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Journal articles on the topic 'UBTD1'

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Author: Grafiati

Published: 6 July 2024

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1

Zhang, Xiao-Wei, Xiao-Feng Wang, Su-Jie Ni, Wei Qin, Li-Qin Zhao, Rui-Xi Hua, You-Wei Lu, Jin Li, Goberdhan P. Dimri, and Wei-Jian Guo. "UBTD1 induces cellular senescence through an UBTD1-Mdm2/p53 positive feedback loop." Journal of Pathology 235, no. 4 (January 7, 2015): 656–67. http://dx.doi.org/10.1002/path.4478.

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2

Uhler, Jay P., Henrik Spåhr, Géraldine Farge, Stéphan Clavel, Nils-Göran Larsson, Maria Falkenberg, Tore Samuelsson, and Claes M. Gustafsson. "The UbL protein UBTD1 stably interacts with the UBE2D family of E2 ubiquitin conjugating enzymes." Biochemical and Biophysical Research Communications 443, no. 1 (January 2014): 7–12. http://dx.doi.org/10.1016/j.bbrc.2013.10.137.

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3

Yang, Nan, Tianxiang Chen, Liang Wang, Runkun Liu, Yongshen Niu, Liankang Sun, Bowen Yao, et al. "CXCR4 mediates matrix stiffness-induced downregulation of UBTD1 driving hepatocellular carcinoma progression via YAP signaling pathway." Theranostics 10, no. 13 (2020): 5790–801. http://dx.doi.org/10.7150/thno.44789.

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4

Blueggel, Mike, Johannes van den Boom, Hemmo Meyer, Peter Bayer, and Christine Beuck. "Structure of the PUB Domain from Ubiquitin Regulatory X Domain Protein 1 (UBXD1) and Its Interaction with the p97 AAA+ ATPase." Biomolecules 9, no. 12 (December 14, 2019): 876. http://dx.doi.org/10.3390/biom9120876.

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AAA+ ATPase p97/valosin-containing protein (VCP)/Cdc48 is a key player in various cellular stress responses in which it unfolds ubiquitinated proteins to facilitate their degradation by the proteasome. P97 works in different cellular processes using alternative sets of cofactors and is implicated in multiple degenerative diseases. Ubiquitin regulatory X domain protein 1 (UBXD1) has been linked to pathogenesis and is unique amongst p97 cofactors because it interacts with both termini of p97. Its N-domain binds to the N-domain and N/D1 interface of p97 and regulates its ATPase activity. The PUB (peptide:N-glycanase and UBA or UBX-containing proteins) domain binds the p97 C-terminus, but how it controls p97 function is still unknown. Here we present the NMR structure of UBXD1-PUB together with binding studies, mutational analysis, and a model of UBXD1-PUB in complex with the p97 C-terminus. While the binding pocket is conserved among PUB domains, UBXD1-PUB features a unique loop and turn regions suggesting a role in coordinating interaction with downstream regulators and substrate processing

5

Tremblay, Michel G., Dany S. Sibai, Melissa Valère, Jean-Clément Mars, Frédéric Lessard, Roderick T. Hori, Mohammad Moshahid Khan, Victor Y. Stefanovsky, Mark S. LeDoux, and Tom Moss. "Ribosomal DNA promoter recognition is determined in vivo by cooperation between UBTF1 and SL1 and is compromised in the UBTF-E210K neuroregression syndrome." PLOS Genetics 18, no. 2 (February 9, 2022): e1009644. http://dx.doi.org/10.1371/journal.pgen.1009644.

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Transcription of the ~200 mouse and human ribosomal RNA genes (rDNA) by RNA Polymerase I (RPI/PolR1) accounts for 80% of total cellular RNA, around 35% of all nuclear RNA synthesis, and determines the cytoplasmic ribosome complement. It is therefore a major factor controlling cell growth and its misfunction has been implicated in hypertrophic and developmental disorders. Activation of each rDNA repeat requires nucleosome replacement by the architectural multi-HMGbox factor UBTF to create a 15.7 kbp nucleosome free region (NFR). Formation of this NFR is also essential for recruitment of the TBP-TAFI factor SL1 and for preinitiation complex (PIC) formation at the gene and enhancer-associated promoters of the rDNA. However, these promoters show little sequence commonality and neither UBTF nor SL1 display significant DNA sequence binding specificity, making what drives PIC formation a mystery. Here we show that cooperation between SL1 and the longer UBTF1 splice variant generates the specificity required for rDNA promoter recognition in cell. We find that conditional deletion of the TAF1B subunit of SL1 causes a striking depletion of UBTF at both rDNA promoters but not elsewhere across the rDNA. We also find that while both UBTF1 and -2 variants bind throughout the rDNA NFR, only UBTF1 is present with SL1 at the promoters. The data strongly suggest an induced-fit model of RPI promoter recognition in which UBTF1 plays an architectural role. Interestingly, a recurrent UBTF-E210K mutation and the cause of a pediatric neurodegeneration syndrome provides indirect support for this model. E210K knock-in cells show enhanced levels of the UBTF1 splice variant and a concomitant increase in active rDNA copies. In contrast, they also display reduced rDNA transcription and promoter recruitment of SL1. We suggest the underlying cause of the UBTF-E210K syndrome is therefore a reduction in cooperative UBTF1-SL1 promoter recruitment that may be partially compensated by enhanced rDNA activation.

6

Zhen, M., R. Heinlein, D. Jones, S. Jentsch, and E. P. Candido. "The ubc-2 gene of Caenorhabditis elegans encodes a ubiquitin-conjugating enzyme involved in selective protein degradation." Molecular and Cellular Biology 13, no. 3 (March 1993): 1371–77. http://dx.doi.org/10.1128/mcb.13.3.1371-1377.1993.

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The ubiquitin-protein conjugation system is involved in a variety of eukaryotic cell functions, including the degradation of abnormal and short-lived proteins, chromatin structure, cell cycle progression, and DNA repair. The ubiquitination of target proteins is catalyzed by a ubiquitin-activating enzyme (E1) and ubiquitin-conjugating enzymes (E2s) and in some cases also requires auxiliary substrate recognition proteins (E3s). Multiple E2s have been found, and these likely possess specificity for different classes of target proteins. Here we report the cloning and characterization of a gene (ubc-2) encoding a ubiquitin-conjugating enzyme which is involved in the selective degradation of abnormal and short-lived proteins in the nematode Caenorhabditis elegans. The nematode ubc-2 gene encodes a 16.7-kDa protein with striking amino acid sequence similarity to Saccharomyces cerevisiae UBC4 and UBC5 and Drosophila UbcD1. When driven by the UBC4 promoter, ubc-2 can functionally substitute for UBC4 in yeast cells; it rescues the slow-growth phenotype of ubc4 ubc5 mutants at normal temperature and restores their ability to grow at elevated temperatures. Western blots (immunoblots) of ubc4 ubc5 yeast cells transformed with ubc-2 reveal a protein of the expected size, which cross-reacts with anti-Drosophila UbcD1 antibody. C. elegans ubc-2 is constitutively expressed at all life cycle stages and, unlike yeast UBC4 and UBC5, is not induced by heat shock. Both trans and cis splicing are involved in the maturation of the ubc-2 transcript. These data suggest that yeast UBC4 and UBC5, Drosophila UbcD1, and C. elegans ubc-2 define a highly conserved gene family which plays fundamental roles in all eukaryotic cells.

7

Zhen, M., R. Heinlein, D. Jones, S. Jentsch, and E. P. Candido. "The ubc-2 gene of Caenorhabditis elegans encodes a ubiquitin-conjugating enzyme involved in selective protein degradation." Molecular and Cellular Biology 13, no. 3 (March 1993): 1371–77. http://dx.doi.org/10.1128/mcb.13.3.1371.

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Abstract:

The ubiquitin-protein conjugation system is involved in a variety of eukaryotic cell functions, including the degradation of abnormal and short-lived proteins, chromatin structure, cell cycle progression, and DNA repair. The ubiquitination of target proteins is catalyzed by a ubiquitin-activating enzyme (E1) and ubiquitin-conjugating enzymes (E2s) and in some cases also requires auxiliary substrate recognition proteins (E3s). Multiple E2s have been found, and these likely possess specificity for different classes of target proteins. Here we report the cloning and characterization of a gene (ubc-2) encoding a ubiquitin-conjugating enzyme which is involved in the selective degradation of abnormal and short-lived proteins in the nematode Caenorhabditis elegans. The nematode ubc-2 gene encodes a 16.7-kDa protein with striking amino acid sequence similarity to Saccharomyces cerevisiae UBC4 and UBC5 and Drosophila UbcD1. When driven by the UBC4 promoter, ubc-2 can functionally substitute for UBC4 in yeast cells; it rescues the slow-growth phenotype of ubc4 ubc5 mutants at normal temperature and restores their ability to grow at elevated temperatures. Western blots (immunoblots) of ubc4 ubc5 yeast cells transformed with ubc-2 reveal a protein of the expected size, which cross-reacts with anti-Drosophila UbcD1 antibody. C. elegans ubc-2 is constitutively expressed at all life cycle stages and, unlike yeast UBC4 and UBC5, is not induced by heat shock. Both trans and cis splicing are involved in the maturation of the ubc-2 transcript. These data suggest that yeast UBC4 and UBC5, Drosophila UbcD1, and C. elegans ubc-2 define a highly conserved gene family which plays fundamental roles in all eukaryotic cells.

8

Prophet, Sarah M., Brigitte S. Naughton, and Christian Schlieker. "p97/UBXD1 Generate Ubiquitylated Proteins That Are Sequestered into Nuclear Envelope Herniations in Torsin-Deficient Cells." International Journal of Molecular Sciences 23, no. 9 (April 21, 2022): 4627. http://dx.doi.org/10.3390/ijms23094627.

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DYT1 dystonia is a debilitating neurological movement disorder that arises upon Torsin ATPase deficiency. Nuclear envelope (NE) blebs that contain FG-nucleoporins (FG-Nups) and K48-linked ubiquitin are the hallmark phenotype of Torsin manipulation across disease models of DYT1 dystonia. While the aberrant deposition of FG-Nups is caused by defective nuclear pore complex assembly, the source of K48-ubiquitylated proteins inside NE blebs is not known. Here, we demonstrate that the characteristic K48-ubiquitin accumulation inside blebs requires p97 activity. This activity is highly dependent on the p97 adaptor UBXD1. We show that p97 does not significantly depend on the Ufd1/Npl4 heterodimer to generate the K48-ubiquitylated proteins inside blebs, nor does inhibiting translation affect the ubiquitin sequestration in blebs. However, stimulating global ubiquitylation by heat shock greatly increases the amount of K48-ubiquitin sequestered inside blebs. These results suggest that blebs have an extraordinarily high capacity for sequestering ubiquitylated protein generated in a p97-dependent manner. The p97/UBXD1 axis is thus a major factor contributing to cellular DYT1 dystonia pathology and its modulation represents an unexplored potential for therapeutic development.

9

Kern, Maximilian, Vanesa Fernandez-Sáiz, Zasie Schäfer, and Alexander Buchberger. "UBXD1 binds p97 through two independent binding sites." Biochemical and Biophysical Research Communications 380, no. 2 (March 2009): 303–7. http://dx.doi.org/10.1016/j.bbrc.2009.01.076.

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10

Ramkumar, Poornima, Bennett A. Smith, Anu C. Akinbamidele, Joseph Kapcia, Stephen L. Beauparlant, and Dale S. Haines. "Generation and Characterization of Novel Monoclonal Antibodies Recognizing UBXD1." Hybridoma 28, no. 6 (December 2009): 459–62. http://dx.doi.org/10.1089/hyb.2009.0035.

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11

Yoo, Soon Ji. "Grim Stimulates Diap1 Poly-Ubiquitination by Binding to UbcD1." Molecules and Cells 20, no. 3 (December 2005): 446–51. http://dx.doi.org/10.1016/s1016-8478(23)13252-3.

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12

Pan, Chenyu, Yue Xiong, Xiangdong Lv, Yuanxin Xia, Shuo Zhang, Hao Chen, Jialin Fan, et al. "UbcD1 regulates Hedgehog signaling by directly modulating Ci ubiquitination and processing." EMBO reports 18, no. 11 (September 8, 2017): 1922–34. http://dx.doi.org/10.15252/embr.201643289.

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13

Cenci, G., R. B. Rawson, G. Belloni, D. H. Castrillon, M. Tudor, R. Petrucci, M. L. Goldberg, S. A. Wasserman, and M. Gatti. "UbcD1, a Drosophila ubiquitin-conjugating enzyme required for proper telomere behavior." Genes & Development 11, no. 7 (April 1, 1997): 863–75. http://dx.doi.org/10.1101/gad.11.7.863.

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14

Ryoo, Hyung Don, Andreas Bergmann, Hedva Gonen, Aaron Ciechanover, and Hermann Steller. "Regulation of Drosophila IAP1 degradation and apoptosis by reaper and ubcD1." Nature Cell Biology 4, no. 6 (May 20, 2002): 432–38. http://dx.doi.org/10.1038/ncb795.

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15

Madsen, Louise, Katrine M. Andersen, Søren Prag, Torben Moos, Colin A. Semple, Michael Seeger, and Rasmus Hartmann-Petersen. "Ubxd1 is a novel co-factor of the human p97 ATPase." International Journal of Biochemistry & Cell Biology 40, no. 12 (January 2008): 2927–42. http://dx.doi.org/10.1016/j.biocel.2008.06.008.

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16

Neufeld, Thomas P., Amy H. Tang, and Gerald M. Rubin. "A Genetic Screen to Identify Components of the sina Signaling Pathway in Drosophila Eye Development." Genetics 148, no. 1 (January 1, 1998): 277–86. http://dx.doi.org/10.1093/genetics/148.1.277.

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Abstract Specification of the R7 photoreceptor cell in the developing Drosophila eye requires the seven in absentia (sina) gene. We demonstrate that ectopic expression of sina in all cells behind the morphogenetic furrow disrupts normal eye development during pupation, resulting in a severely disorganized adult eye. Earlier events of cell fate specification appear unaffected. A genetic screen for dominant enhancers and suppressors of this phenotype identified mutations in a number of genes required for normal eye development, including UbcD1, which encodes a ubiquitin conjugating enzyme; SR3-4a, a gene previously implicated in signaling downstream of Ras1; and a Drosophila homolog of the Sin3A transcriptional repressor.

17

Neufeld, Thomas P., Amy H. Tang, and Gerald M. Rubin. "A Genetic Screen to Identify Components of the sina Signaling Pathway in Drosophila Eye Development." Genetics 148, no. 1 (January 1, 1998): 277–86. http://dx.doi.org/10.1093/genetics/148.1.277a.

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AbstractSpecification of the R7 photoreceptor cell in the developing Drosophila eye requires the seven in absentia (sina) gene. We demonstrate that ectopic expression of sina in all cells behind the morphogenetic furrow disrupts normal eye development during pupation, resulting in a severely disorganized adult eye. Earlier events of cell fate specification appear unaffected. A genetic screen for dominant enhancers and suppressors of this phenotype identified mutations in a number of genes required for normal eye development, including UbcD1, which encodes a ubiquitin conjugating enzyme; SR3-4a, a gene previously implicated in signaling downstream of Ras1; and a Drosophila homolog of the Sin3A transcriptional repressor.

18

Nagahama, Masami, Machi Ohnishi, Yumiko Kawate, Takayuki Matsui, Hitomi Miyake, Keizo Yuasa, Katsuko Tani, Mitsuo Tagaya, and Akihiko Tsuji. "UBXD1 is a VCP-interacting protein that is involved in ER-associated degradation." Biochemical and Biophysical Research Communications 382, no. 2 (May 2009): 303–8. http://dx.doi.org/10.1016/j.bbrc.2009.03.012.

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19

Costantini, Susan, Francesca Capone, Andrea Polo, Palmina Bagnara, and Alfredo Budillon. "Valosin-Containing Protein (VCP)/p97: A Prognostic Biomarker and Therapeutic Target in Cancer." International Journal of Molecular Sciences 22, no. 18 (September 21, 2021): 10177. http://dx.doi.org/10.3390/ijms221810177.

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Valosin-containing protein (VCP)/p97, a member of the AAA+ ATPase family, is a molecular chaperone recruited to the endoplasmic reticulum (ER) membrane by binding to membrane adapters (nuclear protein localization protein 4 (NPL4), p47 and ubiquitin regulatory X (UBX) domain-containing protein 1 (UBXD1)), where it is involved in ER-associated protein degradation (ERAD). However, VCP/p97 interacts with many cofactors to participate in different cellular processes that are critical for cancer cell survival and aggressiveness. Indeed, VCP/p97 is reported to be overexpressed in many cancer types and is considered a potential cancer biomarker and therapeutic target. This review summarizes the role of VCP/p97 in different cancers and the advances in the discovery of small-molecule inhibitors with therapeutic potential, focusing on the challenges associated with cancer-related VCP mutations in the mechanisms of resistance to inhibitors.

20

Treier, M., W. Seufert, and S. Jentsch. "Drosophila UbcD1 encodes a highly conserved ubiquitin-conjugating enzyme involved in selective protein degradation." EMBO Journal 11, no. 1 (January 1992): 367–72. http://dx.doi.org/10.1002/j.1460-2075.1992.tb05059.x.

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21

Zhang, H. Y., W. J. Yang, Y. Z. Luo, and J. L. Han. "Genetic Polymorphisms in a 1.2 kb Long Fragment within Intron 2 of Chicken UBTD2 Gene." International Journal of Poultry Science 12, no. 5 (April 15, 2013): 307–11. http://dx.doi.org/10.3923/ijps.2013.307.311.

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22

Braxton, Julian, Chad Altobelli, Michelle Arkin, and Daniel Southworth. "Cryo-EM structures reveal dramatic remodeling of the p97 hexamer by the multi-domain adapter UBXD1." Acta Crystallographica Section A Foundations and Advances 78, a1 (July 29, 2022): a202. http://dx.doi.org/10.1107/s2053273322097972.

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23

Guo, Xing, and Xin Qi. "VCP cooperates with UBXD1 to degrade mitochondrial outer membrane protein MCL1 in model of Huntington's disease." Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease 1863, no. 2 (February 2017): 552–59. http://dx.doi.org/10.1016/j.bbadis.2016.11.026.

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24

Song, Ai-Xin, Chen-Jie Zhou, Xiao Guan, Kong-Hung Sze, and Hong-Yu Hu. "Solution structure of the N-terminal domain of DC-UbP/UBTD2 and its interaction with ubiquitin." Protein Science 19, no. 5 (March 26, 2010): 1104–9. http://dx.doi.org/10.1002/pro.386.

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25

Duan, Lian, Rui Liu, Xiaoyue Cui, Qiaoling Zhang, Dan Cao, Maoshan Chen, and Aijie Zhang. "Identification of UBFD1 as a prognostic biomarker and molecular target among estrogen receptor-positive breast cancer." Biochemical and Biophysical Research Communications 686 (December 2023): 149171. http://dx.doi.org/10.1016/j.bbrc.2023.149171.

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26

Patel, Radhika K., Ravi K. Shah, Vimal S. Prajapati, Kamlesh C. Patel, and Ujjval B. Trivedi. "Draft Genome Analysis of Acinetobacter indicus Strain UBT1, an Efficient Lipase and Biosurfactant Producer." Current Microbiology 78, no. 4 (February 25, 2021): 1238–44. http://dx.doi.org/10.1007/s00284-021-02380-5.

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27

Song, Ai-Xin, Hui Yang, Yong-Guang Gao, Chen-Jie Zhou, Yu-Hang Zhang, and Hong-Yu Hu. "A Ubiquitin Shuttle DC-UbP/UBTD2 Reconciles Protein Ubiquitination and Deubiquitination via Linking UbE1 and USP5 Enzymes." PLoS ONE 9, no. 9 (September 10, 2014): e107509. http://dx.doi.org/10.1371/journal.pone.0107509.

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28

Gadkari, D., G. Mörsdorf, and O. Meyer. "Chemolithoautotrophic assimilation of dinitrogen by Streptomyces thermoautotrophicus UBT1: identification of an unusual N2-fixing system." Journal of Bacteriology 174, no. 21 (1992): 6840–43. http://dx.doi.org/10.1128/jb.174.21.6840-6843.1992.

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29

Ritz, Danilo, Maja Vuk, Philipp Kirchner, Monika Bug, Sabina Schütz, Arnold Hayer, Sebastian Bremer, et al. "Endolysosomal sorting of ubiquitylated caveolin-1 is regulated by VCP and UBXD1 and impaired by VCP disease mutations." Nature Cell Biology 13, no. 9 (August 7, 2011): 1116–23. http://dx.doi.org/10.1038/ncb2301.

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30

Tchelidze, Pavel, Hervé Kaplan, Christine Terryn, Nathalie Lalun, Dominique Ploton, and Marc Thiry. "Electron tomography reveals changes in spatial distribution of UBTF1 and UBTF2 isoforms within nucleolar components during rRNA synthesis inhibition." Journal of Structural Biology 208, no. 2 (November 2019): 191–204. http://dx.doi.org/10.1016/j.jsb.2019.08.014.

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31

Carim-Todd, Laura, Mònica Escarceller, Xavier Estivill, and Lauro Sumoy. "Identification and characterization of UBXD1, a novel UBX domain-containing gene on human chromosome 19p13, and its mouse ortholog." Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 1517, no. 2 (January 2001): 298–301. http://dx.doi.org/10.1016/s0167-4781(00)00248-7.

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32

Haines, Dale S., J. Eugene Lee, Stephen L. Beauparlant, Dane B. Kyle, Willem den Besten, Michael J. Sweredoski, Robert L. J. Graham, Sonja Hess, and Raymond J. Deshaies. "Protein Interaction Profiling of the p97 Adaptor UBXD1 Points to a Role for the Complex in Modulating ERGIC-53 Trafficking." Molecular & Cellular Proteomics 11, no. 6 (February 14, 2012): M111.016444. http://dx.doi.org/10.1074/mcp.m111.016444.

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33

Schütz, Anne Kathrin, Enrico Rennella, and Lewis E. Kay. "Exploiting conformational plasticity in the AAA+ protein VCP/p97 to modify function." Proceedings of the National Academy of Sciences 114, no. 33 (July 31, 2017): E6822—E6829. http://dx.doi.org/10.1073/pnas.1707974114.

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p97/VCP, a member of the AAA+ (ATPases associated with diverse cellular activities) family of proteins, is implicated in the etiology of a group of degenerative diseases affecting bone and muscle tissue as well as the central nervous system. Methyl-TROSY–based NMR studies have previously revealed how disease-causing mutations deregulate a subtle dynamic conformational equilibrium involving the N-terminal domain (NTD) with implications for the binding of certain adaptors, providing insight into how disease mutations lead to abnormal function. Herein the conformational plasticity of the p97 system is explored in an attempt to identify hotspots that can serve as targets for restoring function in disease mutants by shifting the position of the NTD back to its wild-type location. Although p97 is overall robust with respect to extensive mutagenesis throughout the protein involving conservative substitutions of hydrophobic residues, key positions have been identified that alter the NTD equilibrium; these lie in specific regions that localize to the interface between the NTD and the D1 nucleotide-binding domain of the complex. Notably, for a severe disease mutant involving an R155C substitution the NTD equilibrium can be shifted back to its wild-type position by mutation at a secondary site with restoration of wild-type two-pronged binding of the UBXD1 adaptor protein that is impaired in disease; this underlies the potential for recovering function by targeting p97 disease mutants with drug molecules.

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FAUVARQUE, MARIE-ODILE, PATRICK LAURENTI, ANTOINE BOIVIN, SÉBASTIEN BLOYER, RUTH GRIFFIN-SHEA, HENRI-MARC BOURBON, and JEAN-MAURICE DURA. "Dominant modifiers of the polyhomeotic extra-sex-combs phenotype induced by marked P element insertional mutagenesis in Drosophila." Genetical Research 78, no. 2 (October 2001): 137–48. http://dx.doi.org/10.1017/s0016672301005274.

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Members of the Polycomb group (Pc-G) and trithorax group (trx-G) of genes, as well as the enhancers of trx-G and Pc-G (ETP), function together to maintain segment identity during Drosophila development. In order to obtain new marked P mutations in these genes, we screened for dominant modifiers of the extra-sex-combs phenotype displayed by males mutant for the polyhomeotic (ph) gene, a member of the Pc-G group. Five P{lacW} insertions in four different genes were found to stably suppress ph: two are allelic to trithorax, one is the first allele specific to the Minute(2)21C gene, and the remaining two define new trx-G genes, toutatis (tou) in 48A and taranis (tara) in 89B10-13. tou is predicted to encode a 3109 amino acid sequence protein (TOU), which contains a TAM DNA-binding domain, a WAKZ motif, two PHD zinc fingers and a C-terminal bromodomain, and as such is likely to be involved in regulation of chromatin structure as a subunit of a novel chromatin remodelling complex. In a previous study, we found that insertion of a P{ph} transposable element containing ph regulatory sequences creates a high frequency of mutations modifying ph homeotic phenotypes. One such insertion enhanced the ph phenotype and we show that it is a new allele of UbcD1/eff, a gene encoding a ubiquitin-conjugating enzyme that is involved in telomere association and potentially in chromatin remodelling.

35

Huang, Rui, Zev A. Ripstein, John L. Rubinstein, and Lewis E. Kay. "Cooperative subunit dynamics modulate p97 function." Proceedings of the National Academy of Sciences 116, no. 1 (December 24, 2018): 158–67. http://dx.doi.org/10.1073/pnas.1815495116.

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p97 is an essential hexameric AAA+ ATPase involved in a wide range of cellular processes. Mutations in the enzyme are implicated in the etiology of an autosomal dominant neurological disease in which patients are heterozygous with respect to p97 alleles, containing one copy each of WT and disease-causing mutant genes, so that, in vivo, p97 molecules can be heterogeneous in subunit composition. Studies of p97 have, however, focused on homohexameric constructs, where protomers are either entirely WT or contain a disease-causing mutation, showing that for WT p97, the N-terminal domain (NTD) of each subunit can exist in either a down (ADP) or up (ATP) conformation. NMR studies establish that, in the ADP-bound state, the up/down NTD equilibrium shifts progressively toward the up conformation as a function of disease mutant severity. To understand NTD functional dynamics in biologically relevant p97 heterohexamers comprising both WT and disease-causing mutant subunits, we performed a methyl-transverse relaxation optimized spectroscopy (TROSY) NMR study on a series of constructs in which only one of the protomer types is NMR-labeled. Our results show positive cooperativity of NTD up/down equilibria between neighboring protomers, allowing us to define interprotomer pathways that mediate the allosteric communication between subunits. Notably, the perturbed up/down NTD equilibrium in mutant subunits is partially restored by neighboring WT protomers, as is the two-pronged binding of the UBXD1 adaptor that is affected in disease. This work highlights the plasticity of p97 and how subtle perturbations to its free-energy landscape lead to significant changes in NTD conformation and adaptor binding.

36

Mohr, Dirk, and Mulalo Doyoyo. "Experimental Investigation on the Plasticity of Hexagonal Aluminum Honeycomb Under Multiaxial Loading." Journal of Applied Mechanics 71, no. 3 (May 1, 2004): 375–85. http://dx.doi.org/10.1115/1.1683715.

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Abstract:

A new custom-built universal biaxial testing device (UBTD) is introduced and successfully used to investigate the response of aluminum honeycomb under various combinations of large shear and compressive strains in its tubular direction. At the macroscopic level, different characteristic regimes are identified in the measured shear and normal stress-strain curves: elastic I, elastic II, nucleation, softening, and crushing. The first elastic regime shows a conventional linear elastic response, whereas the second elastic regime is nonlinear due to the generation of elastic buckles in the honeycomb microstructure. Nucleation is the point at which the cellular structure loses its load carrying capacity as a result of plastic collapse. It precedes a rapid drop of stress levels in the softening regime as pronounced plastic collapse bands emerge in the microstructure. Formation and growth of plastic folds dominate the microstructural response in the crushing phase. The mechanical features of this phase are long stress plateaus for both the corresponding shear and compressive stress-strain curves. Based on these observations, honeycomb plasticity is established by making analogies of plastic hinge lines and folding systems in the cellular microstructure with dislocations and slip line systems in a solid lattice, respectively. The initial yield surface is found to take the form of an ellipse in stress space, while the crushing behavior is described by a linear envelope along with a nonassociated flow rule based on total strain increments.

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Trusch, Franziska, Anja Matena, Maja Vuk, Lisa Koerver, Helene Knævelsrud, Paul S. Freemont, Hemmo Meyer, and Peter Bayer. "The N-terminal Region of the Ubiquitin Regulatory X (UBX) Domain-containing Protein 1 (UBXD1) Modulates Interdomain Communication within the Valosin-containing Protein p97." Journal of Biological Chemistry 290, no. 49 (October 16, 2015): 29414–27. http://dx.doi.org/10.1074/jbc.m115.680686.

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Zweitzig, D. R., N. Shcherbik, and D. S. Haines. "Retraction for D. R. Zweitzig, N. Shcherbik, and D. S. Haines: AAA ATPase P97 and Adaptor UBXD1 Suppress MDM2 Ubiquitination and Degradation and Promote Constitutive P53 Turnover." Molecular Biology of the Cell 19, no. 11 (November 2008): 5029. http://dx.doi.org/10.1091/mbc.e08-01-0067.

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Torrino, Stéphanie, Victor Tiroille, Bastien Dolfi, Maeva Dufies, Charlotte Hinault, Laurent Bonesso, Sonia Dagnino, et al. "UBTD1 regulates ceramide balance and endolysosomal positioning to coordinate EGFR signaling." eLife 10 (April 22, 2021). http://dx.doi.org/10.7554/elife.68348.

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Abstract:

To adapt in an ever-changing environment, cells must integrate physical and chemical signals and translate them into biological meaningful information through complex signaling pathways. By combining lipidomic and proteomic approaches with functional analysis, we have shown that ubiquitin domain-containing protein 1 (UBTD1) plays a crucial role in both the epidermal growth factor receptor (EGFR) self-phosphorylation and its lysosomal degradation. On the one hand, by modulating the cellular level of ceramides through N-acylsphingosine amidohydrolase 1 (ASAH1) ubiquitination, UBTD1 controls the ligand-independent phosphorylation of EGFR. On the other hand, UBTD1, via the ubiquitination of Sequestosome 1 (SQSTM1/p62) by RNF26 and endolysosome positioning, participates in the lysosomal degradation of EGFR. The coordination of these two ubiquitin-dependent processes contributes to the control of the duration of the EGFR signal. Moreover, we showed that UBTD1 depletion exacerbates EGFR signaling and induces cell proliferation emphasizing a hitherto unknown function of UBTD1 in EGFR-driven human cell proliferation.

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Torrino, Stéphanie, François‐René Roustan, Lisa Kaminski, Thomas Bertero, Sabrina Pisano, Damien Ambrosetti, Maeva Dufies, et al. "UBTD1 is a mechano‐regulator controlling cancer aggressiveness." EMBO reports 20, no. 4 (February 25, 2019). http://dx.doi.org/10.15252/embr.201846570.

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Blueggel, Mike, Alexander Kroening, Matthias Kracht, Johannes van den Boom, Matthias Dabisch, Anna Goehring, Farnusch Kaschani, et al. "The UBX domain in UBXD1 organizes ubiquitin binding at the C-terminus of the VCP/p97 AAA-ATPase." Nature Communications 14, no. 1 (June 5, 2023). http://dx.doi.org/10.1038/s41467-023-38604-4.

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AbstractThe AAA+ ATPase p97/VCP together with different sets of substrate-delivery adapters and accessory cofactor proteins unfolds ubiquitinated substrates to facilitate degradation by the proteasome. The UBXD1 cofactor is connected to p97-associated multisystem proteinopathy but its biochemical function and structural organization on p97 has remained largely elusive. Using a combination of crosslinking mass spectrometry and biochemical assays, we identify an extended UBX (eUBX) module in UBXD1 related to a lariat in another cofactor, ASPL. Of note, the UBXD1-eUBX intramolecularly associates with the PUB domain in UBXD1 close to the substrate exit pore of p97. The UBXD1 PUB domain can also bind the proteasomal shuttling factor HR23b via its UBL domain. We further show that the eUBX domain has ubiquitin binding activity and that UBXD1 associates with an active p97-adapter complex during substrate unfolding. Our findings suggest that the UBXD1-eUBX module receives unfolded ubiquitinated substrates after they exit the p97 channel and before hand-over to the proteasome. The interplay of full-length UBXD1 and HR23b and their function in the context of an active p97:UBXD1 unfolding complex remains to be studied in future work.

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Zhang, Fengchao, Yao Chen, Jie Shen, and Junzheng Zhang. "The Ubiquitin Conjugating Enzyme UbcD1 is Required for Notch Signaling Activation During Drosophila Wing Development." Frontiers in Genetics 12 (October 12, 2021). http://dx.doi.org/10.3389/fgene.2021.770853.

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Notch signaling pathway plays crucial roles in animal development. Protein ubiquitination contributes to Notch signaling regulation by governing the stability and activity of major signaling components. Studies in Drosophila have identified multiple ubiquitin ligases and deubiquitinating enzymes that modify Notch ligand and receptor proteins. The fate of ubiquitinated substrates depend on topologies of the attached ubiquitin chains, which are determined by the ubiquitin conjugating enzymes (E2 enzymes). However, which E2 enzymes participate in Notch signal transduction remain elusive. Here, we report that the E2 enzyme UbcD1 is required for Notch signaling activation during Drosophila wing development. Mutations of UbcD1 lead to marginal nicks in the adult wing and reduction of Notch signaling targets expression in the wing imaginal disc. Genetic analysis reveal that UbcD1 functions in the signaling receiving cells prior to cleavage of the Notch protein. We provide further evidence suggesting that UbcD1 is likely involved in endocytic trafficking of Notch protein. Our results demonstrate that UbcD1 positively regulates Notch signaling and thus reveal a novel role of UbcD1 in development.

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Braxton, Julian R., Chad R. Altobelli, Maxwell R. Tucker, Eric Tse, Aye C. Thwin, Michelle R. Arkin, and Daniel R. Southworth. "The p97/VCP adaptor UBXD1 drives AAA+ remodeling and ring opening through multi-domain tethered interactions." Nature Structural & Molecular Biology, November 9, 2023. http://dx.doi.org/10.1038/s41594-023-01126-0.

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Abstractp97, also known as valosin-containing protein, is an essential cytosolic AAA+ (ATPases associated with diverse cellular activities) hexamer that unfolds substrate polypeptides to support protein homeostasis and macromolecular disassembly. Distinct sets of p97 adaptors guide cellular functions but their roles in direct control of the hexamer are unclear. The UBXD1 adaptor localizes with p97 in critical mitochondria and lysosome clearance pathways and contains multiple p97-interacting domains. Here we identify UBXD1 as a potent p97 ATPase inhibitor and report structures of intact human p97–UBXD1 complexes that reveal extensive UBXD1 contacts across p97 and an asymmetric remodeling of the hexamer. Conserved VIM, UBX and PUB domains tether adjacent protomers while a connecting strand forms an N-terminal domain lariat with a helix wedged at the interprotomer interface. An additional VIM-connecting helix binds along the second (D2) AAA+ domain. Together, these contacts split the hexamer into a ring-open conformation. Structures, mutagenesis and comparisons to other adaptors further reveal how adaptors containing conserved p97-remodeling motifs regulate p97 ATPase activity and structure.

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Clough, Barbara, Daniel Fisch, Todd H. Mize, Vesela Encheva, Ambrosius Snijders, and Eva-Maria Frickel. "p97/VCP targets Toxoplasma gondii vacuoles for parasite restriction in interferon-stimulated human cells." mSphere, November 17, 2023. http://dx.doi.org/10.1128/msphere.00511-23.

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ABSTRACT Infection with the parasite Toxoplasma gondii leads to production of interferon gamma (IFNγ) that stimulates cells to upregulate defense proteins targeting the parasite for cell intrinsic elimination or growth restriction. Various host defense mechanisms operate at the parasitophorous vacuole (PV) in different human cell types leading to PV disruption, acidification, or membrane envelopment. Ubiquitin and p62 are players in all human host control mechanisms of Toxoplasma , but other unifying proteins have not been identified. Here, we show that p97/valosin-containing protein (VCP), as well as its associated proteins ANKRD13A and UBXD1 control Toxoplasma infection while recruited to the PV in IFNγ-stimulated endothelial cells. Convergent deposition of ANKRD13A, p97/VCP, and UBXD1 onto the same vacuole is dependent on vacuolar ubiquitination and observed within 2 h post-infection. ANKRD13A, p97/VCP, and UBXD1 all drive the acidification mechanism of the vacuole, which is the IFNγ-dependent control pathway of Toxoplasma in endothelial cells. We assessed p97/VCP in Toxoplasma control in various human cells and demonstrate that p97/VCP is a universal IFNγ-dependent host restriction factor targeting the Toxoplasma PV in epithelial (HeLa) and endothelial cells (human umbilical vein endothelial cells), fibroblasts (human foreskin fibroblast), and macrophages (THP1). IMPORTANCE Toxoplasma gondii (Tg) is a ubiquitous parasitic pathogen, infecting about one-third of the global population. Tg is controlled in immunocompetent people by mechanisms that are not fully understood. Tg infection drives the production of the inflammatory cytokine interferon gamma (IFNγ), which upregulates intracellular anti-pathogen defense pathways. In this study, we describe host proteins p97/VCP, UBXD1, and ANKRD13A that control Tg at the parasitophorous vacuole (PV) in IFNγ-stimulated endothelial cells. p97/VCP is an ATPase that interacts with a network of cofactors and is active in a wide range of ubiquitin-dependent cellular processes. We demonstrate that PV ubiquitination is a pre-requisite for recruitment of these host defense proteins, and their deposition directs Tg PVs to acidification in endothelial cells. We show that p97/VCP universally targets PVs in human cells and restricts Tg in different human cell types. Overall, these findings reveal new players of intracellular host defense of a vacuolated pathogen.

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Bento, Ana C., Claudia C. Bippes, Corina Kohler, Charles Hemion, Stephan Frank, and Albert Neutzner. "UBXD1 is a mitochondrial recruitment factor for p97/VCP and promotes mitophagy." Scientific Reports 8, no. 1 (August 17, 2018). http://dx.doi.org/10.1038/s41598-018-30963-z.

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"Erratum: Regulation of Drosophila IAP1 degradation and apoptosis by reaper and ubcD1." Nature Cell Biology 4, no. 7 (July 2002): 546. http://dx.doi.org/10.1038/ncb818.

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"Multidomain interactions and ring opening of the p97 ATPase by the UBXD1 adapter." Nature Structural & Molecular Biology, November 16, 2023. http://dx.doi.org/10.1038/s41594-023-01127-z.

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Wu, Jun-Dong, Liqun Xu, Weibin Chen, Yanchun Zhou, Guiyu Zheng, and Wei Gu. "LncRNA PCAT6 mediates UBFD1 expression via sponging miR-545-3p in breast cancer cells." Non-coding RNA Research, February 2024. http://dx.doi.org/10.1016/j.ncrna.2024.01.019.

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Wang, Chen Yi, Si Ying Li, Yun Xia Xiao, Lin Zhen, Xiao Gao Wei, Xiao Bing Tang, Zheng Wei Yuan, and Yu Zuo Bai. "miR‐141‐3p affects β‐catenin signaling and apoptosis by targeting Ubtd2 in rats with anorectal malformations." Annals of the New York Academy of Sciences, November 3, 2022. http://dx.doi.org/10.1111/nyas.14924.

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Patel, Radhika, Vimal Prajapati, Ujjval Trivedi, and Kamlesh Patel. "Optimization of organic solvent-tolerant lipase production by Acinetobacter sp. UBT1 using deoiled castor seed cake." 3 Biotech 10, no. 12 (November 5, 2020). http://dx.doi.org/10.1007/s13205-020-02501-0.

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