Structural–Functional Interactions of NS1-BP Protein with the Splicing and Mrna Export Machineries for Viral and Host Gene Expression

Total Page:16

File Type:pdf, Size:1020Kb

Structural–Functional Interactions of NS1-BP Protein with the Splicing and Mrna Export Machineries for Viral and Host Gene Expression Structural–functional interactions of NS1-BP protein with the splicing and mRNA export machineries for viral and host gene expression Ke Zhanga, Guijun Shangb, Abhilash Padavannilb, Juan Wanga, Ramanavelan Sakthivela, Xiang Chenc,d, Min Kime, Matthew G. Thompsonf, Adolfo García-Sastreg,h,i, Kristen W. Lynchf, Zhijian J. Chenc,d, Yuh Min Chookb,1, and Beatriz M. A. Fontouraa,1 aDepartment of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390; bDepartment of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390; cDepartment of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390; dHoward Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390; eDepartment of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390; fDepartment of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104; gDepartment of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029; hGlobal Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029; and iDivision of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029 Edited by Thomas E. Shenk, Princeton University, Princeton, NJ, and approved November 13, 2018 (received for review October 23, 2018) The influenza virulence factor NS1 protein interacts with the Viral mRNA splicing requires the cellular spliceosome. Most cellular NS1-BP protein to promote splicing and nuclear export of of cellular splicing occurs in the nucleoplasm, where splicing the viral M mRNAs. The viral M1 mRNA encodes the M1 matrix factors are recruited to nascent transcripts through interaction protein and is alternatively spliced into the M2 mRNA, which is with polymerase II (Pol II). However, there is some evidence translated into the M2 ion channel. These proteins have key that splicing of a subset of mRNAs might be compartmentalized functions in viral trafficking and budding. To uncover the NS1-BP at nuclear speckles (5), which are known to be storage sites of structural and functional activities in splicing and nuclear export, splicing and processing factors (6). We have shown that influenza we performed proteomics analysis of nuclear NS1-BP binding virus M mRNA is targeted to nuclear speckles for splicing and CELL BIOLOGY partners and showed its interaction with constituents of the nuclear export (7). This process requires both viral and cellular splicing and mRNA export machineries. NS1-BP BTB domains form proteins. Our findings suggested a model in which the viral dimers in the crystal. Full-length NS1-BP is a dimer in solution and protein NS1, a virulence factor of influenza, together with its forms at least a dimer in cells. Mutations suggest that dimerization is cellular interacting partner NS1-BP, promotes targeting of the important for splicing. The central BACK domain of NS1-BP interacts influenza M mRNA to nuclear speckles where heterogeneous directly with splicing factors such as hnRNP K and PTBP1 and with the nuclear RNP K (hnRNP K), in conjunction with the nuclear viral NS1 protein. The BACK domain is also the site for interactions speckle assembly factor SON, promotes splicing of M1 mRNA with mRNA export factor Aly/REF and is required for viral M mRNA into M2 mRNA through recruitment of the splicing machinery nuclear export. The crystal structure of the C-terminal Kelch domain (8). Together with previous findings (9, 10), these results showed shows that it forms a β-propeller fold, which is required for the splic- ing function of NS1-BP. This domain interacts with the polymerase II Significance C-terminal domain and SART1, which are involved in recruitment of splicing factors and spliceosome assembly, respectively. NS1-BP func- A subset of cellular and viral RNAs relies on specific proteins to tions are not only critical for processing a subset of viral mRNAs but mediate splicing and nuclear export for proper gene expres- also impact levels and nuclear export of a subset of cellular mRNAs sion. During influenza virus infection, the virulence factor NS1 encoding factors involved in metastasis and immunity. protein binds the cellular protein NS1-BP to promote splicing and nuclear export of a subset of viral mRNAs that encode mRNA export | influenza virus | splicing | NS1 protein | Kelch critical proteins for viral trafficking and budding. Here we present structures of NS1-BP domains and their functional in- ultiple and highly coordinated viral–host interactions with teractions with components of the splicing and mRNA nuclear Mintranuclear pathways dictate the replication of influenza export machineries to promote viral gene expression. Addi- A viruses, which are major human pathogens. The segmented tionally, NS1-BP is important for proper expression of a subset genome of influenza virus, composed of eight single-strand negative- of mRNAs involved in metastasis and immunity. These findings sense RNAs (viral ribonuclear proteins, vRNPs), enters the host reveal basic features of NS1-BP that can be exploited in antiviral cell nucleus for transcription and replication. Two of the viral therapy and to investigate NS1-BP function in tumorigenesis. mRNAs, M and NS mRNAs, undergo alternative splicing to generate critical viral proteins. For example, the M mRNA gen- Author contributions: K.Z., G.S., Z.J.C., Y.M.C., and B.M.A.F. designed research; K.Z., G.S., A.P., J.W., R.S., X.C., M.K., and M.G.T. performed research; A.G.-S. contributed new re- erates the M1 and M2 proteins involved in viral trafficking and agents/analytic tools; K.Z., G.S., A.P., J.W., R.S., X.C., M.K., M.G.T., A.G.-S., K.W.L., Z.J.C., budding. The M1 protein is encoded by the unspliced M1 mRNA, Y.M.C., and B.M.A.F. analyzed data; and K.W.L., Y.M.C., and B.M.A.F. wrote the paper. whereas the M2 mRNA is derived by the removal of an intron. The authors declare no conflict of interest. The M1 protein is associated with the inner surface of the viral This article is a PNAS Direct Submission. envelope where it appears to interact with the viral glycoproteins Published under the PNAS license. and RNPs. The functions of M1 protein include vRNP nuclear Data deposition: The atomic coordinates reported in this paper have been deposited in export and virion assembly at the plasma membrane. The M2 the Protein Data Bank, www.wwpdb.org (PDB ID code 6N34 for BTB domain and 6N3H for protein encodes a proton channel that acidifies the viral particle in Kelch domain). – the endosomes during viral entry, leading to the disruption of M1 1To whom correspondence may be addressed. Email: Yuhmin.Chook@utsouthwestern. vRNP interactions and the release of vRNPs in the cytoplasm, edu or [email protected]. which are subsequently imported into the nucleus (1). M2 also has This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. functions in the late stages of the virus life cycle, including bud- 1073/pnas.1818012115/-/DCSupplemental. ding (2, 3) and autophagy inhibition (4). www.pnas.org/cgi/doi/10.1073/pnas.1818012115 PNAS Latest Articles | 1of10 Downloaded by guest on September 30, 2021 spatial and temporal regulation of M2 expression, which is likely 440 kDa to 669 kDa and above) where specific bindings partners important to prevent premature expression of an ion channel coeluted at different positions. This pattern suggests the formation of that could be detrimental to the host cell during the early stages prespliceosome and spliceosome complexes between NS1-BP and of virus replication. In addition, M2 expression likely should be splicing factors. Fraction 11 contains NS1-BP, U1A, and SART1, coordinated with budding for effective production of infectious whereas fractions 9.5 and 10 likely contain the high molecular mass viral particles. spliceosome where the expected splicing factors and the mRNA While the core components of the spliceosome have been de- export factor Aly/REF coeluted. As mentioned above, Aly/REF fined, regulatory factors of this key machinery for gene expression interacts with the spliceosome to link splicing to mRNA nuclear have not been fully explored. The spliceosome is an enzymatic export (23). The differences in U1A mobility observed between complex composed of five small nuclear RNPs (snRNPs): U1, U2, fractions 9.5 and 11 are likely due to differential phosphorylation U4, U5, and U6 (11). Additional factors interact with these snRNPs (24). Taken together, a pool of NS1-BP binds splicing factors, and to regulate the different stages of the splicing cycle. In the case of the mRNA export factor Aly/REF, and NS1-BP probably associates influenza virus M1 mRNA, we show that the cellular protein NS1- with prespliceosome and spliceosome complexes. BP interacts with the cellular RNA-binding protein hnRNP K to promote splicing of the viral M1 mRNA. NS1-BP belongs to the Dimerization of NS1-BP via Its BTB Domain Is Required for Splicing. Kelch family of proteins. It has a BTB [broad-complex, tramtrack, To understand the mode of action of NS1-BP on splicing, we and bric-a-brac; also known as a “POZ” (Pox virus and zinc finger)] determined the crystal structure of its BTB domain to 2.8-Å domain at its N terminus, followed by a BACK domain and a C- resolution (Fig. 2A and SI Appendix, Table S2). The NS1-BP terminal Kelch domain (Fig. 1A). Many characterized BTB do- BTB forms a homodimer in the crystal (Fig. 2A). The NS1-BP mains are dimers (12); the central BACK domains of Kelch pro- BTB homodimer is comprised of a group of α-helices that are teins contain HEAT repeats that are possibly flexible (13) and bind flanked by four short β-sheets.
Recommended publications
  • Kelch Proteins: Emerging Roles in Skeletal Muscle Development and Diseases
    Kelch proteins: emerging roles in skeletal muscle development and diseases The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Gupta, Vandana A., and Alan H Beggs. 2014. “Kelch proteins: emerging roles in skeletal muscle development and diseases.” Skeletal Muscle 4 (1): 11. doi:10.1186/2044-5040-4-11. http:// dx.doi.org/10.1186/2044-5040-4-11. Published Version doi:10.1186/2044-5040-4-11 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:12406733 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Gupta and Beggs Skeletal Muscle 2014, 4:11 http://www.skeletalmusclejournal.com/content/4/1/11 REVIEW Open Access Kelch proteins: emerging roles in skeletal muscle development and diseases Vandana A Gupta and Alan H Beggs* Abstract Our understanding of genes that cause skeletal muscle disease has increased tremendously over the past three decades. Advances in approaches to genetics and genomics have aided in the identification of new pathogenic mechanisms in rare genetic disorders and have opened up new avenues for therapeutic interventions by identification of new molecular pathways in muscle disease. Recent studies have identified mutations of several Kelch proteins in skeletal muscle disorders. The Kelch superfamily is one of the largest evolutionary conserved gene families. The 66 known family members all possess a Kelch-repeat containing domain and are implicated in diverse biological functions.
    [Show full text]
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • Supplementary Table 1: Adhesion Genes Data Set
    Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like,
    [Show full text]
  • Identification of a Gene Coding for a Protein Possessing Shared Tumor Epitopes Capable of Inducing HLA-A24-Restricted Cytotoxic T Lymphocytes in Cancer Patients1
    [CANCER RESEARCH 59, 4056–4063, August 15, 1999] Identification of a Gene Coding for a Protein Possessing Shared Tumor Epitopes Capable of Inducing HLA-A24-restricted Cytotoxic T Lymphocytes in Cancer Patients1 Damu Yang, Masanobu Nakao, Shigeki Shichijo, Teruo Sasatomi, Hideo Takasu, Hajime Matsumoto, Kazunori Mori, Akihiro Hayashi, Hideaki Yamana, Kazuo Shirouzu, and Kyogo Itoh2 Cancer Vaccine Development Division, Kurume University Research Center for Innovative Cancer Therapy [D. Y., M. N., K. I.], and Departments of Surgery [A. H., H. Y., K. S.], Immunology [S. S., T. S., H. T., H. M., K. I.], and Otolaryngology [K. M.], Kurume University School of Medicine, Kurume, 830-0011, Japan ABSTRACT we report a gene encoding epitopes that are capable of inducing CTLs in PBMCs of patients with SCCs and adenocarcinomas. Genes encoding tumor epitopes that are capable of inducing CTLs against adenocarcinomas and squamous cell carcinomas, two major hu- man cancers histologically observed in various organs, have rarely been MATERIALS AND METHODS identified. Here, we report a new gene from cDNA of esophageal cancer cells that encodes a shared tumor antigen recognized by HLA-A2402- Generation of HLA-A2402-restricted CTLs. HLA-A2402-restricted and restricted and tumor-specific CTLs. The sequence of this gene is almost tumor-specific CTLs were established from the PBMCs of an esophageal identical to that of the KIAA0156 gene, which has been registered in cancer patient (HLA-A2402/A2601) by the standard method of mixed lym- phocyte tumor cell culture,
    [Show full text]
  • Supplementary Materials
    Supplementary materials Supplementary Table S1: MGNC compound library Ingredien Molecule Caco- Mol ID MW AlogP OB (%) BBB DL FASA- HL t Name Name 2 shengdi MOL012254 campesterol 400.8 7.63 37.58 1.34 0.98 0.7 0.21 20.2 shengdi MOL000519 coniferin 314.4 3.16 31.11 0.42 -0.2 0.3 0.27 74.6 beta- shengdi MOL000359 414.8 8.08 36.91 1.32 0.99 0.8 0.23 20.2 sitosterol pachymic shengdi MOL000289 528.9 6.54 33.63 0.1 -0.6 0.8 0 9.27 acid Poricoic acid shengdi MOL000291 484.7 5.64 30.52 -0.08 -0.9 0.8 0 8.67 B Chrysanthem shengdi MOL004492 585 8.24 38.72 0.51 -1 0.6 0.3 17.5 axanthin 20- shengdi MOL011455 Hexadecano 418.6 1.91 32.7 -0.24 -0.4 0.7 0.29 104 ylingenol huanglian MOL001454 berberine 336.4 3.45 36.86 1.24 0.57 0.8 0.19 6.57 huanglian MOL013352 Obacunone 454.6 2.68 43.29 0.01 -0.4 0.8 0.31 -13 huanglian MOL002894 berberrubine 322.4 3.2 35.74 1.07 0.17 0.7 0.24 6.46 huanglian MOL002897 epiberberine 336.4 3.45 43.09 1.17 0.4 0.8 0.19 6.1 huanglian MOL002903 (R)-Canadine 339.4 3.4 55.37 1.04 0.57 0.8 0.2 6.41 huanglian MOL002904 Berlambine 351.4 2.49 36.68 0.97 0.17 0.8 0.28 7.33 Corchorosid huanglian MOL002907 404.6 1.34 105 -0.91 -1.3 0.8 0.29 6.68 e A_qt Magnogrand huanglian MOL000622 266.4 1.18 63.71 0.02 -0.2 0.2 0.3 3.17 iolide huanglian MOL000762 Palmidin A 510.5 4.52 35.36 -0.38 -1.5 0.7 0.39 33.2 huanglian MOL000785 palmatine 352.4 3.65 64.6 1.33 0.37 0.7 0.13 2.25 huanglian MOL000098 quercetin 302.3 1.5 46.43 0.05 -0.8 0.3 0.38 14.4 huanglian MOL001458 coptisine 320.3 3.25 30.67 1.21 0.32 0.9 0.26 9.33 huanglian MOL002668 Worenine
    [Show full text]
  • Product Datasheet SART1 Antibody NBP2-14836
    Product Datasheet SART1 Antibody NBP2-14836 Unit Size: 0.1 ml Store at 4C short term. Aliquot and store at -20C long term. Avoid freeze-thaw cycles. Protocols, Publications, Related Products, Reviews, Research Tools and Images at: www.novusbio.com/NBP2-14836 Updated 10/25/2020 v.20.1 Earn rewards for product reviews and publications. Submit a publication at www.novusbio.com/publications Submit a review at www.novusbio.com/reviews/destination/NBP2-14836 Page 1 of 4 v.20.1 Updated 10/25/2020 NBP2-14836 SART1 Antibody Product Information Unit Size 0.1 ml Concentration 1.3 mg/ml Storage Store at 4C short term. Aliquot and store at -20C long term. Avoid freeze-thaw cycles. Clonality Polyclonal Preservative 0.05% Sodium Azide Isotype IgG Purity Immunogen affinity purified Buffer PBS and 30% Glycerol Product Description Host Rabbit Gene ID 9092 Gene Symbol SART1 Species Human, Mouse Reactivity Notes Human and mouse. Immunogen displays the following percentage of sequence identity for non-tested species: rat (94%). Immunogen A synthetic peptide made to a internal portion of the human SART1 protein (between residues 100-200) [UniProt O43290] Product Application Details Applications Western Blot, Immunohistochemistry, Immunohistochemistry-Paraffin, ICC/IF (Negative) Recommended Dilutions Western Blot 1 ug/ml, Immunohistochemistry 1:200-1:500, Immunohistochemistry-Paraffin 1:200-1:500, ICC/IF (Negative) Application Notes This SART1 antibody is useful for IHC-paraffin embedded sections and Western blot. In Western blot a band is detected ~100 kDa in NIH-3T3 cell lysate. In IHC- P, staining was observed in the nuclei of mouse testes.
    [Show full text]
  • Use of Genome-Wide Expression Data to Mine the "Gray Zone" of GWA Studies Leads to Novel Candidate Obesity Genes
    Use of Genome-Wide Expression Data to Mine the "Gray Zone" of GWA Studies Leads to Novel Candidate Obesity Genes The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Naukkarinen, Jussi et al. “Use of Genome-Wide Expression Data to Mine the “Gray Zone” of GWA Studies Leads to Novel Candidate Obesity Genes.” PLoS Genet 6.6 (2010): e1000976. As Published http://dx.doi.org/10.1371/journal.pgen.1000976 Publisher Public Library of Science Version Final published version Citable link http://hdl.handle.net/1721.1/60388 Terms of Use Creative Commons Attribution Detailed Terms http://creativecommons.org/licenses/by/2.5/ Use of Genome-Wide Expression Data to Mine the ‘‘Gray Zone’’ of GWA Studies Leads to Novel Candidate Obesity Genes Jussi Naukkarinen1,2,3*, Ida Surakka1,2, Kirsi H. Pietila¨inen4,5, Aila Rissanen4, Veikko Salomaa6, Samuli Ripatti1,2, Hannele Yki-Ja¨rvinen7, Cornelia M. van Duijn8, H.-Erich Wichmann9,10,11, Jaakko Kaprio1,5,12, Marja-Riitta Taskinen13, Leena Peltonen1,2,3,14,15, ENGAGE Consortium" 1 FIMM, Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland, 2 Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland, 3 Department of Medical Genetics, University of Helsinki, Helsinki, Finland, 4 Obesity Research Unit, Department of Psychiatry, Helsinki University Central Hospital, Helsinki, Finland, 5 Finnish Twin Cohort Study, Department of Public Health, University of Helsinki, Helsinki, Finland,
    [Show full text]
  • The Genome of Swinepox Virus
    University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Virology Papers Virology, Nebraska Center for 1-1-2002 The Genome of Swinepox Virus C. L. Afonso Agricultural Research Service, U.S. Department of Agriculture E. R. Tulman Agricultural Research Service, U.S. Department of Agriculture Z. Lu Agricultural Research Service, U.S. Department of Agriculture L. Zsak Agricultural Research Service, U.S. Department of Agriculture Fernando A. Osorio University of Nebraska-Lincoln, [email protected] See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/virologypub Part of the Virology Commons Afonso, C. L.; Tulman, E. R.; Lu, Z.; Zsak, L.; Osorio, Fernando A.; Balinsky, C.; Kutish, G. F.; and Rock, D. L., "The Genome of Swinepox Virus" (2002). Virology Papers. 71. https://digitalcommons.unl.edu/virologypub/71 This Article is brought to you for free and open access by the Virology, Nebraska Center for at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Virology Papers by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors C. L. Afonso, E. R. Tulman, Z. Lu, L. Zsak, Fernando A. Osorio, C. Balinsky, G. F. Kutish, and D. L. Rock This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/ virologypub/71 JOURNAL OF VIROLOGY, Jan. 2002, p. 783–790 Vol. 76, No. 2 0022-538X/02/$04.00ϩ0 DOI: 10.1128/JVI.76.2.783–790.2002 The Genome of Swinepox Virus C. L. Afonso,1*E.R.Tulman,1 Z. Lu,1 L. Zsak,1 F.
    [Show full text]
  • Discovery of a Molecular Glue That Enhances Uprmt to Restore
    bioRxiv preprint doi: https://doi.org/10.1101/2021.02.17.431525; this version posted February 17, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Title: Discovery of a molecular glue that enhances UPRmt to restore proteostasis via TRKA-GRB2-EVI1-CRLS1 axis Authors: Li-Feng-Rong Qi1, 2 †, Cheng Qian1, †, Shuai Liu1, 2†, Chao Peng3, 4, Mu Zhang1, Peng Yang1, Ping Wu3, 4, Ping Li1 and Xiaojun Xu1, 2 * † These authors share joint first authorship Running title: Ginsenoside Rg3 reverses Parkinson’s disease model by enhancing mitochondrial UPR Affiliations: 1 State Key Laboratory of Natural Medicines, China Pharmaceutical University, 210009, Nanjing, Jiangsu, China. 2 Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, China Pharmaceutical University, 210009, Nanjing, Jiangsu, China. 3. National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China 4. Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, 201204, China. Corresponding author: Ping Li, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 210009, Nanjing, Jiangsu, China. Email: [email protected], Xiaojun Xu, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, China Pharmaceutical University, 210009, Nanjing, Jiangsu, China. Telephone number: +86-2583271203, E-mail: [email protected]. bioRxiv preprint doi: https://doi.org/10.1101/2021.02.17.431525; this version posted February 17, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.
    [Show full text]
  • Splicing Factors Sf3a2 and Prp31 Have Direct Roles in Mitotic Chromosome Segregation
    RESEARCH ARTICLE Splicing factors Sf3A2 and Prp31 have direct roles in mitotic chromosome segregation Claudia Pellacani1†, Elisabetta Bucciarelli1†, Fioranna Renda2‡, Daniel Hayward3, Antonella Palena1, Jack Chen3, Silvia Bonaccorsi2, James G Wakefield3, Maurizio Gatti1,2*, Maria Patrizia Somma1* 1Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Universita` di Roma, Roma, Italy; 2Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Universita` di Roma, Roma, Italy; 3Biosciences/Living Systems Institute, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom Abstract Several studies have shown that RNAi-mediated depletion of splicing factors (SFs) results in mitotic abnormalities. However, it is currently unclear whether these abnormalities reflect defective splicing of specific pre-mRNAs or a direct role of the SFs in mitosis. Here, we show that two highly conserved SFs, Sf3A2 and Prp31, are required for chromosome segregation in both Drosophila and human cells. Injections of anti-Sf3A2 and anti-Prp31 antibodies into Drosophila *For correspondence: embryos disrupt mitotic division within 1 min, arguing strongly against a splicing-related mitotic [email protected] (MG); function of these factors. We demonstrate that both SFs bind spindle microtubules (MTs) and the [email protected] Ndc80 complex, which in Sf3A2- and Prp31-depleted cells is not tightly associated with the (MPS) kinetochores; in HeLa cells the Ndc80/HEC1-SF interaction is restricted to the M phase.
    [Show full text]
  • (12) United States Patent (10) Patent No.: US 6,989,232 B2 Burgess Et Al
    USOO6989232B2 (12) United States Patent (10) Patent No.: US 6,989,232 B2 Burgess et al. (45) Date of Patent: Jan. 24, 2006 (54) PROTEINS AND NUCLEIC ACIDS Adams et al, Nature 377 (Suppl), 3 (1995).* ENCODING SAME Nakayama et al, Genomics 51(1), 27(1998).* Mahairas et al. Accession No. B45150 (Oct. 21, 1997).* (75) Inventors: Catherine E. Burgess, Wethersfield, Wallace et al, Methods Enzymol. 152: 432 (1987).* CT (US); Pamela B. Conley, Palo Alto, GenBank Accession No.: CAB01233 (Jun. 20, 2001). CA (US); William M. Grosse, SWALL (SPTR) Accession No.: Q9N4G7 (Oct. 1, 2000). Branford, CT (US); Matthew Hart, San GenBank Accession No.: Z77666 (Jun. 20, 2001). Francisco, CA (US); Ramesh Kekuda, GenBank Accession No. XM 038002 (Oct. 16, 2001). Stamford, CT (US); Richard A. GenBank Accession No. XM 039746 (Oct. 16, 2001). Shimkets, West Haven, CT (US); GenBank Accession No.: AAF51854 (Oct. 4, 2000). Kimberly A. Spytek, New Haven, CT GenBank Accession No.: AAF52569 (Oct. 4, 2000). (US); Edward Szekeres, Jr., Branford, GenBank Accession No.: AAF53188 (Oct. 4, 2000). CT (US); James E. Tomlinson, GenBank Accession No.: AAF55 108 (Oct. 5, 2000). Burlingame, CA (US); James N. GenBank Accession No.: AAF58048 (Oct. 4, 2000). Topper, Los Altos, CA (US); Ruey-Bin GenBank Accession No.: AAF59281 (Oct. 4, 2000). Yang, San Mateo, CA (US) GenBank Accession No.: AE003598 (Oct. 4, 2000). GenBank Accession No.: AE003619 (Oct. 4, 2000). (73) Assignees: Millennium Pharmaceuticals, Inc., GenBank Accession No.: AE003636 (Oct. 4, 2000). Cambridge, MA (US); Curagen GenBank Accession No.: AE003706 (Oct. 5, 2000). Corporation, New Haven, CT (US) GenBank Accession No.: AE003808 (Oct.
    [Show full text]
  • Supplementary Figure 1. Network Map Associated with Upregulated Canonical Pathways Shows Interferon Alpha As a Key Regulator
    Supplementary Figure 1. Network map associated with upregulated canonical pathways shows interferon alpha as a key regulator. IPA core analysis determined interferon-alpha as an upstream regulator in the significantly upregulated genes from RNAseq data from nasopharyngeal swabs of COVID-19 patients (GSE152075). Network map was generated in IPA, overlaid with the Coronavirus Replication Pathway. Supplementary Figure 2. Network map associated with Cell Cycle, Cellular Assembly and Organization, DNA Replication, Recombination, and Repair shows relationships among significant canonical pathways. Significant pathways were identified from pathway analysis of RNAseq from PBMCs of COVID-19 patients. Coronavirus Pathogenesis Pathway was also overlaid on the network map. The orange and blue colors in indicate predicted activation or predicted inhibition, respectively. Supplementary Figure 3. Significant biological processes affected in brochoalveolar lung fluid of severe COVID-19 patients. Network map was generated by IPA core analysis of differentially expressed genes for severe vs mild COVID-19 patients in bronchoalveolar lung fluid (BALF) from scRNA-seq profile of GSE145926. Orange color represents predicted activation. Red boxes highlight important cytokines involved. Supplementary Figure 4. 10X Genomics Human Immunology Panel filtered differentially expressed genes in each immune subset (NK cells, T cells, B cells, and Macrophages) of severe versus mild COVID-19 patients. Three genes (HLA-DQA2, IFIT1, and MX1) were found significantly and consistently differentially expressed. Gene expression is shown per the disease severity (mild, severe, recovered) is shown on the top row and expression across immune cell subsets are shown on the bottom row. Supplementary Figure 5. Network map shows interactions between differentially expressed genes in severe versus mild COVID-19 patients.
    [Show full text]