of the recognition or transit of macromolecules through the NPC.

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12

Arshad, Maria, Nazefah Abdul Hamid, Mun Chiang Chan, Fuad Ismail, Geok Chin Tan, Francesco Pezzella, and Ka-Liong Tan. "NUB1 and FAT10 Proteins as Potential Novel Biomarkers in Cancer: A Translational Perspective." Cells 10, no. 9 (August 24, 2021): 2176. http://dx.doi.org/10.3390/cells10092176.

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Cancer increases the global disease burden substantially, but it remains a challenge to manage it. The search for novel biomarkers is essential for risk assessment, diagnosis, prognosis, prediction of treatment response, and cancer monitoring. This paper examined NEDD8 ultimate buster-1 (NUB1) and F-adjacent transcript 10 (FAT10) proteins as novel biomarkers in cancer. This literature review is based on the search of the electronic database, PubMed. NUB1 is an interferon-inducible protein that mediates apoptotic and anti-proliferative actions in cancer, while FAT10 is a ubiquitin-like modifier that promotes cancer. The upregulated expression of both NUB1 and FAT10 has been observed in various cancers. NUB1 protein binds to FAT10 non-covalently to promote FAT10 degradation. An overexpressed FAT10 stimulates nuclear factor-kappa β, activates the inflammatory pathways, and induces the proliferation of cancer. The FAT10 protein interacts with the mitotic arrest deficient 2 protein, causing chromosomal instability and breast tumourigenesis. FAT10 binds to the proliferating cell nuclear antigen protein and inhibits the DNA damage repair response. In addition, FAT10 involves epithelial–mesenchymal transition, invasion, apoptosis, and multiplication in hepatocellular carcinoma. Our knowledge about them is still limited. There is a need to further develop NUB1 and FAT10 as novel biomarkers.

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13

Aron, Rebecca, Andrey Tsvetkov, and Steven Finkbeiner. "NUB1 snubs huntingtin toxicity." Nature Neuroscience 16, no. 5 (April 25, 2013): 523–25. http://dx.doi.org/10.1038/nn.3380.

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14

Sulistinah, Nunik. "KEMAMPUAN Flavobacterium sp NUB1 DALAM MENGGUNAKAN ALIFATIK NITRIL UNTUK PERTUMBUHANNYA." Jurnal Teknologi Lingkungan 11, no. 3 (December 2, 2016): 425. http://dx.doi.org/10.29122/jtl.v11i3.1188.

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A bacteria isolate capable utilizing 1% (v/v) acetonitrile and butironitrile as thesolesource of carbon and nitrogen was isolated from industrial effluents ofPTPetrokimia-Gresik and identified as Flavobacterium sp NUB1. The bacteriaisolatewas able to grow in both acetonitrile and butironitrile at concentrationofup to 4% (v/v). The highest growth was reached at 1% concentration ofacetonitrileand butironitrile, but the bacteria isolate was not able to grow onacrilonitrile.The specific growth rate (μ) of the isolate was 0,029 h-1. Themajorobjective of this study was to explore the abilities of the isolate to utilizesomealiphatic nitriles and then further evaluate the metabolite product of thenitriledegradation.Key words: aliphatic nitrile, biodegradation, Flavobacterium sp. NUB1

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15

Garvey Brickner, Donna, and Jason H. Brickner. "Cdk Phosphorylation of a Nucleoporin Controls Localization of Active Genes through the Cell Cycle." Molecular Biology of the Cell 21, no. 19 (October 2010): 3421–32. http://dx.doi.org/10.1091/mbc.e10-01-0065.

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Many inducible genes in yeast are targeted to the nuclear pore complex when active. We find that the peripheral localization of the INO1 and GAL1 genes is regulated through the cell cycle. Active INO1 and GAL1 localized at the nuclear periphery during G1, became nucleoplasmic during S-phase, and then returned to the nuclear periphery during G2/M. Loss of peripheral targeting followed the initiation of DNA replication and was lost in cells lacking a cyclin-dependent kinase (Cdk) inhibitor. Furthermore, the Cdk1 kinase and two Cdk phosphorylation sites in the nucleoporin Nup1 were required for peripheral targeting of INO1 and GAL1. Introduction of aspartic acid residues in place of either of these two sites in Nup1 bypassed the requirement for Cdk1 and resulted in targeting of INO1 and GAL1 to the nuclear periphery during S-phase. Thus, phosphorylation of a nuclear pore component by cyclin dependent kinase controls the localization of active genes to the nuclear periphery through the cell cycle.

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16

Lamba, Jatinder, Lata Chauhan, Christophe Echeverri, Kerstin Korn, Kartini Kochar, Xueyuan Cao, and Stanley Pounds. "High-Throughput, High-Content siRNA/Drug Modifier Screen for Validation of Transcriptional Profiles Predictive of Cytarabine Response in AML." Blood 124, no. 21 (December 6, 2014): 3615. http://dx.doi.org/10.1182/blood.v124.21.3615.3615.

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Abstract Cytarabine is the backbone of modern AML chemotherapy. However, extensive inter-patient variation in treatment response, development of resistance, and severe toxicity remain as major hurdles to effective cytarabine chemotherapy. Although the genes involved in cytarabine’s activation/inactivation and transport are well defined, we still lack in understanding of the PD genes of relevance. So far several efforts have been made to identify cytarabine response genes have some of these utilized transcriptional profiling to identify gene expression signatures that differentiate sensitive and resistant cell lines; others have utilized gene expression profiles from diagnostic specimens, to identify transcripts predictive of therapeutic outcome. To identify genes that show a biologically meaningful pattern of association with multiple pharmacologic and clinical variables, we have recently developed and applied the innovative PROMISE (PRojection Onto the Most Interesting Statistical Evidence) statistical analysis procedure. In our preliminary study using PROMISE, we identified transcriptional signatures (consisting of 60 genes) that were predictive of therapeutically beneficial (n=46 genes) or detrimental (n=14 genes) patterns of association with multiple clinical parameters. We then used this information, combined with genes reported in literature as being important to ara-C pharmacology and/or identified in relevant genome-wide screens, to define a high-priority list of 300 candidate genes, which we subjected to a multi-phased, high throughput siRNA/ cytarabine modifier screening campaign in human AML cells. The first screening phase used 3 individual siRNAs to target each of the 300 selected candidate genes in THP1 cells, tested alongside standard transfection controls in 384 well plates. Post siRNA transfection, cells were treated with different concentrations of cytarabine (0µM; 0.1µM-IC10; 0.8µM-IC50; and 10µM-IC90) followed by multi-parametric nuclear morphometry assays using automated microscopy to document the individual and combined phenotypic effects of siRNA gene silencing and cytarabine on cell growth and proliferation. Genes were classified as suppressors if their siRNA knockdown inhibited the drug response (i.e increased resistance) and enhancers if the knockdown enhanced the drug response (i.e increased drug sensitivity). This analysis yielded 72 candidate cytarabine modifier genes, which were then subjected to further technical and biological validation tests to document experimental reproducibility, siRNA targeting specificity and cell line specificity of observed phenotypes in THP1 (0, 0.8 and 10µM) and Kasumi cells (0, 0.05 and 1µM for IC50 and IC90 concentrations for Kasumi). Targeting specificity was assessed by comparing microscopy phenotypes to target knock-down as measured by RT-qPCR for candidate hit siRNAs and matched non-cleaving “C911” control siRNAs. Our results yielded clear validation of ara-C modifier effects for several genes with known functions in ara-C-relevant pathways, including DNA damage repair response factors and deoxynucleotide metabolism/catabolism enzymes. As such, these results confirm the patho-physiological relevance of our screening campaign in strengthening the predictive value of markers previously identified by transcriptional profiling analyses from AML patient samples. They also confirm our screen design’s potential for identifying novel modulators of cytarabine -induced phenotypes. Indeed, even from this relatively small screen of only 300 high-priority genes, our validation data supported ara-C suppressor effects from knocking down APOBEC3G, ANXA5, (DCK: involved in activation of cytarabine), KPNA2, NCF1, PLEKHM1, REPIN1 and XRCC1, as well as enhancer effects from knocking down CFLAR, CHEK1, DERA, EIF4F2, EXO1, GNB5, GRPEL1, IER3IP1, IQGAP1, MAPK11, NFKB2, NKX2, NUBP1, RPL31. These genes represent valuable biomarker candidates whose expression levels in AML patients may predict ara-C responsiveness. The identified enhancer genes also represent novel therapeutic target candidates for developing more effective ara-C combination treatments for AML. Disclosures Echeverri: Cenix BioScience Inc: Employment, Equity Ownership. Korn:Cenix BioScience Inc: Employment. Kochar:Cenix BioScience Inc: Employment.

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17

Richet, Emma, Amy M. Pooler, Teresa Rodriguez, Sergey S. Novoselov, Gunter Schmidtke, Marcus Groettrup, Diane P. Hanger, Michael E. Cheetham та Jacqueline van der Spuy. "NUB1 modulation of GSK3β reduces tau aggregation". Human Molecular Genetics 21, № 24 (10 вересня 2012): 5254–67. http://dx.doi.org/10.1093/hmg/dds376.

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18

Flight, Monica Hoyos. "Hunting out the NUB1 of the matter." Nature Reviews Neuroscience 14, no. 5 (April 10, 2013): 308–9. http://dx.doi.org/10.1038/nrn3493.

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19

Richet, Emma, Mike Cheetham, and Jacqueline Van Der Spuy. "P1-347: NUB1 modulation of tau aggregation." Alzheimer's & Dementia 6 (July 2010): S273—S274. http://dx.doi.org/10.1016/j.jalz.2010.05.900.

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20

Dantoft, Widad, Daniel Lundin, Shiva Seyedoleslami Esfahani, and Ylva Engström. "The POU/Oct Transcription Factor Pdm1/nub Is Necessary for a Beneficial Gut Microbiota and Normal Lifespan of Drosophila." Journal of Innate Immunity 8, no. 4 (2016): 412–26. http://dx.doi.org/10.1159/000446368.

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Maintenance of a stable gut microbial community relies on a delicate balance between immune defense and immune tolerance. We have used Drosophila to study how the microbial gut flora is affected by changes in host genetic factors and immunity. Flies with a constitutively active gut immune system, due to a mutation in the POU transcriptional regulator Pdm1/nubbin (nub) gene, had higher loads of bacteria and a more diverse taxonomic composition than controls. In addition, the microbial composition shifted considerably during the short lifespan of the nub1 mutants. This shift was characterized by a loss of relatively few OTUs (operational taxonomic units) and a remarkable increase in a large number of Acetobacter spp. and Leuconostoc spp. Treating nub1 mutant flies with antibiotics prolonged their lifetime survival by more than 100%. Immune gene expression was also persistently high in the presence of antibiotics, indicating that the early death was not a direct consequence of an overactive immune defense but rather an indirect consequence of the microbial load and composition. Thus, changes in host genotype and an inability to regulate the normal growth and composition of the gut microbiota leads to a shift in the microbial community, dysbiosis and early death.

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21

van der Spuy, Jacqueline, and Michael E. Cheetham. "The Leber Congenital Amaurosis Protein AIPL1 Modulates the Nuclear Translocation of NUB1 and Suppresses Inclusion Formation by NUB1 Fragments." Journal of Biological Chemistry 279, no. 46 (August 30, 2004): 48038–47. http://dx.doi.org/10.1074/jbc.m407871200.

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22

Hildreth, S. B., E. A. Gehman, H. Yang, R. H. Lu, R. K C, K. C. Harich, S. Yu, et al. "Tobacco nicotine uptake permease (NUP1) affects alkaloid metabolism." Proceedings of the National Academy of Sciences 108, no. 44 (October 17, 2011): 18179–84. http://dx.doi.org/10.1073/pnas.1108620108.

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23

Tanji, Kunikazu, Tomoaki Tanaka, and Tetsu Kamitani. "Interaction of NUB1 with the proteasome subunit S5a." Biochemical and Biophysical Research Communications 337, no. 1 (November 2005): 116–20. http://dx.doi.org/10.1016/j.bbrc.2005.09.014.

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24

Belanger, K. D., M. A. Kenna, S. Wei, and L. I. Davis. "Genetic and physical interactions between Srp1p and nuclear pore complex proteins Nup1p and Nup2p." Journal of Cell Biology 126, no. 3 (August 1, 1994): 619–30. http://dx.doi.org/10.1083/jcb.126.3.619.

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Nup1p is a yeast nuclear pore complex protein (nucleoporin) required for nuclear protein import, mRNA export and maintenance of normal nuclear architecture. We have used a genetic approach to identify other proteins that interact functionally with Nup1p. Here we describe the isolation of seventeen mutants that confer a requirement for Nup1p in a background in which this protein is normally not essential. Some of the mutants require wild-type Nup1p, while others are viable in combination with specific nup1 alleles. Several of the mutants show nonallelic noncomplementation, suggesting that the products may be part of a hetero-oligomeric complex. One is allelic to srp1 which, although it was identified in an unrelated screen, was shown to encode a protein that is localized to the nuclear envelope (Yano, R., M. Oakes, M. Yamaghishi, J. A. Dodd, and M. Nomura. 1992. Mol. Cell. Biol. 12:5640-5651). We have used immunoprecipitation and fusion protein precipitation to show that Srp1p forms distinct complexes with both Nup1p and the related nucleoporin Nup2p, indicating that Srp1p is a component of the nuclear pore complex. The distant sequence similarity between Srp1p and the beta-catenin/desmoplakin family, coupled with the altered structure of the nuclear envelope in nup1 mutants, suggests that Srp1p may function in attachment of the nuclear pore complex to an underlying nuclear skeleton.

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25

Mottok, Anja, Bruce W. Woolcock, Fong Chun Chan, Adele Telenius, Elizabeth A. Chavez, Merrill Boyle, Susana Ben-Neriah, et al. "Genetic Alterations of the MHC Class II Transactivator CIITA Are Frequent in Primary Mediastinal Large B-Cell Lymphoma and Associated with Diminished MHC Class II Expression." Blood 124, no. 21 (December 6, 2014): 3040. http://dx.doi.org/10.1182/blood.v124.21.3040.3040.

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Abstract Introduction: Constitutive MHC class II expression is a hallmark of antigen-presenting cells, including B cells, and is indispensable for the initiation of antigen specific immune responses. It has been shown that certain B cell lymphoma entities are able to evade immune recognition by downregulation of MHC molecules on the tumor cell surface. We have previously identified recurrent chromosomal rearrangements of CIITA, the master regulator of MHC class II transcription, as one possible mechanism to reduce MHC class II expression in primary mediastinal large B-cell lymphoma (PMBCL) and classical Hodgkin lymphoma (cHL) (Steidl et al., Nature 2011). Furthermore, we have recently described a 1.6kb breakpoint cluster region within intron 1 of CIITA and have shown in a small sample set of PMBCL cases that deletions, insertions and single nucleotide variants (SNV) are commonly found within this genomic region (Steidl, ASH abstract # 437, 2011). Therefore, we aimed to explore the frequency of these alterations and the correlation with CIITA and MHC class II protein expression in a larger cohort of PMBCL cases and to further characterize their functional significance. Methods: We have comprehensively analyzed 45 diagnostic PMBCL samples for the presence of coding sequence mutations as well as alterations within the promoter III region and the first 3kb of intron 1 using deep amplicon sequencing (Illumina TruSeq) and/or Sanger sequencing. In addition, we characterized the PMBCL-derived cell lines U2940 and Med-B1 by whole transcriptome paired-end sequencing (RNA-seq). To elucidate the functional consequences of the coding sequence mutations identified in these two cell lines we performed retroviral transductions of wild type CIITA and CIITA mutants in a CIITA and HLA-DR expression-negative cell line (DEV, nodular lymphocyte predominant Hodgkin lymphoma-derived). We subsequently analyzed CIITA mRNA expression using qRT-PCR and HLA-DR surface expression using flow cytometry. Furthermore, we applied immunohistochemistry (IHC) to determine expression levels of CIITA and HLA-DR in a large cohort of PMBCL samples represented on two tissue microarrays (TMA, n=149). The TMAs were also used for fluorescence in-situ hybridization (FISH) to evaluate the presence of copy number alterations or translocations of the CIITA locus. Results: FISH was interpretable in 115 samples with a CIITA break-apart (CIITA-ba) frequency of 33.9% (39/115). Correlative analyses revealed that decreased CIITA protein expression by IHC was significantly correlated with the presence of CIITA-ba (P=0.019), whereas HLA-DR expression was not correlated with CIITA-ba status alone (P=0.219). However, we could demonstrate a positive correlation between protein expression of CIITA and HLA-DR (Pearson r=0.45, P<0.0001). Within the subset of 45 PMBCL cases that were analyzed for the presence of genomic alterations, 39% were CIITA-ba positive (16/41), and in 31.8% (14/44) we observed coding sequence mutations and/or alterations affecting the promoter III region. 45.5% (20/44) of the cases presented indels and/or SNVs in intron 1. Using RNA-seq, we have detected two missense mutations in the Med-B1 cell line affecting both alleles in functionally relevant protein domains. Furthermore, we identified a novel NUBP1-CIITA fusion transcript in U2940 also harboring an SNV on the other allele resulting in the transcription of an elongated protein due to the loss of the original stop codon. Ectopic expression of these CIITA mutants in DEV, which has been shown to have undetectable levels of CIITA and HLA-DR due to a biallelic CIITA inactivation, revealed that these individual SNVs showed a diminished capability to restore HLA-DR surface expression in comparison to wild type CIITA as measured by flow cytometry. Conclusions: Here we show that the presence of CIITA rearrangements is significantly associated with low CIITA protein levels, and we could demonstrate that protein expression of CIITA and HLA-DR are positively correlated in PMBCL. Furthermore, CIITA is frequently targeted by coding sequence mutations and intronic deletions in PMBCL cell lines and clinical samples. Functional studies demonstrate that genomic alterations in CIITA contribute to downregulation of MHC class II expression in malignant lymphomas and therefore represent a potent mechanism of acquired immune privilege and escape from immune surveillance. Disclosures No relevant conflicts of interest to declare.

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26

Kato, Keita, Nobukazu Shitan, Tsubasa Shoji, and Takashi Hashimoto. "Tobacco NUP1 transports both tobacco alkaloids and vitamin B6." Phytochemistry 113 (May 2015): 33–40. http://dx.doi.org/10.1016/j.phytochem.2014.05.011.

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27

Bogerd, A. M., J. A. Hoffman, D. C. Amberg, G. R. Fink, and L. I. Davis. "nup1 mutants exhibit pleiotropic defects in nuclear pore complex function." Journal of Cell Biology 127, no. 2 (October 15, 1994): 319–32. http://dx.doi.org/10.1083/jcb.127.2.319.

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The NUP1 gene of Saccharomyces cerevisiae encodes one member of a family of nuclear pore complex proteins (nucleoporins) conserved from yeast to vertebrates. We have used mutational analysis to investigate the function of Nup1p. Deletion of either the amino- or carboxy-terminal domain confers a lethal phenotype, but partial truncations at either end affect growth to varying extents. Amino-terminal truncation causes mislocalization and degradation of the mutant protein, suggesting that this domain is required for targeting Nup1p to the nuclear pore complex. Carboxy-terminal mutants are stable but do not have wild-type function, and confer a temperature sensitive phenotype. Both import of nuclear proteins and export of poly(A) RNA are defective at the nonpermissive temperature. In addition, nup1 mutant cells become multinucleate at all temperatures, a phenotype suggestive of a defect in nuclear migration. Tubulin staining revealed that the mitotic spindle appears to be oriented randomly with respect to the bud, in spite of the presence of apparently normal cytoplasmic microtubules connecting one spindle pole body to the bud tip. EM analysis showed that the nuclear envelope forms long projections extending into the cytoplasm, which appear to have detached from the bulk of the nucleus. Our results suggest that Nup1p may be required to retain the structural integrity between the nuclear envelope and an underlying nuclear scaffold, and that this connection is required to allow reorientation of the nucleus in response to cytoskeletal forces.

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28

Sala, L. Molero, R. Garcia Rodriguez, R. Garcia Delgado, L. Toledo, I. S. Garcia, A. A. Santana, J. Perez Gonzalez, I. Ortega Cárdenes, and J. C. Lopez. "VP24.01: Fetal lenticulostriatal vasculopathy associated to pathogenic variant in NUBPL gene." Ultrasound in Obstetrics & Gynecology 58, S1 (October 2021): 200. http://dx.doi.org/10.1002/uog.24388.

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29

Tenisch, E. V., A. S. Lebre, D. Grevent, P. de Lonlay, M. Rio, M. Zilbovicius, B. Funalot, et al. "Massive and exclusive pontocerebellar damage in mitochondrial disease and NUBPL mutations." Neurology 79, no. 4 (July 23, 2012): 391. http://dx.doi.org/10.1212/wnl.0b013e3182611232.

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30

DiStasio, Andrew, David Paulding, Praneet Chaturvedi, and Rolf W. Stottmann. "Nubp2 is required for cranial neural crest survival in the mouse." Developmental Biology 458, no. 2 (February 2020): 189–99. http://dx.doi.org/10.1016/j.ydbio.2019.10.039.

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31

Bonacci, Thomas, Stéphane Audebert, Luc Camoin, Emilie Baudelet, Juan-Lucio Iovanna, and Philippe Soubeyran. "Regulation of NUB1 Activity through Non-Proteolytic Mdm2-Mediated Ubiquitination." PLOS ONE 12, no. 1 (January 18, 2017): e0169988. http://dx.doi.org/10.1371/journal.pone.0169988.

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32

Kenna, M. A., J. G. Petranka, J. L. Reilly, and L. I. Davis. "Yeast N1e3p/Nup170p is required for normal stoichiometry of FG nucleoporins within the nuclear pore complex." Molecular and Cellular Biology 16, no. 5 (May 1996): 2025–36. http://dx.doi.org/10.1128/mcb.16.5.2025.

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The FG nucleoporins are a conserved family of proteins, some of which bind to the nuclear localization sequence receptor, karyopherin. Distinct members of this family are found in each region of the nuclear pore complex (NPC), spanning from the cytoplasmically disposed filaments to the distal end of the nuclear basket. Movement of karyopherin from one FG nucleoporin to the next may be required for translocation of substrates across the NPC. So far, nothing is known about how the FG nucleoporins are localized within the NPC. To identify proteins that interact functionally with one member of this family, the Saccharomyces cerevisiae protein Nup1p, we previously identified 16 complementation groups containing mutants that are lethal in the absence of NUP1 These mutants were referred to as nle (Nup-lethal) mutants. Mutants in the nle3/nlel7 complementation group are lethal in combination with amino-terminal nup1 truncation mutants, which we have previously shown to be defective for localization to the NPC. Here we show that NLE3 (which is allelic to NUP170) encodes a protein with similarity to the mammalian nucleoporin Nup155. We show that Nle3p coprecipitates with glutathione S-transferase fusions containing the amino-terminal domain of Nup1p. Furthermore, a deletion of Nle3p leads to changes in the stoichiometry of several of the XFXFG nucleoporins, including the loss of Nup1p and Nup2p. These results suggest that Nle3p plays a role in localizing specific FG nucleoporins within the NPC. The broad spectrum of synthetic phenotypes observed with the nle3delta mutant provides support for this model. We also identify a redundant yeast homolog that can partially substitute for Nle3p and show that together these proteins are required for viability.

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33

LAUFFART, Brenda, Scott J. HOWELL, Jason E. TASCH, John K. COWELL, and Ivan H. STILL. "Interaction of the transforming acidic coiled-coil 1 (TACC1) protein with ch-TOG and GAS41/NuBI1 suggests multiple TACC1-containing protein complexes in human cells." Biochemical Journal 363, no. 1 (March 22, 2002): 195–200. http://dx.doi.org/10.1042/bj3630195.

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Dysregulation of the human transforming acidic coiled-coil (TACC) proteins is thought to be important in the evolution of breast cancer and multiple myeloma. However, the exact role of these proteins in the oncogenic process is currently unknown. Using the full-length TACC1 protein as bait to screen a human mammary epithelial cDNA library, we have identified two genes that are also amplified and overexpressed in tumours derived from different cellular origins. TACC1 interacts with the C-terminus of both the microtubule-associated colonic and hepatic tumour overexpressed (ch-TOG) protein, and the oncogenic transcription factor glioma amplified sequence 41/NuMA binding protein 1 (GAS41/NuBI1; where NuMA stands for nuclear mitotic apparatus protein 1). This suggests that the TACC proteins can form multiple complexes, dysregulation of which may be an important step during tumorigenesis.

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34

Kamitani, Tetsu, Katsumi Kito, Taeko Fukuda-Kamitani, and Edward T. H. Yeh. "Targeting of NEDD8 and Its Conjugates for Proteasomal Degradation by NUB1." Journal of Biological Chemistry 276, no. 49 (October 3, 2001): 46655–60. http://dx.doi.org/10.1074/jbc.m108636200.

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35

Kevelam, S. H., R. J. Rodenburg, N. I. Wolf, P. Ferreira, R. J. Lunsing, L. G. Nijtmans, A. Mitchell, et al. "NUBPL mutations in patients with complex I deficiency and a distinct MRI pattern." Neurology 80, no. 17 (April 3, 2013): 1577–83. http://dx.doi.org/10.1212/wnl.0b013e31828f1914.

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36

Vodicka, Petr, Kathryn Chase, Maria Iuliano, Dana T. Valentine, Ellen Sapp, Boxun Lu, Kimberly B. Kegel-Gleason, Miguel Sena-Esteves, Neil Aronin, and Marian DiFiglia. "Effects of Exogenous NUB1 Expression in the Striatum of HDQ175/Q7 Mice." Journal of Huntington's Disease 5, no. 2 (July 1, 2016): 163–74. http://dx.doi.org/10.3233/jhd-160195.

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37

Tanji, Kunikazu, Fumiaki Mori, Akiyoshi Kakita, Haixin Zhang, Katsumi Kito, Tetsu Kamitani, Hitoshi Takahashi, and Koichi Wakabayashi. "Immunohistochemical localization of NUB1, a synphilin-1-binding protein, in neurodegenerative disorders." Acta Neuropathologica 114, no. 4 (June 5, 2007): 365–71. http://dx.doi.org/10.1007/s00401-007-0238-1.

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38

Kanaya, Koichi, Melanie M. Sohocki, and Tetsu Kamitani. "Abolished interaction of NUB1 with mutant AIPL1 involved in Leber congenital amaurosis." Biochemical and Biophysical Research Communications 317, no. 3 (May 2004): 768–73. http://dx.doi.org/10.1016/j.bbrc.2004.03.108.

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39

Tanaka, Tomoaki, Edward T. H. Yeh, and Tetsu Kamitani. "NUB1-mediated targeting of the ubiquitin precursor UbC1 for its C-terminal hydrolysis." European Journal of Biochemistry 271, no. 5 (February 5, 2004): 972–82. http://dx.doi.org/10.1111/j.1432-1033.2004.03999.x.

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40

Tan, K. L., S. Haider, C. Zois, H. Turley, R. Leek, A. Harris, F. Buffa, O. Acuto, and F. Pezzella. "NUB1 protein regulates cullins and E3 ligases in estrogen receptor negative breast cancers." European Journal of Cancer 61 (July 2016): S190. http://dx.doi.org/10.1016/s0959-8049(16)61672-6.

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41

Davis, Laura I., and Gerald R. Fink. "The NUP1 gene encodes an essential component of the yeast nuclear pore complex." Cell 61, no. 6 (June 1990): 965–78. http://dx.doi.org/10.1016/0092-8674(90)90062-j.

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42

Sun, Haixia, Junling Liu, Yuxin Su, Fang Li, Mingyue Zhang, Jia Li, and Meiling Song. "The role and mechanism of NDST1/NULP1 regulating right ventricular hypertrophy in hypoxic pulmonary hypertension." General physiology and biophysics 41, no. 05 (2022): 407–16. http://dx.doi.org/10.4149/gpb_2022032.

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43

Balint, B., G. Charlesworth, M. Stamelou, L. Carr, N. E. Mencacci, N. W. Wood, and K. P. Bhatia. "Mitochondrial complex I NUBPL mutations cause combined dystonia with bilateral striatal necrosis and cerebellar atrophy." European Journal of Neurology 26, no. 9 (April 20, 2019): 1240–43. http://dx.doi.org/10.1111/ene.13956.

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44

Calvo, Sarah E., Elena J. Tucker, Alison G. Compton, Denise M. Kirby, Gabriel Crawford, Noel P. Burtt, Manuel Rivas, et al. "High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency." Nature Genetics 42, no. 10 (September 5, 2010): 851–58. http://dx.doi.org/10.1038/ng.659.

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45

Wang, Yuhui, Nan Wu, Donglin Sun, Haiming Sun, Dandan Tong, Duo Liu, Bo Pang, et al. "NUBPL , a novel metastasis-related gene, promotes colorectal carcinoma cell motility by inducing epithelial-mesenchymal transition." Cancer Science 108, no. 6 (June 2017): 1169–76. http://dx.doi.org/10.1111/cas.13243.

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46

Tucker, Elena J., Masakazu Mimaki, Alison G. Compton, Matthew McKenzie, Michael T. Ryan, and David R. Thorburn. "Next-generation sequencing in molecular diagnosis: NUBPL mutations highlight the challenges of variant detection and interpretation." Human Mutation 33, no. 2 (December 22, 2011): 411–18. http://dx.doi.org/10.1002/humu.21654.

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47

Lu, Boxun, Ismael Al-Ramahi, Antonio Valencia, Qiong Wang, Frada Berenshteyn, Haidi Yang, Tatiana Gallego-Flores, et al. "Identification of NUB1 as a suppressor of mutant Huntingtin toxicity via enhanced protein clearance." Nature Neuroscience 16, no. 5 (March 24, 2013): 562–70. http://dx.doi.org/10.1038/nn.3367.

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48

Liu, G., and D. P. Xirodimas. "NUB1 promotes cytoplasmic localization of p53 through cooperation of the NEDD8 and ubiquitin pathways." Oncogene 29, no. 15 (January 25, 2010): 2252–61. http://dx.doi.org/10.1038/onc.2009.494.

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49

Tanji, Kunikazu, Yasuo Miki, Atsushi Maruyama, Fumiaki Mori, Junsei Mimura, Ken Itoh, Tetsu Kamitani та Koichi Wakabayashi. "The role of NUB1 in α-synuclein degradation in Lewy body disease model mice". Biochemical and Biophysical Research Communications 470, № 3 (лютий 2016): 635–42. http://dx.doi.org/10.1016/j.bbrc.2016.01.093.

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50

Akey, D. T. "The inherited blindness associated protein AIPL1 interacts with the cell cycle regulator protein NUB1." Human Molecular Genetics 11, no. 22 (October 15, 2002): 2723–33. http://dx.doi.org/10.1093/hmg/11.22.2723.

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