Skip to content
Licensed Unlicensed Requires Authentication Published by De Gruyter December 14, 2020

Transcription, translation, and DNA repair: new insights from emerging noncanonical substrates of RNA helicases

  • Matthew P. Russon , Kirsten M. Westerhouse and Elizabeth J. Tran ORCID logo EMAIL logo
From the journal Biological Chemistry

Abstract

RNA helicases are enzymes that exist in all domains of life whose canonical functions include ATP-dependent remodeling of RNA structures and displacement of proteins from ribonucleoprotein complexes (RNPs). These enzymes play roles in virtually all processes of RNA metabolism, including pre-mRNA splicing, rRNA processing, nuclear mRNA export, translation and RNA decay. Here we review emerging noncanonical substrates of RNA helicases including RNA-DNA hybrids (R-loops) and RNA and DNA G-quadruplexes and discuss their biological significance.


Corresponding author: Elizabeth J. Tran, Department of Biochemistry, Purdue University, BCHM A343, 175 S. University Street, West Lafayette, IN, 47907, USA; and Purdue University Center for Cancer Research, Purdue University, Hansen Life Sciences Research Building, Room 141, 201 S. University Street, West Lafayette, IN, 47907, USA, E-mail:

Funding source: Purdue University Center for Cancer Research

Award Identifier / Grant number: P30 CA023168

Award Identifier / Grant number: R01GM097332

Acknowledgements

We would like to thank Tran laboratory members Sara Cloutier and Youssef Hegazy for helpful input on this manuscript.

  1. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: This work was supported by funds from the Department of Biochemistry and Purdue University Center for Cancer Research (NIH grant P30 CA023168) and NIH R01GM097332 to E.J.T.

  3. Conflict of interest statement: The authors declare no conflicts of interest regarding this article.

References

Argaud, D., Boulanger, M.C., Chignon, A., Mkannez, G., and Mathieu, P. (2019). Enhancer-mediated enrichment of interacting JMJD3-DDX21 to ENPP2 locus prevents R-loop formation and promotes transcription. Nucleic Acids Res. 47: 8424–8438, https://doi.org/10.1093/nar/gkz560.Search in Google Scholar PubMed PubMed Central

Booy, E.P., Howard, R., Marushchak, O., Ariyo, E.O., Meier, M., Novakowski, S.K., Deo, S.R., Dzananovic, E., Stetefeld, J., and McKenna, S.A. (2014). The RNA helicase RHAU (DHX36) suppresses expression of the transcription factor PITX1. Nucleic Acids Res. 42: 3346–3361, https://doi.org/10.1093/nar/gkt1340.Search in Google Scholar PubMed PubMed Central

Boros-Oláh, B., Dobos, N., Hornyák, L., Szabó, Z., Karányi, Z., Halmos, G., Roszik, J., and Székvölgyi, L. (2019). Drugging the R-loop interactome: RNA-DNA hybrid binding proteins as targets for cancer therapy. DNA Repair 84: 102642, https://doi.org/10.1016/j.dnarep.2019.102642.Search in Google Scholar PubMed

Byrd, A.K., Bell, M.R., and Raney, K.D. (2018). Pif1 helicase unfolding of G-quadruplex DNA is highly dependent on sequence and reaction conditions. J. Biol. Chem. 293: 17792–17802, https://doi.org/10.1074/jbc.ra118.004499.Search in Google Scholar

Cammas, A. and Millevoi, S. (2017). RNA G-quadruplexes: emerging mechanisms in disease. Nucleic Acids Res.10.1093/nar/gkw1280Search in Google Scholar PubMed PubMed Central

Capasso, A., Bagby, S.M., Dailey, K.L., Currimjee, N., Yacob, B.W., Ionkina, A., Frank, J.G., Kim, D.J., George, C., Lee, Y.B., et al.. (2019). First-in-class phosphorylated-p68 inhibitor RX-5902 inhibits β-catenin signaling and demonstrates antitumor activity in triple-negative breast cancer. Mol. Canc. Therapeut. 18: 1916–1925, https://doi.org/10.1158/1535-7163.mct-18-1334.Search in Google Scholar PubMed PubMed Central

Chakraborty, P. and Grosse, F. (2011). Human DHX9 helicase preferentially unwinds RNA-containing displacement loops (R-loops) and G-quadruplexes. DNA Repair 10: 654–665, https://doi.org/10.1016/j.dnarep.2011.04.013.Search in Google Scholar PubMed

Chakraborty, P., Huang, J.T.J., and Hiom, K. (2018). DHX9 helicase promotes R-loop formation in cells with impaired RNA splicing. Nat. Commun. 9: 1–4, https://doi.org/10.1038/s41467-018-06677-1.Search in Google Scholar PubMed PubMed Central

Chambers, V.S., Marsico, G., Boutell, J.M., Di Antonio, M., Smith, G.P., and Balasubramanian, S. (2015). High-throughput sequencing of DNA G-quadruplex structures in the human genome. Nat. Biotechnol 33: 877–881, https://doi.org/10.1038/nbt.3295.Search in Google Scholar PubMed

Chen, M.C., Tippana, R., Demeshkina, N.A., Murat, P., Balasubramanian, S., Myong, S., and Ferré-D’amaré, A.R. (2018). Structural basis of G-quadruplex unfolding by the DEAH/RHA helicase DHX36. Nature 558: 465–483, https://doi.org/10.1038/s41586-018-0209-9.Search in Google Scholar PubMed PubMed Central

Cloutier, S.C., Wang, S., Ma, W.K., Petell, C.J., and Tran, E.J. (2013). Long noncoding RNAs promote transcriptional poising of inducible genes. PLoS Biol. 11: e1001715, https://doi.org/10.1371/journal.pbio.1001715.Search in Google Scholar PubMed PubMed Central

Cloutier, S.C., Wang, S., Ma, W.K., Husini, N.Al, Dhoondia, Z., Ansari, A., Pascuzzi, P.E., and Tran, E.J. (2016). Regulated formation of lncRNA-DNA hybrids enables faster transcriptional induction and environmental adaptation. Mol. Cell 61: 393–404, https://doi.org/10.1016/j.molcel.2015.12.024.Search in Google Scholar PubMed PubMed Central

Cramer, P. (2019). Organization and regulation of gene transcription. Nature 573: 45–54, https://doi.org/10.1038/s41586-019-1517-4.Search in Google Scholar PubMed

Fuller-Pace, F.V. (2006). DExD/H box RNA helicases: multifunctional proteins with important roles in transcriptional regulation. Nucleic Acids Res. 34: 4206–4215, https://doi.org/10.1093/nar/gkl460.Search in Google Scholar PubMed PubMed Central

Gao, J., Byrd, A.K., Zybailov, B.L., Marecki, J.C., Guderyon, M.J., Edwards, A.D., Chib, S., West, K.L., Waldrip, Z.J., Mackintosh, S.G., et al.. (2019). DEAD-box RNA helicases Dbp2, Ded1 and Mss116 bind to G-quadruplex nucleic acids and destabilize G-quadruplex RNA. Chem. Commun. 55: 4467–4470, https://doi.org/10.1039/c8cc10091h.Search in Google Scholar PubMed PubMed Central

Gilman, B., Tijerina, P., and Russell, R. (2017). Distinct RNA-unwinding mechanisms of DEAD-box and DEAH-box RNA helicase proteins in remodeling structured RNAs and RNPs. Biochem. Soc. Trans. 45: 1313–1321, https://doi.org/10.1042/bst20170095.Search in Google Scholar PubMed PubMed Central

Giraud, G., Terrone, S., and Bourgeois, C.F. (2018). Functions of DEAD box RNA helicases DDX5 and DDX17 in chromatin organization and transcriptional regulation. BMB Rep. 51: 613–622, https://doi.org/10.5483/bmbrep.2018.51.12.234.Search in Google Scholar

Giri, B., Smaldino, P.J., Thys, R.G., Creacy, S.D., Routh, E.D., Hantgan, R.R., Lattmann, S., Nagamine, Y., Akman, S.A., and Vaughn, J.P. (2011). G4 Resolvase 1 tightly binds and unwinds unimolecular G4-DNA. Nucleic Acids Res 39: 7161–7178,https://doi.org/10.1093/nar/gkr234.Search in Google Scholar PubMed PubMed Central

Guenther, U.-P., Weinberg, D.E., Zubradt, M.M., Tedeschi, F.A., Stawicki, B.N., Zagore, L.L., Brar, G.A., Brar, G.A., Licatalosi, D.D., Bartel, D.P., et al.. (2018). The helicase Ded1p controls use of near-cognate translation initiation codons in 5′ UTRs. Nature 559: 130–134, https://doi.org/10.1038/s41586-018-0258-0.Search in Google Scholar PubMed PubMed Central

Guo, J.U. and Bartel, D.P. (2016). RNA G-quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria. Science 353: aaf5371, https://doi.org/10.1126/science.aaf5371.Search in Google Scholar PubMed PubMed Central

Heddi, B., Cheong, V.V., Martadinata, H., and Phan, A.T. (2015). Insights into G-quadruplex specific recognition by the DEAH-box helicase RHAU: solution structure of a peptide-quadruplex complex. Proc. Natl. Acad. Sci. U.S.A., https://doi.org/10.2210/pdb2n16/pdb.Search in Google Scholar

Heerma van Voss, M.R., Diest, P.J.van, and Raman, V (2017). Targeting RNA helicases in cancer: the translation trap. Biochim. Biophys. Acta Rev. Canc 1868: 510–520, https://doi.org/10.1016/j.bbcan.2017.09.006.Search in Google Scholar PubMed PubMed Central

Hegazy, Y.A., Fernando, C.M., and Tran, E.J. (2020). The balancing act of R-loop biology: the good, the bad, and the ugly. J. Biol. Chem. 295: 905–913, https://doi.org/10.1074/jbc.rev119.011353.Search in Google Scholar

Herdy, B., Mayer, C., Varshney, D., Marsico, G., Murat, P., Taylor, C., D’Santos, C., Tannahill, D., and Balasubramanian, S. (2018). Analysis of NRAS RNA G-quadruplex binding proteins reveals DDX3X as a novel interactor of cellular G-quadruplex containing transcripts. Nucleic Acids Res. 46: 11592–11604, https://doi.org/10.1093/nar/gky861.Search in Google Scholar PubMed PubMed Central

Hodroj, D., Recolin, B., Serhal, K., Martinez, S., Tsanov, N., Abou Merhi, R., and Maiorano, D. (2017). An ATR ‐dependent function for the Ddx19 RNA helicase in nuclear R‐loop metabolism. EMBO J. 36: 1182–1198, https://doi.org/10.15252/embj.201695131.Search in Google Scholar PubMed PubMed Central

Huppert, J.L., Bugaut, A., Kumari, S., and Balasubramanian, S. (2008). G-quadruplexes: the beginning and end of UTRs. Nucleic Acids Res. 36: 6260–6268, https://doi.org/10.1093/nar/gkn511.Search in Google Scholar PubMed PubMed Central

Jankowsky, E. (2011). RNA helicases at work: binding and rearranging. Trends Biochem. Sci. 36: 19–29, https://doi.org/10.1016/j.tibs.2010.07.008.Search in Google Scholar PubMed PubMed Central

Jarmoskaite, I. and Russell, R. (2014). RNA helicase proteins as chaperones and remodelers. Annu. Rev. Biochem. 83: 697–725, https://doi.org/10.1146/annurev-biochem-060713-035546.Search in Google Scholar PubMed PubMed Central

Kwok, C.K., Marsico, G., Sahakyan, A.B., Chambers, V.S., and Balasubramanian, S. (2016). RG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome. Nat. Methods 13: 841–844, https://doi.org/10.1038/nmeth.3965.Search in Google Scholar PubMed

Lai, Y.-H., Choudhary, K., Cloutier, S.C., Xing, Z., Aviran, S., and Tran, E.J. (2019). Genome-wide discovery of DEAD-box RNA helicase targets reveals RNA structural remodeling in transcription termination. Genetics 212: 153–174, https://doi.org/10.1534/genetics.119.302058.Search in Google Scholar PubMed PubMed Central

Lattmann, S., Giri, B., Vaughn, J.P., Akman, S.A., and Nagamine, Y. (2010). Role of the amino terminal RHAU-specific motif in the recognition and resolution of guanine quadruplex-RNA by the DEAH-box RNA helicase RHAU. Nucleic Acids Res. 38: 6219–6233, https://doi.org/10.1093/nar/gkq372.Search in Google Scholar PubMed PubMed Central

Li, L., Germain, D.R., Poon, H.-Y., Hildebrandt, M.R., Monckton, E.A., McDonald, D., Hendzel, M.J., and Godbout, R. (2016). DEAD box 1 facilitates removal of RNA and homologous recombination at DNA double-strand breaks. Mol. Cell Biol. 36: 2794–2810, https://doi.org/10.1128/mcb.00415-16.Search in Google Scholar PubMed PubMed Central

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 PubMed PubMed Central

McRae, E.K.S., Booy, E.P., Moya-Torres, A., Ezzati, P., Stetefeld, J., and McKenna, S.A. (2017). Human DDX21 binds and unwinds RNA guanine quadruplexes. Nucleic Acids Res. 45: 6656–6668, https://doi.org/10.1093/nar/gkx380.Search in Google Scholar PubMed PubMed Central

Mersaoui, S.Y., Yu, Z., Coulombe, Y., Karam, M., Busatto, F.F., Masson, J., and Richard, S. (2019). Arginine methylation of the DDX 5 helicase RGG / RG motif by PRMT 5 regulates resolution of RNA:DNA hybrids. EMBO J. 38: 1–20, https://doi.org/10.15252/embj.2018100986.Search in Google Scholar PubMed PubMed Central

Murat, P., Marsico, G., Herdy, B., Ghanbarian, A., Portella, G., and Balasubramanian, S. (2018). RNA G-quadruplexes at upstream open reading frames cause DHX36- and DHX9-dependent translation of human mRNAs. Genome Biol. 19: 1–24, https://doi.org/10.1186/s13059-018-1602-2.Search in Google Scholar PubMed PubMed Central

Pérez-Calero, C., Bayona-Feliu, A., Xue, X., Barroso, S.I., Muñoz, S., González-Basallote, V.M., Sung, P., and Aguilera, A. (2020). UAP56/DDX39B is a major cotranscriptional RNA–DNA helicase that unwinds harmful R loops genome-wide. Genes Dev. 34: 898–912, https://doi.org/10.1101/gad.336024.119.Search in Google Scholar PubMed PubMed Central

Porrua, O. and Libri, D. (2015). Transcription termination and the control of the transcriptome: why, where and how to stop. Nat. Rev. Mol. Cell Biol. 16: 190–202, https://doi.org/10.1038/nrm3943.Search in Google Scholar PubMed

Ribeiro de Almeida, C., Dhir, S., Dhir, A., Moghaddam, A.E., Sattentau, Q., Meinhart, A., and Proudfoot, N.J. (2018). RNA helicase DDX1 converts RNA G-quadruplex structures into R-loops to promote IgH class switch recombination. Mol. Cell 70: 650–662.e8, https://doi.org/10.1016/j.molcel.2018.04.001.Search in Google Scholar PubMed PubMed Central

Sauer, M., Juranek, S.A., Marks, J., Magis, A.De, Kazemier, H.G., Hilbig, D., Benhalevy, D.,Wang, X., Hafner, M., and Paeschke, K. (2019). DHX36 prevents the accumulation of translationally inactive mRNAs with G4-structures in untranslated regions. Nat. Commun. 10: 2421, https://doi.org/10.1038/s41467-019-10432-5.Search in Google Scholar PubMed PubMed Central

Sharma, D. and Jankowsky, E. (2014). The Ded1/DDX3 subfamily of DEAD-box RNA helicases. Crit. Rev. Biochem. Mol. Biol. 49: 343–360, https://doi.org/10.3109/10409238.2014.931339.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

Song, C., Hotz-Wagenblatt, A., Voit, R., and Grummt, I. (2017). SIRT7 and the DEAD-box helicase DDX21 cooperate to resolve genomic R loops and safeguard genome stability. Genes Dev. 31: 1370–1381, https://doi.org/10.1101/gad.300624.117.Search in Google Scholar PubMed PubMed Central

Soto-Rifo, R., Rubilar, P.S., Limousin, T., Breyne, S.De, Décimo, D., and Ohlmann, T. (2012). DEAD-box protein DDX3 associates with eIF4F to promote translation of selected mRNAs. EMBO J. 31: 3745–3756, https://doi.org/10.1038/emboj.2012.220.Search in Google Scholar PubMed PubMed Central

Sridhara, S.C., Carvalho, S., Grosso, A.R., Gallego-Paez, L.M., Carmo-Fonseca, M., and de Almeida, S.F. (2017). Transcription dynamics prevent RNA-mediated genomic instability through SRPK2-dependent DDX23 phosphorylation. Cell Rep. 18: 334–343, https://doi.org/10.1016/j.celrep.2016.12.050.Search in Google Scholar PubMed

Tedeschi, F.A., Cloutier, S.C., Tran, E.J., and Jankowsky, E. (2018). The DEAD-box protein Dbp2p is linked to noncoding RNAs, the helicase Sen1p, and R-loops. RNA 24: 1693–1705, https://doi.org/10.1261/rna.067249.118.Search in Google Scholar PubMed PubMed Central

Tippana, R., Hwang, H., Opresko, P.L., Bohr, V.A., and Myong, S. (2016). Single-molecule imaging reveals a common mechanism shared by G-quadruplex-resolving helicases. Proc. Natl. Acad. Sci. U.S.A. 113: 8448–8453, https://doi.org/10.1073/pnas.1603724113.Search in Google Scholar PubMed PubMed Central

Tippana, R., Chen, M.C., Demeshkina, N.A., Ferré-D’Amaré, A.R., and Myong, S. (2019). RNA G-quadruplex is resolved by repetitive and ATP-dependent mechanism of DHX36. Nat. Commun. 10: 1–10, https://doi.org/10.1038/s41467-019-09802-w.Search in Google Scholar PubMed PubMed Central

Varshney, D., Spiegel, J., Zyner, K., Tannahill, D., and Balasubramanian, S. (2020). The regulation and functions of DNA and RNA G-quadruplexes. Nat. Rev. Mol. Cell Biol. 21: 459–474, https://doi.org/10.1038/s41580-020-0236-x.Search in Google Scholar PubMed PubMed Central

Vaughn, J.P., Creacy, S.D., Routh, E.D., Joyner-Butt, C., Jenkins, G.S., Pauli, S., Nagamine, Y., and Akman, S.A. (2005). The DEXH protein product of the DHX36 gene is the major source of tetramolecular quadruplex G4-DNA resolving activity in HeLa cell lysates. J. Biol. Chem. 280: 38117–38120, https://doi.org/10.1074/jbc.c500348200.Search in Google Scholar PubMed

Vester, K., Eravci, M., Serikawa, T., Schütze, T., Weise, C., and Kurreck, J. (2019). RNAi-mediated knockdown of the Rhau helicase preferentially depletes proteins with a Guanine-quadruplex motif in the 5’-UTR of their mRNA. Biochem. Biophys. Res. Commun. 508: 756–761, https://doi.org/10.1016/j.bbrc.2018.11.186.Search in Google Scholar PubMed

Villarreal, O.D., Mersaoui, S.Y., Yu, Z., Masson, J.Y., and Richard, S. (2020). Genome-wide R-loop analysis defines unique roles for DDX5, XRN2, and PRMT5 in DNA/RNA hybrid resolution. Life Sci. Alliance 3: 1–14, https://doi.org/10.26508/lsa.202000762.Search in Google Scholar PubMed PubMed Central

Waldron, J.A., Raza, F., and Le Quesne, J. (2018). eIF4A alleviates the translational repression mediated by classical secondary structures more than by G-quadruplexes. Nucleic Acids Res. 46: 3075–3087, https://doi.org/10.1093/nar/gky108.Search in Google Scholar PubMed PubMed Central

Wolfe, A.L., Singh, K., Zhong, Y., Drewe, P., Rajasekhar, V.K., Sanghvi, V.R., Mavrakis, K.J., Jiang, M., Roderick, J.E., Van der Meulen, J., et al.. (2014). RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer. Nature 513: 65–70, https://doi.org/10.1038/nature13485.Search in Google Scholar PubMed PubMed Central

Wu, G., Xing, Z., Tran, E.J., and Yang, D. (2019). DDX5 helicase resolves G-quadruplex and is involved in MYC gene transcriptional activation. Proc. Natl. Acad. Sci. U.S.A. 116: 20453–20461, https://doi.org/10.1073/pnas.1909047116.Search in Google Scholar PubMed PubMed Central

Xing, Z., Wang, S., and Tran, E.J. (2017). Characterization of the mammalian DEAD-box protein DDX5 reveals functional conservation with S. cerevisiae ortholog Dbp2 in transcriptional control and glucose metabolism. RNA 23: 1125–1138, https://doi.org/10.1261/rna.060335.116.Search in Google Scholar PubMed PubMed Central

Yang, Q., Del Campo, M., Lambowitz, A.M., and Jankowsky, E. (2007). DEAD-box proteins unwind duplexes by local strand separation. Mol. Cell 28: 253–263, https://doi.org/10.1016/j.molcel.2007.08.016.Search in Google Scholar PubMed

Yangyuoru, P.M., Bradburn, D.A., Liu, Z., Xiao, T.S., and Russell, R. (2018). The G-quadruplex (G4) resolvase DHX36 efficiently and specifically disrupts DNA G4s via a translocation-based helicase mechanism. J. Biol. Chem. 293: 1924–1932, https://doi.org/10.1074/jbc.m117.815076.Search in Google Scholar

You, H., Lattmann, S., Rhodes, D., and Yan, J. (2017). RHAU helicase stabilizes G4 in its nucleotide-free state and destabilizes G4 upon ATP hydrolysis. Nucleic Acids Res. 45: 206–214, https://doi.org/10.1093/nar/gkw881.Search in Google Scholar PubMed PubMed Central

Zyner, K.G., Mulhearn, D.S., Adhikari, S., Cuesta, S.M., Di Antonio, M., Erard, N., Hannon, G.J., Tannahill, D., and Balasubramanian, S. (2019). Genetic interactions of G-quadruplexes in humans. eLife 8: 1–40, https://doi.org/10.7554/elife.46793.Search in Google Scholar

Received: 2020-10-05
Accepted: 2020-11-23
Published Online: 2020-12-14
Published in Print: 2021-04-27

© 2020 Walter de Gruyter GmbH, Berlin/Boston

Downloaded on 16.4.2024 from https://www.degruyter.com/document/doi/10.1515/hsz-2020-0333/html
Scroll to top button