Regulation of RNA helicase activity: principles and examples

References

Absmeier, E., Becke, C., Wollenhaupt, J., Santos, K.F., and Wahl, M.C. (2017). Interplay of cis- and trans-regulatory mechanisms in the spliceosomal RNA helicase Brr2. Cell Cycle 16: 100–112. https://doi.org/10.1080/15384101.2016.1255384.Search in Google Scholar PubMed PubMed Central

Absmeier, E., Rosenberger, L., Apelt, L., Becke, C., Santos, K.F., Stelzl, U., and Wahl, M.C. (2015a). A noncanonical PWI domain in the N-terminal helicase-associated region of the spliceosomal Brr2 protein. Acta Crystallogr. D Biol. Crystallogr. 71: 762–771. https://doi.org/10.1107/S1399004715001005.Search in Google Scholar PubMed

Absmeier, E., Santos, K.F., and Wahl, M.C. (2016). Functions and regulation of the Brr2 RNA helicase during splicing. Cell Cycle 15: 3362–3377. https://doi.org/10.1080/15384101.2016.1249549.Search in Google Scholar PubMed PubMed Central

Absmeier, E., Santos, K.F., and Wahl, M.C. (2020). Molecular mechanism underlying inhibition of intrinsic ATPase activity in a Ski2-like RNA helicase. Structure 28: 236–243. https://doi.org/10.1016/j.str.2019.11.014.Search in Google Scholar PubMed

Absmeier, E., Wollenhaupt, J., Mozaffari-Jovin, S., Becke, C., Lee, C.T., Preussner, M., Heyd, F., Urlaub, H., Luhrmann, R., Santos, K.F., et al.. (2015b). The large N-terminal region of the Brr2 RNA helicase guides productive spliceosome activation. Genes Dev. 29: 2576–2587. https://doi.org/10.1101/gad.271528.115.Search in Google Scholar PubMed PubMed Central

Agafonov, D.E., Deckert, J., Wolf, E., Odenwalder, P., Bessonov, S., Will, C.L., Urlaub, H., and Luhrmann, R. (2011). Semiquantitative proteomic analysis of the human spliceosome via a novel two-dimensional gel electrophoresis method. Mol. Cell Biol. 31: 2667–2682. https://doi.org/10.1128/MCB.05266-11.Search in Google Scholar PubMed PubMed Central

Agafonov, D.E., Kastner, B., Dybkov, O., Hofele, R.V., Liu, W.T., Urlaub, H., Luhrmann, R., and Stark, H. (2016). Molecular architecture of the human U4/U6.U5 tri-snRNP. Science 351: 1416–1420. https://doi.org/10.1126/science.aad2085.Search in Google Scholar PubMed

Alexandrov, A., Colognori, D., and Steitz, J.A. (2011). Human eIF4AIII interacts with an eIF4G-like partner, NOM1, revealing an evolutionarily conserved function outside the exon junction complex. Genes Dev. 25: 1078–1090. https://doi.org/10.1101/gad.2045411.Search in Google Scholar PubMed PubMed Central

Andersen, C.B., Ballut, L., Johansen, J.S., Chamieh, H., Nielsen, K.H., Oliveira, C.L., Pedersen, J.S., Seraphin, B., Le Hir, H., and Andersen, G.R. (2006). Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA. Science 313: 1968–1972. https://doi.org/10.1126/science.1131981.Search in Google Scholar PubMed

Andreou, A.Z., Harms, U., and Klostermeier, D. (2016). eIF4B stimulates eIF4A ATPase and unwinding activities by direct interaction through its 7-repeats region. RNA Biol. 14: 113–123. https://doi.org/10.1080/15476286.2016.1259782.Search in Google Scholar PubMed PubMed Central

Andreou, A.Z., Harms, U., and Klostermeier, D. (2019). Single-stranded regions modulate conformational dynamics and ATPase activity of eIF4A to optimize 5′-UTR unwinding. Nucleic Acids Res. 47: 5260–5275. https://doi.org/10.1093/nar/gkz254.Search in Google Scholar PubMed PubMed Central

Andreou, A.Z. and Klostermeier, D. (2014). eIF4B and eIF4G jointly stimulate eIF4A ATPase and unwinding activities by modulation of the eIF4A conformational cycle. J. Mol. Biol. 426: 51–61. https://doi.org/10.1016/j.jmb.2013.09.027.Search in Google Scholar PubMed

Aravind, L. and Koonin, E.V. (1999). G-patch: a new conserved domain in eukaryotic RNA-processing proteins and type D retroviral polyproteins. Trends Biochem. Sci. 24: 342–344. https://doi.org/10.1016/S0968-0004(99)01437-1.Search in Google Scholar PubMed

Aregger, R. and Klostermeier, D. (2009). The DEAD-box helicase YxiN maintains a closed conformation during ATP hydrolysis. Biochemistry 48: 10679–10681. https://doi.org/10.1021/bi901278p.Search in Google Scholar PubMed

Arenas, J.E. and Abelson, J.N. (1997). Prp43: an RNA helicase-like factor involved in spliceosome disassembly. Proc. Natl. Acad. Sci. U. S. A. 94: 11798–11802.10.1073/pnas.94.22.11798Search in Google Scholar PubMed PubMed Central

Bai, R., Wan, R., Yan, C., Lei, J., and Shi, Y. (2018). Structures of the fully assembled Saccharomyces cerevisiae spliceosome before activation. Science 360: 1423–1429. https://doi.org/10.1126/science.aau0325.Search in Google Scholar PubMed

Banerjee, D., McDaniel, P.M., and Rymond, B.C. (2015). Limited portability of G-patch domains in regulators of the Prp43 RNA helicase required for pre-mRNA splicing and ribosomal RNA maturation in Saccharomyces cerevisiae. Genetics 200: 135–147. https://doi.org/10.1534/genetics.115.176461.Search in Google Scholar PubMed PubMed Central

Berke, I.C., Yu, X., Modis, Y., and Egelman, E.H. (2012). MDA5 assembles into a polar helical filament on dsRNA. Proc. Natl. Acad. Sci. U. S. A. 109: 18437–18441.10.1073/pnas.1212186109Search in Google Scholar PubMed PubMed Central

Bertram, K., Agafonov, D.E., Dybkov, O., Haselbach, D., Leelaram, M.N., Will, C.L., Urlaub, H., Kastner, B., Luhrmann, R., and Stark, H. (2017). Cryo-EM structure of a pre-catalytic human spliceosome primed for activation. Cell 170: 701–713 e711. https://doi.org/10.1016/j.cell.2017.07.011.Search in Google Scholar PubMed

Bertram, K., El Ayoubi, L., Dybkov, O., Agafonov, D.E., Will, C.L., Hartmuth, K., Urlaub, H., Kastner, B., Stark, H., and Luhrmann, R. (2020). Structural insights into the roles of metazoan-specific splicing factors in the human step 1 spliceosome. Mol. Cell 80: 127–139 e126. https://doi.org/10.1016/j.molcel.2020.09.012.Search in Google Scholar PubMed

Biyanee, A., Ohnheiser, J., Singh, P., and Klempnauer, K.H. (2014). A novel mechanism for the control of translation of specific mRNAs by tumor suppressor protein Pdcd4: inhibition of translation elongation. Oncogene 34: 1384–1392. https://doi.org/10.1038/onc.2014.83.Search in Google Scholar PubMed

Bohnsack, M.T., Martin, R., Granneman, S., Ruprecht, M., Schleiff, E., and Tollervey, D. (2009). Prp43 bound at different sites on the pre-rRNA performs distinct functions in ribosome synthesis. Mol. Cell 36: 583–592. https://doi.org/10.1016/j.molcel.2009.09.039.Search in Google Scholar PubMed PubMed Central

Bohnsack, K.E., Ficner, R., Bohnsack, M.T., and Jonas, S. (2021). Regulation of DEAH-box RNA helicases by G-patch proteins. Biological Chemistry, 402: 561–579.10.1515/hsz-2020-0338Search in Google Scholar PubMed

Bono, F., Ebert, J., Lorentzen, E., and Conti, E. (2006). The crystal structure of the exon junction complex reveals how it maintains a stable grip on mRNA. Cell 126: 713–725. https://doi.org/10.1016/j.cell.2006.08.006.Search in Google Scholar PubMed

Breitwieser, W., Markussen, F.H., Horstmann, H., and Ephrussi, A. (1996). Oskar protein interaction with Vasa represents an essential step in polar granule assembly. Genes Dev. 10: 2179–2188. https://doi.org/10.1101/gad.10.17.2179.Search in Google Scholar PubMed

Brito Querido, J., Sokabe, M., Kraatz, S., Gordiyenko, Y., Skehel, J.M., Fraser, C.S., and Ramakrishnan, V. (2020). Structure of a human 48S translational initiation complex. Science 369: 1220–1227.10.1126/science.aba4904Search in Google Scholar PubMed PubMed Central

Bruns, A.M., Leser, G.P., Lamb, R.A., and Horvath, C.M. (2014). The innate immune sensor LGP2 activates antiviral signaling by regulating MDA5-RNA interaction and filament assembly. Mol. Cell 55: 771–781. https://doi.org/10.1016/j.molcel.2014.07.003.Search in Google Scholar PubMed PubMed Central

Buchwald, G., Schussler, S., Basquin, C., Le Hir, H., and Conti, E. (2013). Crystal structure of the human eIF4AIII-CWC22 complex shows how a DEAD-box protein is inhibited by a MIF4G domain. Proc. Natl. Acad. Sci. U. S. A. 110: E4611–E4618.10.1073/pnas.1314684110Search in Google Scholar PubMed PubMed Central

Busa, V.F., Rector, M.J., and Russell, R. (2017). The DEAD-box protein CYT-19 Uses arginine residues in its C-tail to tether RNA substrates. Biochemistry 56: 3571–3578. https://doi.org/10.1021/acs.biochem.7b00362.Search in Google Scholar PubMed PubMed Central

Buttner, K., Nehring, S., and Hopfner, K.P. (2007). Structural basis for DNA duplex separation by a superfamily-2 helicase. Nat. Struct. Mol. Biol. 14: 647–652. https://doi.org/10.1038/nsmb1246.Search in Google Scholar PubMed

Cao, W., Coman, M.M., Ding, S., Henn, A., Middleton, E.R., Bradley, M.J., Rhoades, E., Hackney, D.D., Pyle, A.M., and De La Cruz, E.M. (2011). Mechanism of Mss116 ATPase reveals functional diversity of DEAD-Box proteins. J. Mol. Biol. 409: 399–414. https://doi.org/10.1016/j.jmb.2011.04.004.Search in Google Scholar PubMed PubMed Central

Caruthers, J.M. and McKay, D.B. (2002). Helicase structure and mechanism. Curr. Opin. Struct. Biol. 12: 123–133. https://doi.org/10.1016/S0959-440X(02)00298-1.Search in Google Scholar

Chang, J.H., Cho, Y.H., Sohn, S.Y., Choi, J.M., Kim, A., Kim, Y.C., Jang, S.K., and Cho, Y. (2009). Crystal structure of the eIF4A-PDCD4 complex. Proc. Natl. Acad. Sci. U. S. A. 106: 3148–3153.10.1073/pnas.0808275106Search in Google Scholar PubMed PubMed Central

Charenton, C., Wilkinson, M.E., and Nagai, K. (2019). Mechanism of 5′ splice site transfer for human spliceosome activation. Science 364: 362–367.10.1126/science.aax3289Search in Google Scholar PubMed PubMed Central

Charollais, J., Dreyfus, M., and Iost, I. (2004). CsdA, a cold-shock RNA helicase from Escherichia coli, is involved in the biogenesis of 50S ribosomal subunit. Nucleic Acids Res. 32: 2751–2759. https://doi.org/10.1093/nar/gkh603.Search in Google Scholar PubMed PubMed Central

Chen, Y., Boland, A., Kuzuoglu-Ozturk, D., Bawankar, P., Loh, B., Chang, C.T., Weichenrieder, O., and Izaurralde, E. (2014). A DDX6-CNOT1 complex and W-binding pockets in CNOT9 reveal direct links between miRNA target recognition and silencing. Mol. Cell 54: 737–750. https://doi.org/10.1016/j.molcel.2014.03.034.Search in Google Scholar PubMed

Christian, H., Hofele, R.V., Urlaub, H., and Ficner, R. (2014). Insights into the activation of the helicase Prp43 by biochemical studies and structural mass spectrometry. Nucleic Acids Res. 42: 1162–1179. https://doi.org/10.1093/nar/gkt985.Search in Google Scholar PubMed PubMed Central

Collins, R., Karlberg, T., Lehtio, L., Schutz, P., van den Berg, S., Dahlgren, L.G., Hammarstrom, M., Weigelt, J., and Schuler, H. (2009). The DExD/H-box RNA helicase DDX19 is regulated by an alpha -helical switch. J. Biol. Chem. 284: 10296–10300. https://doi.org/10.1074/jbc.C900018200.Search in Google Scholar PubMed PubMed Central

Combs, D.J., Nagel, R.J., Ares, M.Jr., and Stevens, S.W. (2006). Prp43p is a DEAH-box spliceosome disassembly factor essential for ribosome biogenesis. Mol. Cell Biol. 26: 523–534. https://doi.org/10.1128/MCB.26.2.523-534.2006.Search in Google Scholar PubMed PubMed Central

Cordin, O. and Beggs, J.D. (2013). RNA helicases in splicing. RNA Biol. 10: 83–95. https://doi.org/10.4161/rna.22547.Search in Google Scholar PubMed PubMed Central

Cordin, O., Tanner, N.K., Doere, M., Linder, P., and Banroques, J. (2004). The newly discovered Q motif of DEAD-box RNA helicases regulates RNA-binding and helicase activity. EMBO J. 23: 2478–2487.10.1038/sj.emboj.7600272Search in Google Scholar PubMed PubMed Central

Cui, S., Eisenacher, K., Kirchhofer, A., Brzozka, K., Lammens, A., Lammens, K., Fujita, T., Conzelmann, K.K., Krug, A., and Hopfner, K.P. (2008). The C-terminal regulatory domain is the RNA 5′-triphosphate sensor of RIG-I. Mol. Cell 29: 169–179. https://doi.org/10.1016/j.molcel.2007.10.032.Search in Google Scholar PubMed

Daugeron, M.C., Prouteau, M., Lacroute, F., and Seraphin, B. (2011). The highly conserved eukaryotic DRG factors are required for efficient translation in a manner redundant with the putative RNA helicase Slh1. Nucleic Acids Res. 39: 2221–2233. https://doi.org/10.1093/nar/gkq898.Search in Google Scholar PubMed PubMed Central

Davila Gallesio, J., Hackert, P., Bohnsack, K.E., and Bohnsack, M.T. (2020). Sgd1 is an MIF4G domain-containing cofactor of the RNA helicase Fal1 and associates with the 5′ domain of the 18S rRNA sequence. RNA Biol. 17: 539–553. https://doi.org/10.1080/15476286.2020.1716540.Search in Google Scholar PubMed PubMed Central

de la Cruz, J., Kressler, D., and Linder, P. (1999). Unwinding RNA in Saccharomyces cerevisiae: DEAD-box proteins and related families. Trends Biochem. Sci. 24: 192–198. https://doi.org/10.1016/S0968-0004(99)01376-6.Search in Google Scholar PubMed

Del Campo, M. and Lambowitz, A.M. (2009). Structure of the yeast DEAD-box protein Mss116p reveals two wedges that crimp RNA. Mol. Cell 35: 598–609. https://doi.org/10.1016/j.molcel.2009.07.032.Search in Google Scholar PubMed PubMed Central

Del Campo, M., Mohr, S., Jiang, Y., Jia, H., Jankowsky, E., and Lambowitz, A.M. (2009). Unwinding by local strand separation is critical for the function of DEAD-box proteins as RNA chaperones. J. Mol. Biol. 389: 674–693. https://doi.org/10.1016/j.jmb.2009.04.043.Search in Google Scholar PubMed PubMed Central

del Toro Duany, Y., Wu, B., and Hur, S. (2015). MDA5-filament, dynamics and disease. Curr. Opin. Virol. 12: 20–25. https://doi.org/10.1016/j.coviro.2015.01.011.Search in Google Scholar PubMed PubMed Central

Diges, C.M. and Uhlenbeck, O.C. (2001). Escherichia coli DbpA is an RNA helicase that requires hairpin 92 of 23S rRNA. EMBO J. 20: 5503–5512.10.1093/emboj/20.19.5503Search in Google Scholar PubMed PubMed Central

Dominguez, D., Altmann, M., Benz, J., Baumann, U., and Trachsel, H. (1999). Interaction of translation initiation factor eIF4G with eIF4A in the yeast Saccharomyces cerevisiae. J. Biol. Chem. 274: 26720–26726. https://doi.org/10.1074/jbc.274.38.26720.Search in Google Scholar PubMed

Donsbach, P., Yee, B.A., Sanchez-Hevia, D., Berenguer, J., Aigner, S., Yeo, G.W., and Klostermeier, D. (2020). The Thermus thermophilus DEAD-box protein Hera is a general RNA binding protein and plays a key role in tRNA metabolism. RNA 26: 1557–1574. https://doi.org/10.1261/rna.075580.075120.Search in Google Scholar

Fairman-Williams, M.E., Guenther, U.P., and Jankowsky, E. (2010). SF1 and SF2 helicases: family matters. Curr. Opin. Struct. Biol. 20: 313–324. https://doi.org/10.1016/j.sbi.2010.03.011.Search in Google Scholar PubMed PubMed Central

Fan, J.S., Cheng, Z., Zhang, J., Noble, C., Zhou, Z., Song, H., and Yang, D. (2009). Solution and crystal structures of mRNA exporter Dbp5p and its interaction with nucleotides. J. Mol. Biol. 388: 1–10. https://doi.org/10.1016/j.jmb.2009.03.004.Search in Google Scholar PubMed

Ferraiuolo, M.A., Lee, C.S., Ler, L.W., Hsu, J.L., Costa-Mattioli, M., Luo, M.J., Reed, R., and Sonenberg, N. (2004). A nuclear translation-like factor eIF4AIII is recruited to the mRNA during splicing and functions in nonsense-mediated decay. Proc. Natl. Acad. Sci. U. S. A. 101: 4118–4123.10.1073/pnas.0400933101Search in Google Scholar PubMed PubMed Central

Fica, S.M., Oubridge, C., Wilkinson, M.E., Newman, A.J., and Nagai, K. (2019). A human postcatalytic spliceosome structure reveals essential roles of metazoan factors for exon ligation. Science 363: 710–714.10.1126/science.aaw5569Search in Google Scholar PubMed PubMed Central

Fica, S.M., Tuttle, N., Novak, T., Li, N.S., Lu, J., Koodathingal, P., Dai, Q., Staley, J.P., and Piccirilli, J.A. (2013). RNA catalyses nuclear pre-mRNA splicing. Nature 503: 229–234. https://doi.org/10.1038/nature12734.Search in Google Scholar PubMed PubMed Central

Fischer, N. and Weis, K. (2002). The DEAD box protein Dhh1 stimulates the decapping enzyme Dcp1. EMBO J. 21: 2788–2797.10.1093/emboj/21.11.2788Search in Google Scholar PubMed PubMed Central

Floor, S.N., Condon, K.J., Sharma, D., Jankowsky, E., and Doudna, J.A. (2015). Autoinhibitory interdomain interactions and subfamily-specific extensions redefine the catalytic core of the human DEAD-box protein DDX3. J. Biol. Chem. 291: 2412–2421. https://doi.org/10.1074/jbc.M115.700625.Search in Google Scholar PubMed PubMed Central

Galej, W.P., Wilkinson, M.E., Fica, S.M., Oubridge, C., Newman, A.J., and Nagai, K. (2016). Cryo-EM structure of the spliceosome immediately after branching. Nature 537: 197–201. https://doi.org/10.1038/nature19316.Search in Google Scholar PubMed PubMed Central

Gao, Z., Putnam, A.A., Bowers, H.A., Guenther, U.P., Ye, X., Kindsfather, A., Hilliker, A.K., and Jankowsky, E. (2016). Coupling between the DEAD-box RNA helicases Ded1p and eIF4A. eLife 5: e16408. https://doi.org/10.7554/eLife.16408.Search in Google Scholar PubMed PubMed Central

Gorbalenya, A.E. and Koonin, E.V. (1993). Helicases: amino acid sequence comparisons and structure-function relationships. Curr. Opin. Struct. Biol. 3: 419–429. https://doi.org/10.1016/S0959-440X(05)80116-2.Search in Google Scholar

Grohman, J.K., Campo, M.D., Bhaskaran, H., Tijerina, P., Lambowitz, A.M., and Russell, R. (2007). Probing the mechanisms of DEAD-box proteins as general RNA chaperones: the C-terminal domain of CYT-19 mediates general recognition of RNA. Biochemistry 46: 3013–3022. https://doi.org/10.1021/bi0619472.Search in Google Scholar PubMed PubMed Central

Gulay, S., Gupta, N., Lorsch, J.R., and Hinnebusch, A.G. (2020). Distinct interactions of eIF4A and eIF4E with RNA helicase Ded1 stimulate translation in vivo. eLife 9: e58243. https://doi.org/10.7554/eLife.58243.Search in Google Scholar PubMed PubMed Central

Hahn, D. and Beggs, J.D. (2010). Brr2p RNA helicase with a split personality: insights into structure and function. Biochem. Soc. Trans. 38: 1105–1109. https://doi.org/10.1042/BST0381105.Search in Google Scholar PubMed

Hahn, D., Kudla, G., Tollervey, D., and Beggs, J.D. (2012). Brr2p-mediated conformational rearrangements in the spliceosome during activation and substrate repositioning. Genes Dev. 26: 2408–2421. https://doi.org/10.1101/gad.199307.112.Search in Google Scholar PubMed PubMed Central

Halbach, F., Reichelt, P., Rode, M., and Conti, E. (2013). The yeast ski complex: crystal structure and RNA channeling to the exosome complex. Cell 154: 814–826. https://doi.org/10.1016/j.cell.2013.07.017.Search in Google Scholar PubMed

Halbach, F., Rode, M., and Conti, E. (2012). The crystal structure of S. cerevisiae Ski2, a DExH helicase associated with the cytoplasmic functions of the exosome. RNA 18: 124–134. https://doi.org/10.1261/rna.029553.111.Search in Google Scholar PubMed PubMed Central

Halls, C., Mohr, S., Del Campo, M., Yang, Q., Jankowsky, E., and Lambowitz, A.M. (2007). Involvement of DEAD-box proteins in group I and group II intron splicing. Biochemical characterization of Mss116p, ATP hydrolysis-dependent and -independent mechanisms, and general RNA chaperone activity. J. Mol. Biol. 365: 835–855. https://doi.org/10.1016/j.jmb.2006.09.083.Search in Google Scholar PubMed PubMed Central

Hamann, F., Enders, M., and Ficner, R. (2019). Structural basis for RNA translocation by DEAH-box ATPases. Nucleic Acids Res. 47: 4349–4362. https://doi.org/10.1093/nar/gkz150.Search in Google Scholar PubMed PubMed Central

Hamann, F., Schmitt, A., Favretto, F., Hofele, R., Neumann, P., Xiang, S., Urlaub, H., Zweckstetter, M., and Ficner, R. (2020). Structural analysis of the intrinsically disordered splicing factor Spp2 and its binding to the DEAH-box ATPase Prp2. Proc. Natl. Acad. Sci. U. S. A. 117: 2948–2956.10.1073/pnas.1907960117Search in Google Scholar PubMed PubMed Central

Hardwick, S.W. and Luisi, B.F. (2012). Rarely at rest: RNA helicases and their busy contributions to RNA degradation, regulation and quality control. RNA Biol. 10: 56–70. https://doi.org/10.4161/rna.22270.Search in Google Scholar PubMed PubMed Central

Harms, U., Andreou, A.Z., Gubaev, A., and Klostermeier, D. (2014). eIF4B, eIF4G and RNA regulate eIF4A activity in translation initiation by modulating the eIF4A conformational cycle. Nucleic Acids Res. 42: 7911–7922. https://doi.org/10.1093/nar/gku440.Search in Google Scholar PubMed PubMed Central

Haselbach, D., Komarov, I., Agafonov, D.E., Hartmuth, K., Graf, B., Dybkov, O., Urlaub, H., Kastner, B., Luhrmann, R., and Stark, H. (2018). Structure and conformational dynamics of the human spliceosomal B(act) complex. Cell 172: 454–464 e411. https://doi.org/10.1016/j.cell.2018.01.010.Search in Google Scholar PubMed

Hausmann, S., Geiser, J., Vadas, O., Ducret, V., Perron, K., and Valentini, M. (2020). Auxiliary domains of the HrpB bacterial DExH-box helicase shape its RNA preferences. RNA Biol. 17: 637–650. https://doi.org/10.1080/15476286.2020.1720376.Search in Google Scholar PubMed PubMed Central

He, Y., Andersen, G.R., and Nielsen, K.H. (2009). Structural basis for the function of DEAH helicases. EMBO Rep. 11: 180–186.10.1038/embor.2010.11Search in Google Scholar PubMed PubMed Central

Heininger, A.U., Hackert, P., Andreou, A.Z., Boon, K.L., Memet, I., Prior, M., Clancy, A., Schmidt, B., Urlaub, H., Schleiff, E., et al.. (2016). Protein cofactor competition regulates the action of a multifunctional RNA helicase in different pathways. RNA Biol. 13: 320–330. https://doi.org/10.1080/15476286.2016.1142038.Search in Google Scholar PubMed PubMed Central

Henis-Korenblit, S., Shani, G., Sines, T., Marash, L., Shohat, G., and Kimchi, A. (2002). The caspase-cleaved DAP5 protein supports internal ribosome entry site-mediated translation of death proteins. Proc. Natl. Acad. Sci. U. S. A. 99: 5400–5405.10.1073/pnas.082102499Search in Google Scholar PubMed PubMed Central

Henis-Korenblit, S., Strumpf, N.L., Goldstaub, D., and Kimchi, A. (2000). A novel form of DAP5 protein accumulates in apoptotic cells as a result of caspase cleavage and internal ribosome entry site-mediated translation. Mol. Cell Biol. 20: 496–506. https://doi.org/10.1128/MCB.20.2.496-506.2000.Search in Google Scholar PubMed PubMed Central

Henn, A., Bradley, M.J., and De La Cruz, E.M. (2012). ATP utilization and RNA conformational rearrangement by DEAD-box proteins. Annu. Rev. Biophys. 41: 247–267. https://doi.org/10.1146/annurev-biophys-050511-102243.Search in Google Scholar PubMed PubMed Central

Henn, A., Cao, W., Hackney, D.D., and De La Cruz, E.M. (2008). The ATPase cycle mechanism of the DEAD-box rRNA helicase, DbpA. J. Mol. Biol. 377: 193–205. https://doi.org/10.1016/j.jmb.2007.12.046.Search in Google Scholar PubMed PubMed Central

Henn, A., Cao, W., Licciardello, N., Heitkamp, S.E., Hackney, D.D., and De La Cruz, E.M. (2009). Pathway of ATP utilization and duplex rRNA unwinding by the DEAD-box helicase, DbpA. Proc. Natl. Acad. Sci. U. S. A. 107: 4046–4050.10.1073/pnas.0913081107Search in Google Scholar PubMed PubMed Central

Henning, L.M., Santos, K.F., Sticht, J., Jehle, S., Lee, C.T., Wittwer, M., Urlaub, H., Stelzl, U., Wahl, M.C., and Freund, C. (2017). A new role for FBP21 as regulator of Brr2 helicase activity. Nucleic Acids Res. 45: 7922–7937. https://doi.org/10.1093/nar/gkx535.Search in Google Scholar PubMed PubMed Central

Hilbert, M., Kebbel, F., Gubaev, A., and Klostermeier, D. (2011). eIF4G stimulates the activity of the DEAD box protein eIF4A by a conformational guidance mechanism. Nucleic Acids Res. 39: 2260–2270. https://doi.org/10.1093/nar/gkq1127.Search in Google Scholar PubMed PubMed Central

Hilliker, A., Gao, Z., Jankowsky, E., and Parker, R. (2011). The DEAD-box protein Ded1 modulates translation by the formation and resolution of an eIF4F-mRNA complex. Mol. Cell 43: 962–972. https://doi.org/10.1016/j.molcel.2011.08.008.Search in Google Scholar PubMed PubMed Central

Hogbom, M., Collins, R., van den Berg, S., Jenvert, R.M., Karlberg, T., Kotenyova, T., Flores, A., Hedestam, G.B., and Schiavone, L.H. (2007). Crystal structure of conserved domains 1 and 2 of the human DEAD-box helicase DDX3X in complex with the mononucleotide AMP. J. Mol. Biol. 372: 150–159. https://doi.org/10.1016/j.jmb.2007.06.050.Search in Google Scholar PubMed

Hondele, M., Sachdev, R., Heinrich, S., Wang, J., Vallotton, P., Fontoura, B.M.A., and Weis, K. (2019). DEAD-box ATPases are global regulators of phase-separated organelles. Nature 573: 144–148. https://doi.org/10.1038/s41586-019-1502-y.Search in Google Scholar PubMed

Huen, J., Lin, C.L., Golzarroshan, B., Yi, W.L., Yang, W.Z., and Yuan, H.S. (2017). Structural insights into a unique dimeric DEAD-box helicase CshA that promotes RNA decay. Structure 25: 469–481. https://doi.org/10.1016/j.str.2017.01.012.Search in Google Scholar PubMed

Hundsdoerfer, P., Thoma, C., and Hentze, M.W. (2005). Eukaryotic translation initiation factor 4GI and p97 promote cellular internal ribosome entry sequence-driven translation. Proc. Natl. Acad. Sci. U. S. A. 102: 13421–13426.10.1073/pnas.0506536102Search in Google Scholar PubMed PubMed Central

Hunger, K., Beckering, C.L., Wiegeshoff, F., Graumann, P.L., and Marahiel, M.A. (2006). Cold-induced putative DEAD box RNA helicases CshA and CshB are essential for cold adaptation and interact with cold shock protein B in Bacillus subtilis. J. Bacteriol. 188: 240–248. https://doi.org/10.1128/JB.188.1.240-248.2006.Search in Google Scholar PubMed PubMed Central

Imataka, H., Olsen, H.S., and Sonenberg, N. (1997). A new translational regulator with homology to eukaryotic translation initiation factor 4G. EMBO J. 16: 817–825.10.1093/emboj/16.4.817Search in Google Scholar PubMed PubMed Central

Imataka, H. and Sonenberg, N. (1997). Human eukaryotic translation initiation factor 4G (eIF4G) possesses two separate and independent binding sites for eIF4A. Mol. Cell Biol. 17: 6940–6947. https://doi.org/10.1128/MCB.17.12.6940.Search in Google Scholar PubMed PubMed Central

Iwasaki, S., Floor, S.N., and Ingolia, N.T. (2016). Rocaglates convert DEAD-box protein eIF4A into a sequence-selective translational repressor. Nature 534: 558–561. https://doi.org/10.1038/nature17978.Search in Google Scholar PubMed PubMed Central

Iwasaki, S., Iwasaki, W., Takahashi, M., Sakamoto, A., Watanabe, C., Shichino, Y., Floor, S.N., Fujiwara, K., Mito, M., Dodo, K., et al.. (2019). The translation inhibitor Rocaglamide targets a bimolecular cavity between eIF4A and polypurine RNA. Mol. Cell 73: 738–748 e739. https://doi.org/10.1016/j.molcel.2018.11.026.Search in Google Scholar PubMed PubMed Central

Jackson, R.N., Klauer, A.A., Hintze, B.J., Robinson, H., van Hoof, A., and Johnson, S.J. (2010). The crystal structure of Mtr4 reveals a novel arch domain required for rRNA processing. EMBO J. 29: 2205–2216.10.1038/emboj.2010.107Search in Google Scholar PubMed PubMed Central

Jain, S., Wheeler, J.R., Walters, R.W., Agrawal, A., Barsic, A., and Parker, R. (2016). ATPase-modulated stress granules contain a diverse proteome and substructure. Cell 164: 487–498. https://doi.org/10.1016/j.cell.2015.12.038.Search in Google Scholar PubMed PubMed Central

Jeske, M., Bordi, M., Glatt, S., Muller, S., Rybin, V., Muller, C.W., and Ephrussi, A. (2015). The crystal structure of the Drosophila germline inducer Oskar identifies two domains with distinct Vasa helicase- and RNA-binding activities. Cell Rep. 12: 587–598. https://doi.org/10.1016/j.celrep.2015.06.055.Search in Google Scholar PubMed

Jeske, M., Muller, C.W., and Ephrussi, A. (2017). The LOTUS domain is a conserved DEAD-box RNA helicase regulator essential for the recruitment of Vasa to the germ plasm and nuage. Genes Dev. 31: 939–952. https://doi.org/10.1101/gad.297051.117.Search in Google Scholar PubMed PubMed Central

Jiang, F., Ramanathan, A., Miller, M.T., Tang, G.Q., Gale, M.Jr., Patel, S.S., and Marcotrigiano, J. (2011). Structural basis of RNA recognition and activation by innate immune receptor RIG-I. Nature 479: 423–427. https://doi.org/10.1038/nature10537.Search in Google Scholar PubMed PubMed Central

Johnson, S.J. and Jackson, R.N. (2012). Ski2-like RNA helicase structures: common themes and complex assemblies. RNA Biol. 10: 33–43. https://doi.org/10.4161/rna.22101.Search in Google Scholar PubMed PubMed Central

Karginov, F.V., Caruthers, J.M., Hu, Y., McKay, D.B., and Uhlenbeck, O.C. (2005). YxiN is a modular protein combining a DEx(D/H) core and a specific RNA-binding domain. J. Biol. Chem. 280: 35499–35505. https://doi.org/10.1074/jbc.M506815200.Search in Google Scholar PubMed

Karow, A.R. and Klostermeier, D. (2010). A structural model for the DEAD box helicase YxiN in solution: localization of the RNA-binding domain. J. Mol. Biol. 402: 629–637. https://doi.org/10.1016/j.jmb.2010.07.049.Search in Google Scholar PubMed

Kertesz, M., Wan, Y., Mazor, E., Rinn, J.L., Nutter, R.C., Chang, H.Y., and Segal, E. (2010). Genome-wide measurement of RNA secondary structure in yeast. Nature 467: 103–107. https://doi.org/10.1038/nature09322.Search in Google Scholar PubMed PubMed Central

Kim, D.H. and Rossi, J.J. (1999). The first ATPase domain of the yeast 246-kDa protein is required for in vivo unwinding of the U4/U6 duplex. RNA 5: 959–971.10.1017/S135583829999012XSearch in Google Scholar PubMed PubMed Central

Klostermeier, D. and Rudolph, M.G. (2009). A novel dimerization motif in the C-terminal domain of the Thermus thermophilus DEAD box helicase Hera confers substantial flexibility. Nucleic Acids Res. 37: 421–430. https://doi.org/10.1093/nar/gkn947.Search in Google Scholar PubMed PubMed Central

Kohlway, A., Luo, D., Rawling, D.C., Ding, S.C., and Pyle, A.M. (2013). Defining the functional determinants for RNA surveillance by RIG-I. EMBO Rep. 14: 772–779.10.1038/embor.2013.108Search in Google Scholar PubMed PubMed Central

Kossen, K., Karginov, F.V., and Uhlenbeck, O.C. (2002). The carboxy-terminal domain of the DExDH protein YxiN is sufficient to confer specificity for 23S rRNA. J. Mol. Biol. 324: 625–636. https://doi.org/10.1016/S0022-2836(02)01140-3.Search in Google Scholar

Kota, K.P., Wagner, S.R., Huerta, E., Underwood, J.M., and Nickerson, J.A. (2008). Binding of ATP to UAP56 is necessary for mRNA export. J. Cell Sci. 121: 1526–1537. https://doi.org/10.1242/jcs.021055.Search in Google Scholar PubMed

Kowalinski, E., Lunardi, T., McCarthy, A.A., Louber, J., Brunel, J., Grigorov, B., Gerlier, D., and Cusack, S. (2011). Structural basis for the activation of innate immune pattern-recognition receptor RIG-I by viral RNA. Cell 147: 423–435. https://doi.org/10.1016/j.cell.2011.09.039.Search in Google Scholar PubMed

Kubikova, J., Reinig, R., Salgania, H.K., and Jeske, M. (2020). LOTUS-domain proteins – developmental effectors from a molecular perspective. Biol. Chem. 402: 7–23. https://doi.org/10.1515/hsz-2020-0270.Search in Google Scholar PubMed

Laggerbauer, B., Achsel, T., and Luhrmann, R. (1998). The human U5-200kD DEXH-box protein unwinds U4/U6 RNA duplices in vitro. Proc. Natl. Acad. Sci. U. S. A. 95: 4188–4192.10.1073/pnas.95.8.4188Search in Google Scholar PubMed PubMed Central

Lau, P.W., Guiley, K.Z., De, N., Potter, C.S., Carragher, B., and Macrae, I.J. (2012). The molecular architecture of human Dicer. Nat. Struct. Mol. Biol. 19: 436–440. https://doi.org/10.1038/nsmb.2268.Search in Google Scholar PubMed PubMed Central

Lebaron, S., Papin, C., Capeyrou, R., Chen, Y.L., Froment, C., Monsarrat, B., Caizergues-Ferrer, M., Grigoriev, M., and Henry, Y. (2009). The ATPase and helicase activities of Prp43p are stimulated by the G-patch protein Pfa1p during yeast ribosome biogenesis. EMBO J. 28: 3808–3819.10.1038/emboj.2009.335Search in Google Scholar PubMed PubMed Central

Lewis, S.M., Cerquozzi, S., Graber, T.E., Ungureanu, N.H., Andrews, M., and Holcik, M. (2008). The eIF4G homolog DAP5/p97 supports the translation of select mRNAs during endoplasmic reticulum stress. Nucleic Acids Res. 36: 168–178. https://doi.org/10.1093/nar/gkm1007.Search in Google Scholar PubMed PubMed Central

Li, X., Ranjith-Kumar, C.T., Brooks, M.T., Dharmaiah, S., Herr, A.B., Kao, C., and Li, P. (2009). The RIG-I-like receptor LGP2 recognizes the termini of double-stranded RNA. J. Biol. Chem. 284: 13881–13891. https://doi.org/10.1074/jbc.M900818200.Search in Google Scholar PubMed PubMed Central

Linder, P. and Jankowsky, E. (2011). From unwinding to clamping – the DEAD box RNA helicase family. Nat. Rev. Mol. Cell Biol. 12: 505–516. https://doi.org/10.1038/nrm3154.Search in Google Scholar PubMed

Liu, F., Putnam, A., and Jankowsky, E. (2008). ATP hydrolysis is required for DEAD-box protein recycling but not for duplex unwinding. Proc. Natl. Acad. Sci. U. S. A. 51: 20209–20214.10.1073/pnas.0811115106Search in Google Scholar PubMed PubMed Central

Liu, S., Li, X., Zhang, L., Jiang, J., Hill, R.C., Cui, Y., Hansen, K.C., Zhou, Z.H., and Zhao, R. (2017). Structure of the yeast spliceosomal postcatalytic P complex. Science 358: 1278–1283.10.1126/science.aar3462Search in Google Scholar PubMed PubMed Central

Lorsch, J.R. and Herschlag, D. (1998a). The DEAD box protein eIF4A. 1. A minimal kinetic and thermodynamic framework reveals coupled binding of RNA and nucleotide. Biochemistry 37: 2180–2193. https://doi.org/10.1021/bi972430g.Search in Google Scholar PubMed

Lorsch, J.R. and Herschlag, D. (1998b). The DEAD box protein eIF4A. 2. A cycle of nucleotide and RNA-dependent conformational changes. Biochemistry 37: 2194–2206. https://doi.org/10.1021/bi9724319.Search in Google Scholar PubMed

Lu, C., Ranjith-Kumar, C.T., Hao, L., Kao, C.C., and Li, P. (2010). Crystal structure of RIG-I C-terminal domain bound to blunt-ended double-strand RNA without 5′ triphosphate. Nucleic Acids Res. 39: 1565–1575. https://doi.org/10.1093/nar/gkq974.Search in Google Scholar PubMed PubMed Central

Luo, D., Ding, S.C., Vela, A., Kohlway, A., Lindenbach, B.D., and Pyle, A.M. (2011). Structural insights into RNA recognition by RIG-I. Cell 147: 409–422. https://doi.org/10.1016/j.cell.2011.09.023.Search in Google Scholar

Luo, D., Kohlway, A., Vela, A., and Pyle, A.M. (2012). Visualizing the determinants of viral RNA recognition by innate immune sensor RIG-I. Structure 20: 1983–1988. https://doi.org/10.1016/j.str.2012.08.029.Search in Google Scholar

Maeder, C., Kutach, A.K., and Guthrie, C. (2009). ATP-dependent unwinding of U4/U6 snRNAs by the Brr2 helicase requires the C terminus of Prp8. Nat. Struct. Mol. Biol. 16: 42–48. https://doi.org/10.1038/nsmb.1535.Search in Google Scholar

Mallam, A.L., Del Campo, M., Gilman, B., Sidote, D.J., and Lambowitz, A.M. (2012). Structural basis for RNA-duplex recognition and unwinding by the DEAD-box helicase Mss116p. Nature 490: 121–125. https://doi.org/10.1038/nature11402.Search in Google Scholar

Mallam, A.L., Jarmoskaite, I., Tijerina, P., Del Campo, M., Seifert, S., Guo, L., Russell, R., and Lambowitz, A.M. (2011). Solution structures of DEAD-box RNA chaperones reveal conformational changes and nucleic acid tethering by a basic tail. Proc. Natl. Acad. Sci. U. S. A. 108: 12254–12259.10.1073/pnas.1109566108Search in Google Scholar

Mallam, A.L., Sidote, D.J., and Lambowitz, A.M. (2014). Molecular insights into RNA and DNA helicase evolution from the determinants of specificity for a DEAD-box RNA helicase. eLife 3: e04630. https://doi.org/10.7554/eLife.04630.Search in Google Scholar

Marcotrigiano, J., Lomakin, I.B., Sonenberg, N., Pestova, T.V., Hellen, C.U., and Burley, S.K. (2001). A conserved HEAT domain within eIF4G directs assembly of the translation initiation machinery. Mol. Cell 7: 193–203. https://doi.org/10.1016/S1097-2765(01)00167-8.Search in Google Scholar

Marintchev, A. (2013). Roles of helicases in translation initiation: a mechanistic view. Biochim. Biophys. Acta 1829: 799–809. https://doi.org/10.1016/j.bbagrm.2013.01.005.Search in Google Scholar

Martegani, E., Vanoni, M., Mauri, I., Rudoni, S., Saliola, M., and Alberghina, L. (1997). Identification of gene encoding a putative RNA-helicase, homologous to SKI2, in chromosome VII of Saccharomyces cerevisiae. Yeast 13: 391–397. https://doi.org/10.1002/(SICI)1097-0061(19970330)13:4<391::AID-YEA92>3.0.CO;2-Q.10.1002/(SICI)1097-0061(19970330)13:4<391::AID-YEA92>3.0.CO;2-QSearch in Google Scholar

Martin, R., Straub, A.U., Doebele, C., and Bohnsack, M.T. (2012). DExD/H-box RNA helicases in ribosome biogenesis. RNA Biol. 9: 1173–1182. https://doi.org/10.4161/rna.21879.Search in Google Scholar

Mathys, H., Basquin, J., Ozgur, S., Czarnocki-Cieciura, M., Bonneau, F., Aartse, A., Dziembowski, A., Nowotny, M., Conti, E., and Filipowicz, W. (2014). Structural and biochemical insights to the role of the CCR4-NOT complex and DDX6 ATPase in microRNA repression. Mol. Cell 54: 751–765. https://doi.org/10.1016/j.molcel.2014.03.036.Search in Google Scholar PubMed

Mayerle, M. and Guthrie, C. (2016). Prp8 retinitis pigmentosa mutants cause defects in the transition between the catalytic steps of splicing. RNA 22: 793–809. https://doi.org/10.1261/rna.055459.115.Search in Google Scholar PubMed PubMed Central

Mohr, G., Del Campo, M., Mohr, S., Yang, Q., Jia, H., Jankowsky, E., and Lambowitz, A.M. (2008). Function of the C-terminal domain of the DEAD-box protein Mss116p analyzed in vivo and in vitro. J. Mol. Biol. 375: 1344–1364. https://doi.org/10.1016/j.jmb.2007.11.041.Search in Google Scholar PubMed PubMed Central

Montpetit, B., Thomsen, N.D., Helmke, K.J., Seeliger, M.A., Berger, J.M., and Weis, K. (2011). A conserved mechanism of DEAD-box ATPase activation by nucleoporins and InsP6 in mRNA export. Nature 472: 238–242. https://doi.org/10.1038/nature09862.Search in Google Scholar PubMed PubMed Central

Morlang, S., Weglohner, W., and Franceschi, F. (1999). Hera from Thermus thermophilus: the first thermostable DEAD-box helicase with an RNase P protein motif. J. Mol. Biol. 294: 795–805. https://doi.org/10.1006/jmbi.1999.3282.Search in Google Scholar PubMed

Mosallanejad, K., Sekine, Y., Ishikura-Kinoshita, S., Kumagai, K., Nagano, T., Matsuzawa, A., Takeda, K., Naguro, I., and Ichijo, H. (2014). The DEAH-box RNA helicase DHX15 activates NF-kappaB and MAPK signaling downstream of MAVS during antiviral responses. Sci. Signal. 7: ra40. https://doi.org/10.1126/scisignal.2004841.Search in Google Scholar PubMed

Mozaffari-Jovin, S., Santos, K.F., Hsiao, H.H., Will, C.L., Urlaub, H., Wahl, M.C., and Luhrmann, R. (2012). The Prp8 RNase H-like domain inhibits Brr2-mediated U4/U6 snRNA unwinding by blocking Brr2 loading onto the U4 snRNA. Genes Dev. 26: 2422–2434. https://doi.org/10.1101/gad.200949.112.Search in Google Scholar PubMed PubMed Central

Mozaffari-Jovin, S., Wandersleben, T., Santos, K.F., Will, C.L., Luhrmann, R., and Wahl, M.C. (2013). Inhibition of RNA helicase Brr2 by the C-terminal tail of the spliceosomal protein Prp8. Science 341: 80–84.10.1126/science.1237515Search in Google Scholar PubMed

Mugler, C.F., Hondele, M., Heinrich, S., Sachdev, R., Vallotton, P., Koek, A.Y., Chan, L.Y., and Weis, K. (2016). ATPase activity of the DEAD-box protein Dhh1 controls processing body formation. eLife 5: e18746. https://doi.org/10.7554/eLife.18746.Search in Google Scholar PubMed PubMed Central

Myong, S., Cui, S., Cornish, P.V., Kirchhofer, A., Gack, M.U., Jung, J.U., Hopfner, K.P., and Ha, T. (2009). Cytosolic viral sensor RIG-I is a 5′-triphosphate-dependent translocase on double-stranded RNA. Science 323: 1070–1074.10.1126/science.1168352Search in Google Scholar PubMed PubMed Central

Napetschnig, J., Kassube, S.A., Debler, E.W., Wong, R.W., Blobel, G., and Hoelz, A. (2009). Structural and functional analysis of the interaction between the nucleoporin Nup214 and the DEAD-box helicase Ddx19. Proc. Natl. Acad. Sci. U. S. A. 106: 3089–3094.10.1073/pnas.0813267106Search in Google Scholar PubMed PubMed Central

Nevins, T.A., Harder, Z.M., Korneluk, R.G., and Holcik, M. (2003). Distinct regulation of internal ribosome entry site-mediated translation following cellular stress is mediated by apoptotic fragments of eIF4G translation initiation factor family members eIF4GI and p97/DAP5/NAT1. J. Biol. Chem. 278: 3572–3579. https://doi.org/10.1074/jbc.M206781200.Search in Google Scholar PubMed

Nguyen, T.H., Li, J., Galej, W.P., Oshikane, H., Newman, A.J., and Nagai, K. (2013). Structural basis of Brr2-Prp8 interactions and implications for U5 snRNP biogenesis and the spliceosome active site. Structure 21: 910–919. https://doi.org/10.1016/j.str.2013.04.017.Search in Google Scholar PubMed PubMed Central

Nguyen, T.H.D., Galej, W.P., Bai, X.C., Oubridge, C., Newman, A.J., Scheres, S.H.W., and Nagai, K. (2016). Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 A resolution. Nature 530: 298–302. https://doi.org/10.1038/nature16940.Search in Google Scholar PubMed PubMed Central

Nielsen, K.H., Behrens, M.A., He, Y., Oliveira, C.L., Sottrup Jensen, L., Hoffmann, S.V., Pedersen, J.S., and Andersen, G.R. (2011). Synergistic activation of eIF4A by eIF4B and eIF4G. Nucleic Acids Res. 15: 67–75. https://doi.org/10.1093/nar/gkq1206.Search in Google Scholar PubMed PubMed Central

Oberer, M., Marintchev, A., and Wagner, G. (2005). Structural basis for the enhancement of eIF4A helicase activity by eIF4G. Genes Dev. 19: 2212–2223. https://doi.org/10.1101/gad.1335305.Search in Google Scholar PubMed PubMed Central

Patil, V.S., Anand, A., Chakrabarti, A., and Kai, T. (2014). The Tudor domain protein Tapas, a homolog of the vertebrate Tdrd7, functions in the piRNA pathway to regulate retrotransposons in germline of Drosophila melanogaster. BMC Biol. 12: 61. https://doi.org/10.1186/s12915-014-0061-9.Search in Google Scholar PubMed PubMed Central

Patil, V.S. and Kai, T. (2010). Repression of retroelements in Drosophila germline via piRNA pathway by the Tudor domain protein Tejas. Curr. Biol. 20: 724–730. https://doi.org/10.1016/j.cub.2010.02.046.Search in Google Scholar PubMed

Patrick, E.M., Srinivasan, S., Jankowsky, E., and Comstock, M.J. (2017). The RNA helicase Mtr4p is a duplex-sensing translocase. Nat. Chem. Biol. 13: 99–104. https://doi.org/10.1038/nchembio.2234.Search in Google Scholar PubMed

Peisley, A., Jo, M.H., Lin, C., Wu, B., Orme-Johnson, M., Walz, T., Hohng, S., and Hur, S. (2012). Kinetic mechanism for viral dsRNA length discrimination by MDA5 filaments. Proc. Natl. Acad. Sci. U. S. A. 109: E3340–E3349.10.1073/pnas.1208618109Search in Google Scholar PubMed PubMed Central

Peisley, A., Lin, C., Wu, B., Orme-Johnson, M., Liu, M., Walz, T., and Hur, S. (2011). Cooperative assembly and dynamic disassembly of MDA5 filaments for viral dsRNA recognition. Proc. Natl. Acad. Sci. U. S. A. 108: 21010–21015.10.1073/pnas.1113651108Search in Google Scholar PubMed PubMed Central

Pena, V., Jovin, S.M., Fabrizio, P., Orlowski, J., Bujnicki, J.M., Luhrmann, R., and Wahl, M.C. (2009). Common design principles in the spliceosomal RNA helicase Brr2 and in the Hel308 DNA helicase. Mol. Cell 35: 454–466. https://doi.org/10.1016/j.molcel.2009.08.006.Search in Google Scholar PubMed

Pietrzyk-Brzezinska, A.J., Absmeier, E., Klauck, E., Wen, Y., Antelmann, H., and Wahl, M.C. (2018). Crystal structure of the Escherichia coli DExH-box NTPase HrpB. Structure 26: 1462–1473. https://doi.org/10.1016/j.str.2018.07.013.Search in Google Scholar PubMed

Pippig, D.A., Hellmuth, J.C., Cui, S., Kirchhofer, A., Lammens, K., Lammens, A., Schmidt, A., Rothenfusser, S., and Hopfner, K.P. (2009). The regulatory domain of the RIG-I family ATPase LGP2 senses double-stranded RNA. Nucleic Acids Res. 37: 2014–2025. https://doi.org/10.1093/nar/gkp059.Search in Google Scholar PubMed PubMed Central

Plaschka, C., Lin, P.C., and Nagai, K. (2017). Structure of a pre-catalytic spliceosome. Nature 546: 617–621. https://doi.org/10.1038/nature22799.Search in Google Scholar PubMed PubMed Central

Ponting, C.P. (2000). Novel eIF4G domain homologues linking mRNA translation with nonsense-mediated mRNA decay. Trends Biochem. Sci. 25: 423–426. https://doi.org/10.1016/S0968-0004(00)01628-5.Search in Google Scholar PubMed

Prabu, J.R., Muller, M., Thomae, A.W., Schussler, S., Bonneau, F., Becker, P.B., and Conti, E. (2015). Structure of the RNA helicase MLE reveals the molecular mechanisms for uridine specificity and RNA-ATP coupling. Mol. Cell 60: 487–499. https://doi.org/10.1016/j.molcel.2015.10.011.Search in Google Scholar PubMed

Putnam, A.A., Gao, Z., Liu, F., Jia, H., Yang, Q., and Jankowsky, E. (2015). Division of labor in an oligomer of the DEAD-box RNA helicase Ded1p. Mol. Cell 59: 541–452. https://doi.org/10.1016/j.molcel.2015.06.030.Search in Google Scholar PubMed PubMed Central

Putnam, A.A. and Jankowsky, E. (2013). AMP sensing by DEAD-box RNA helicases. J. Mol. Biol. 1829: 884–893. https://doi.org/10.1016/j.jmb.2013.05.006.Search in Google Scholar PubMed PubMed Central

Pyle, A.M. (2008). Translocation and unwinding mechanisms of RNA and DNA helicases. Annu. Rev. Biophys. 37: 317–336. https://doi.org/10.1146/annurev.biophys.37.032807.125908.Search in Google Scholar PubMed

Raghunathan, P.L. and Guthrie, C. (1998). RNA unwinding in U4/U6 snRNPs requires ATP hydrolysis and the DEIH-box splicing factor Brr2. Curr. Biol. 8: 847–855. https://doi.org/10.1016/S0960-9822(07)00345-4.Search in Google Scholar

Rauhut, R., Fabrizio, P., Dybkov, O., Hartmuth, K., Pena, V., Chari, A., Kumar, V., Lee, C.T., Urlaub, H., Kastner, B., et al.. (2016). Molecular architecture of the Saccharomyces cerevisiae activated spliceosome. Science 353: 1399–1405.10.1126/science.aag1906Search in Google Scholar PubMed

Ray, B.K., Lawson, T.G., Kramer, J.C., Cladaras, M.H., Grifo, J.A., Abramson, R.D., Merrick, W.C., and Thach, R.E. (1985). ATP-dependent unwinding of messenger RNA structure by eukaryotic initiation factors. J. Biol. Chem. 260: 7651–7658. https://doi.org/10.1016/S0021-9258(17)39658-8.Search in Google Scholar

Rhine, K., Vidaurre, V., and Myong, S. (2020). RNA droplets. Annu. Rev. Biophys. 49: 247–265. https://doi.org/10.1146/annurev-biophys-052118-115508.Search in Google Scholar PubMed PubMed Central

Robert-Paganin, J., Rety, S., and Leulliot, N. (2015). Regulation of DEAH/RHA helicases by G-patch proteins. BioMed Res. Int. 2015: 931857.10.1155/2015/931857Search in Google Scholar PubMed PubMed Central

Rogers, G.W.Jr., Lima, W.F., and Merrick, W.C. (2001a). Further characterization of the helicase activity of eIF4A. Substrate specificity. J. Biol. Chem. 276: 12598–12608. https://doi.org/10.1074/jbc.M007560200.Search in Google Scholar PubMed

Rogers, G.W.Jr., Richter, N.J., Lima, W.F., and Merrick, W.C. (2001b). Modulation of the helicase activity of eIF4A by eIF4B, eIF4H, and eIF4F. J. Biol. Chem. 276: 30914–30922. https://doi.org/10.1074/jbc.M100157200.Search in Google Scholar PubMed

Rogers, G.W.Jr., Richter, N.J., and Merrick, W.C. (1999). Biochemical and kinetic characterization of the RNA helicase activity of eukaryotic initiation factor 4A. J. Biol. Chem. 274: 12236–12244. https://doi.org/10.1074/jbc.274.18.12236.Search in Google Scholar PubMed

Rothenfusser, S., Goutagny, N., DiPerna, G., Gong, M., Monks, B.G., Schoenemeyer, A., Yamamoto, M., Akira, S., and Fitzgerald, K.A. (2005). The RNA helicase Lgp2 inhibits TLR-independent sensing of viral replication by retinoic acid-inducible gene-I. J. Immunol. 175: 5260–5268. https://doi.org/10.4049/jimmunol.175.8.5260.Search in Google Scholar PubMed

Rudolph, M.G., Heissmann, R., Wittmann, J.G., and Klostermeier, D. (2006). Crystal structure and nucleotide binding of the Thermus thermophilus RNA helicase Hera N-terminal domain. J. Mol. Biol. 361: 731–743. https://doi.org/10.1016/j.jmb.2006.06.065.Search in Google Scholar PubMed

Rudolph, M.G. and Klostermeier, D. (2009). The Thermus thermophilus DEAD box helicase Hera contains a modified RNA recognition motif domain loosely connected to the helicase core. RNA 15: 1993–2001. https://doi.org/10.1261/rna.1820009.Search in Google Scholar PubMed PubMed Central

Rudolph, M.G. and Klostermeier, D. (2015). When core competence is not enough: functional interplay of the DEAD-box helicase core with ancillary domains and auxiliary factors in RNA binding and unwinding. Biol. Chem. 396: 849–865. https://doi.org/10.1515/hsz-2014-0277.Search in Google Scholar PubMed

Sachdev, R., Hondele, M., Linsenmeier, M., Vallotton, P., Mugler, C.F., Arosio, P., and Weis, K. (2019). Pat1 promotes processing body assembly by enhancing the phase separation of the DEAD-box ATPase Dhh1 and RNA. eLife 8: e41415. https://doi.org/10.7554/eLife.41415.Search in Google Scholar PubMed PubMed Central

Saito, T., Hirai, R., Loo, Y.M., Owen, D., Johnson, C.L., Sinha, S.C., Akira, S., Fujita, T., and Gale, M.Jr. (2007). Regulation of innate antiviral defenses through a shared repressor domain in RIG-I and LGP2. Proc. Natl. Acad. Sci. U. S. A. 104: 582–587.10.1073/pnas.0606699104Search in Google Scholar PubMed PubMed Central

Samatanga, B., Andreou, A.Z., and Klostermeier, D. (2017). Allosteric regulation of helicase core activities of the DEAD-box helicase YxiN by RNA binding to its RNA recognition motif. Nucleic Acids Res. 45: 1994–2006. https://doi.org/10.1093/nar/gkx014.Search in Google Scholar PubMed PubMed Central

Samatanga, B. and Klostermeier, D. (2014). DEAD-box RNA helicase domains exhibit a continuum between complete functional independence and high thermodynamic coupling in nucleotide and RNA duplex recognition. Nucleic Acids Res. 42: 10644–10654. https://doi.org/10.1093/nar/gku747.Search in Google Scholar PubMed PubMed Central

Santos, K.F., Jovin, S.M., Weber, G., Pena, V., Luhrmann, R., and Wahl, M.C. (2012). Structural basis for functional cooperation between tandem helicase cassettes in Brr2-mediated remodeling of the spliceosome. Proc. Natl. Acad. Sci. U. S. A. 109: 17418–17423.10.1073/pnas.1208098109Search in Google Scholar PubMed PubMed Central

Schmidt, C., Kowalinski, E., Shanmuganathan, V., Defenouillere, Q., Braunger, K., Heuer, A., Pech, M., Namane, A., Berninghausen, O., Fromont-Racine, M., et al.. (2016). The cryo-EM structure of a ribosome-Ski2-Ski3-Ski8 helicase complex. Science 354: 1431–1433.10.1126/science.aaf7520Search in Google Scholar PubMed

Schmitt, A., Hamann, F., Neumann, P., and Ficner, R. (2018). Crystal structure of the spliceosomal DEAH-box ATPase Prp2. Acta Crystallogr. D Struct. Biol. 74: 643–654. https://doi.org/10.1107/S2059798318006356.Search in Google Scholar PubMed PubMed Central

Schutz, P., Bumann, M., Oberholzer, A.E., Bieniossek, C., Trachsel, H., Altmann, M., and Baumann, U. (2008). Crystal structure of the yeast eIF4A-eIF4G complex: an RNA-helicase controlled by protein-protein interactions. Proc. Natl. Acad. Sci. U. S. A. 105: 9564–9569.10.1073/pnas.0800418105Search in Google Scholar PubMed PubMed Central

Schutz, P., Karlberg, T., van den Berg, S., Collins, R., Lehtio, L., Hogbom, M., Holmberg-Schiavone, L., Tempel, W., Park, H.W., Hammarstrom, M., et al.. (2010). Comparative structural analysis of human DEAD-box RNA helicases. PloS One 5: e12731. https://doi.org/10.1371/journal.pone.0012791.Search in Google Scholar PubMed PubMed Central

Semlow, D.R., Blanco, M.R., Walter, N.G., and Staley, J.P. (2016). Spliceosomal DEAH-box ATPases remodel pre-mRNA to activate alternative splice sites. Cell 164: 985–998. https://doi.org/10.1016/j.cell.2016.01.025.Search in Google Scholar PubMed PubMed Central

Sengoku, T., Nureki, O., Nakamura, A., Kobayashi, S., and Yokoyama, S. (2006). Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa. Cell 125: 287–300. https://doi.org/10.1016/j.cell.2006.01.054.Search in Google Scholar PubMed

Sharma, D., Putnam, A.A., and Jankowsky, E. (2017). Biochemical differences and similarities between the DEAD-box helicase orthologs DDX3X and Ded1p. J. Mol. Biol. 429: 3730–3742. https://doi.org/10.1016/j.jmb.2017.10.008.Search in Google Scholar PubMed PubMed Central

Sheth, U. and Parker, R. (2003). Decapping and decay of messenger RNA occur in cytoplasmic processing bodies. Science 300: 805–808.10.1126/science.1082320Search in Google Scholar PubMed PubMed Central

Sitron, C.S., Park, J.H., and Brandman, O. (2017). Asc1, Hel2, and Slh1 couple translation arrest to nascent chain degradation. RNA 23: 798–810. https://doi.org/10.1261/rna.060897.117.Search in Google Scholar PubMed PubMed Central

Small, E.C., Leggett, S.R., Winans, A.A., and Staley, J.P. (2006). The EF-G-like GTPase Snu114p regulates spliceosome dynamics mediated by Brr2p, a DExD/H box ATPase. Mol. Cell 23: 389–399. https://doi.org/10.1016/j.molcel.2006.05.043.Search in Google Scholar PubMed PubMed Central

Song, H. and Ji, X. (2019). The mechanism of RNA duplex recognition and unwinding by DEAD-box helicase DDX3X. Nat. Commun. 10: 3085. https://doi.org/10.1038/s41467-019-11083-2.Search in Google Scholar PubMed PubMed Central

Steimer, L., Wurm, J.P., Linden, M.H., Rudolph, M.G., Wohnert, J., and Klostermeier, D. (2013). Recognition of two distinct elements in the RNA substrate by the RNA binding domain of the T. thermophilus DEAD box helicase Hera. Nucleic Acids Res. 41: 6259–6272. https://doi.org/10.1093/nar/gkt323.Search in Google Scholar PubMed PubMed Central

Studer, M.K., Ivanovic, L., Weber, M.E., Marti, S., and Jonas, S. (2020). Structural basis for DEAH-helicase activation by G-patch proteins. Proc. Natl. Acad. Sci. U. S. A. 117: 7159–7170.10.1073/pnas.1913880117Search in Google Scholar PubMed PubMed Central

Takahasi, K., Kumeta, H., Tsuduki, N., Narita, R., Shigemoto, T., Hirai, R., Yoneyama, M., Horiuchi, M., Ogura, K., Fujita, T., et al.. (2009). Solution structures of cytosolic RNA sensor MDA5 and LGP2 C-terminal domains: identification of the RNA recognition loop in RIG-I-like receptors. J. Biol. Chem. 284: 17465–17474. https://doi.org/10.1074/jbc.M109.007179.Search in Google Scholar PubMed PubMed Central

Tanaka, N., Aronova, A., and Schwer, B. (2007). Ntr1 activates the Prp43 helicase to trigger release of lariat-intron from the spliceosome. Genes Dev. 21: 2312–2325. https://doi.org/10.1101/gad.1580507.Search in Google Scholar PubMed PubMed Central

Tanaka, N. and Schwer, B. (2005). Characterization of the NTPase, RNA-binding, and RNA helicase activities of the DEAH-box splicing factor Prp22. Biochemistry 44: 9795–9803. https://doi.org/10.1021/bi050407m.Search in Google Scholar PubMed

Tanner, N.K., Cordin, O., Banroques, J., Doere, M., and Linder, P. (2003). The Q motif: a newly identified motif in DEAD box helicases may regulate ATP binding and hydrolysis. Mol. Cell 11: 127–138. https://doi.org/10.1016/S1097-2765(03)00006-6.Search in Google Scholar PubMed

Tauber, D., Tauber, G., Khong, A., Van Treeck, B., Pelletier, J., and Parker, R. (2020). Modulation of RNA condensation by the DEAD-box protein eIF4A. Cell 180: 411–426 e416. https://doi.org/10.1016/j.cell.2019.12.031.Search in Google Scholar PubMed PubMed Central

Tauchert, M.J., Fourmann, J.B., Luhrmann, R., and Ficner, R. (2017). Structural insights into the mechanism of the DEAH-box RNA helicase Prp43. eLife 6: e21510. https://doi.org/10.7554/eLife.21510.Search in Google Scholar PubMed PubMed Central

Taylor, L.L., Jackson, R.N., Rexhepaj, M., King, A.K., Lott, L.K., van Hoof, A., and Johnson, S.J. (2014). The Mtr4 ratchet helix and arch domain both function to promote RNA unwinding. Nucleic Acids Res. 42: 13861–13872. https://doi.org/10.1093/nar/gku1208.Search in Google Scholar PubMed PubMed Central

Teixeira, D., Sheth, U., Valencia-Sanchez, M.A., Brengues, M., and Parker, R. (2005). Processing bodies require RNA for assembly and contain nontranslating mRNAs. RNA 11: 371–382. https://doi.org/10.1261/rna.7258505.Search in Google Scholar PubMed PubMed Central

Theissen, B., Karow, A.R., Kohler, J., Gubaev, A., and Klostermeier, D. (2008). Cooperative binding of ATP and RNA induces a closed conformation in a DEAD box RNA helicase. Proc. Natl. Acad. Sci. U. S. A. 105: 548–553.10.1073/pnas.0705488105Search in Google Scholar PubMed PubMed Central

Theuser, M., Hobartner, C., Wahl, M.C., and Santos, K.F. (2016). Substrate-assisted mechanism of RNP disruption by the spliceosomal Brr2 RNA helicase. Proc. Natl. Acad. Sci. U. S. A. 113: 7798–7803.10.1073/pnas.1524616113Search in Google Scholar PubMed PubMed Central

Tijerina, P., Bhaskaran, H., and Russell, R. (2006). Nonspecific binding to structured RNA and preferential unwinding of an exposed helix by the CYT-19 protein, a DEAD-box RNA chaperone. Proc. Natl. Acad. Sci. U. S. A. 103: 16698–16703.10.1073/pnas.0603127103Search in Google Scholar PubMed PubMed Central

Tsai, R.T., Fu, R.H., Yeh, F.L., Tseng, C.K., Lin, Y.C., Huang, Y.H., and Cheng, S.C. (2005). Spliceosome disassembly catalyzed by Prp43 and its associated components Ntr1 and Ntr2. Genes Dev. 19: 2991–3003. https://doi.org/10.1101/gad.1377405.Search in Google Scholar PubMed PubMed Central

Tsai, R.T., Tseng, C.K., Lee, P.J., Chen, H.C., Fu, R.H., Chang, K.J., Yeh, F.L., and Cheng, S.C. (2007). Dynamic interactions of Ntr1-Ntr2 with Prp43 and with U5 govern the recruitment of Prp43 to mediate spliceosome disassembly. Mol. Cell Biol. 27: 8027–8037. https://doi.org/10.1128/MCB.01213-07.Search in Google Scholar PubMed PubMed Central

Tsu, C.A., Kossen, K., and Uhlenbeck, O.C. (2001). The Escherichia coli DEAD protein DbpA recognizes a small RNA hairpin in 23S rRNA. RNA 7: 702–709.10.1017/S1355838201010135Search in Google Scholar PubMed PubMed Central

Uchikawa, E., Lethier, M., Malet, H., Brunel, J., Gerlier, D., and Cusack, S. (2016). Structural analysis of dsRNA binding to anti-viral pattern recognition receptors LGP2 and MDA5. Mol. Cell 62: 586–602. https://doi.org/10.1016/j.molcel.2016.04.021.Search in Google Scholar PubMed PubMed Central

Vester, K., Santos, K.F., Kuropka, B., Weise, C., and Wahl, M.C. (2019). The inactive C-terminal cassette of the dual-cassette RNA helicase BRR2 both stimulates and inhibits the activity of the N-terminal helicase unit. J. Biol. Chem. 295: 2097–2112. https://doi.org/10.1074/jbc.RA119.010964.Search in Google Scholar PubMed PubMed Central

Virgili, G., Frank, F., Feoktistova, K., Sawicki, M., Sonenberg, N., Fraser, C.S., and Nagar, B. (2013). Structural analysis of the DAP5 MIF4G domain and its interaction with eIF4A. Structure 21: 517–527. https://doi.org/10.1016/j.str.2013.01.015.Search in Google Scholar PubMed PubMed Central

von Moeller, H., Basquin, C., and Conti, E. (2009). The mRNA export protein DBP5 binds RNA and the cytoplasmic nucleoporin NUP214 in a mutually exclusive manner. Nat. Struct. Mol. Biol. 16: 247–254. https://doi.org/10.1038/nsmb.1561.Search in Google Scholar PubMed

Wagner, J.D., Jankowsky, E., Company, M., Pyle, A.M., and Abelson, J.N. (1998). The DEAH-box protein PRP22 is an ATPase that mediates ATP-dependent mRNA release from the spliceosome and unwinds RNA duplexes. EMBO J. 17: 2926–2937.10.1093/emboj/17.10.2926Search in Google Scholar PubMed PubMed Central

Wan, R., Yan, C., Bai, R., Wang, L., Huang, M., Wong, C.C., and Shi, Y. (2016). The 3.8 A structure of the U4/U6.U5 tri-snRNP: insights into spliceosome assembly and catalysis. Science 351: 466–475.10.1126/science.aad6466Search in Google Scholar PubMed

Wang, S., Hu, Y., Overgaard, M.T., Karginov, F.V., Uhlenbeck, O.C., and McKay, D.B. (2006). The domain of the Bacillus subtilis DEAD-box helicase YxiN that is responsible for specific binding of 23S rRNA has an RNA recognition motif fold. RNA 12: 959–967. https://doi.org/10.1261/rna.5906.Search in Google Scholar PubMed PubMed Central

Wang, Y., Ludwig, J., Schuberth, C., Goldeck, M., Schlee, M., Li, H., Juranek, S., Sheng, G., Micura, R., Tuschl, T., et al.. (2010). Structural and functional insights into 5′-ppp RNA pattern recognition by the innate immune receptor RIG-I. Nat. Struct. Mol. Biol. 17: 781–787. https://doi.org/10.1038/nsmb.1863.Search in Google Scholar PubMed PubMed Central

Waters, L.C., Strong, S.L., Ferlemann, E., Oka, O., Muskett, F.W., Veverka, V., Banerjee, S., Schmedt, T., Henry, A.J., Klempnauer, K.H., et al.. (2011). Structure of the tandem MA-3 region of Pdcd4 protein and characterization of its interactions with eIF4A and eIF4G: molecular mechanisms of a tumor suppressor. J. Biol. Chem. 286: 17270–17280. https://doi.org/10.1074/jbc.M110.166157.Search in Google Scholar PubMed PubMed Central

Weick, E.M., Puno, M.R., Januszyk, K., Zinder, J.C., DiMattia, M.A., and Lima, C.D. (2018). Helicase-dependent RNA decay illuminated by a cryo-EM structure of a human nuclear RNA exosome-MTR4 complex. Cell 173: 1663–1677 e1621. https://doi.org/10.1016/j.cell.2018.05.041.Search in Google Scholar PubMed PubMed Central

Weir, J.R., Bonneau, F., Hentschel, J., and Conti, E. (2010). Structural analysis reveals the characteristic features of Mtr4, a DExH helicase involved in nuclear RNA processing and surveillance. Proc. Natl. Acad. Sci. U. S. A. 107: 12139–12144.10.1073/pnas.1004953107Search in Google Scholar PubMed PubMed Central

Wollenhaupt, J., Henning, L.M., Sticht, J., Becke, C., Freund, C., Santos, K.F., and Wahl, M.C. (2018). Intrinsically disordered protein Ntr2 modulates the spliceosomal RNA helicase Brr2. Biophys. J. 114: 788–799. https://doi.org/10.1016/j.bpj.2017.12.033.Search in Google Scholar PubMed PubMed Central

Wu, B., Peisley, A., Richards, C., Yao, H., Zeng, X., Lin, C., Chu, F., Walz, T., and Hur, S. (2013). Structural basis for dsRNA recognition, filament formation, and antiviral signal activation by MDA5. Cell 152: 276–289. https://doi.org/10.1016/j.cell.2012.11.048.Search in Google Scholar PubMed

Xu, L., Wang, L., Peng, J., Li, F., Wu, L., Zhang, B., Lv, M., Zhang, J., Gong, Q., Zhang, R., et al.. (2017). Insights into the structure of dimeric RNA helicase CsdA and indispensable role of its C-terminal regions. Structure 25: 1795–1808 e1795. https://doi.org/10.1016/j.str.2017.09.013.Search in Google Scholar PubMed

Yan, C., Wan, R., Bai, R., Huang, G., and Shi, Y. (2016). Structure of a yeast activated spliceosome at 3.5 A resolution. Science 353: 904–911.10.1126/science.aag0291Search in Google Scholar PubMed

Yang, H.S., Jansen, A.P., Komar, A.A., Zheng, X., Merrick, W.C., Costes, S., Lockett, S.J., Sonenberg, N., and Colburn, N.H. (2003). The transformation suppressor Pdcd4 is a novel eukaryotic translation initiation factor 4A binding protein that inhibits translation. Mol. Cell Biol. 23: 26–37. https://doi.org/10.1128/MCB.23.1.26-37.2003.Search in Google Scholar PubMed PubMed Central

Yang, Q. and Jankowsky, E. (2006). The DEAD-box protein Ded1 unwinds RNA duplexes by a mode distinct from translocating helicases. Nat. Struct. Mol. Biol. 13: 981–986. https://doi.org/10.1038/nsmb1165.Search in Google Scholar PubMed

Yoneyama, M., Kikuchi, M., Natsukawa, T., Shinobu, N., Imaizumi, T., Miyagishi, M., Taira, K., Akira, S., and Fujita, T. (2004). The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses. Nat. Immunol. 5: 730–737. https://doi.org/10.1038/ni1087.Search in Google Scholar PubMed

Yoneyama, M., Onomoto, K., Jogi, M., Akaboshi, T., and Fujita, T. (2015). Viral RNA detection by RIG-I-like receptors. Curr. Opin. Immunol. 32: 48–53. https://doi.org/10.1016/j.coi.2014.12.012.Search in Google Scholar PubMed

Yu, Q., Qu, K., and Modis, Y. (2018). Cryo-EM structures of MDA5-dsRNA filaments at different stages of ATP hydrolysis. Mol. Cell 72: 999–1012 e1016. https://doi.org/10.1016/j.molcel.2018.10.012.Search in Google Scholar PubMed PubMed Central

Zhan, X., Yan, C., Zhang, X., Lei, J., and Shi, Y. (2018). Structures of the human pre-catalytic spliceosome and its precursor spliceosome. Cell Res. 28: 1129–1140. https://doi.org/10.1038/s41422-018-0094-7.Search in Google Scholar PubMed PubMed Central

Zhang, L., Xu, T., Maeder, C., Bud, L.O., Shanks, J., Nix, J., Guthrie, C., Pleiss, J.A., and Zhao, R. (2009). Structural evidence for consecutive Hel308-like modules in the spliceosomal ATPase Brr2. Nat. Struct. Mol. Biol. 16: 731–739. https://doi.org/10.1038/nsmb.1625.Search in Google Scholar PubMed PubMed Central

Zhang, X., Yan, C., Hang, J., Finci, L.I., Lei, J., and Shi, Y. (2017). An atomic structure of the human spliceosome. Cell 169: 918–929 e914. https://doi.org/10.1016/j.cell.2017.04.033.Search in Google Scholar PubMed

Zhang, X., Yan, C., Zhan, X., Li, L., Lei, J., and Shi, Y. (2018). Structure of the human activated spliceosome in three conformational states. Cell Res. 28: 307–322. https://doi.org/10.1038/cr.2018.14.Search in Google Scholar PubMed PubMed Central

Zhang, X., Zhan, X., Yan, C., Zhang, W., Liu, D., Lei, J., and Shi, Y. (2019). Structures of the human spliceosomes before and after release of the ligated exon. Cell Res. 29: 274–285. https://doi.org/10.1038/s41422-019-0143-x.Search in Google Scholar PubMed PubMed Central

Zhu, Z., Zhang, X., Wang, G., and Zheng, H. (2014). The laboratory of genetics and physiology 2: emerging insights into the controversial functions of this RIG-I-like receptor. BioMed Res. Int. 2014: 960190.10.1155/2014/960190Search in Google Scholar PubMed PubMed Central