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.