DOI QR코드

DOI QR Code

The translational landscape as regulated by the RNA helicase DDX3

  • Park, Joon Tae (Division of Life Sciences, Incheon National University) ;
  • Oh, Sekyung (Department of Medical Science, Catholic Kwandong University College of Medicine)
  • 투고 : 2021.12.07
  • 심사 : 2022.02.16
  • 발행 : 2022.03.31

초록

Continuously renewing the proteome, translation is exquisitely controlled by a number of dedicated factors that interact with the ribosome. The RNA helicase DDX3 belonging to the DEAD box family has emerged as one of the critical regulators of translation, the failure of which is frequently observed in a wide range of proliferative, degenerative, and infectious diseases in humans. DDX3 unwinds double-stranded RNA molecules with coupled ATP hydrolysis and thereby remodels complex RNA structures present in various protein-coding and noncoding RNAs. By interacting with specific features on messenger RNAs (mRNAs) and 18S ribosomal RNA (rRNA), DDX3 facilitates translation, while repressing it under certain conditions. We review recent findings underlying these properties of DDX3 in diverse modes of translation, such as cap-dependent and cap-independent translation initiation, usage of upstream open reading frames, and stress-induced ribonucleoprotein granule formation. We further discuss how disease-associated DDX3 variants alter the translation landscape in the cell.

키워드

과제정보

The authors thank members of the Park and the Oh laboratories for critical reading of the manuscript. This research was funded by The National Research Foundation of Korea (NRF-2018R1D1A1B07045410 and NRF-2021R1A2C1011293 to S.O.).

참고문헌

  1. Schwanhausser B, Busse D, Li N et al (2011) Global quantification of mammalian gene expression control. Nature 473, 337-342. https://doi.org/10.1038/nature10098
  2. Tahmasebi S, Khoutorsky A, Mathews MB and Sonenberg N (2018) Translation deregulation in human disease. Nat Rev Mol Cell Biol 19, 791-807 https://doi.org/10.1038/s41580-018-0034-x
  3. Ruggero D (2013) Translational control in cancer etiology. Cold Spring Harb Perspect Biol 5, a012336 https://doi.org/10.1101/cshperspect.a012336
  4. Buttgereit F and Brand MD (1995) A hierarchy of ATP-consuming processes in mammalian cells. Biochem J 312, 163-167 https://doi.org/10.1042/bj3120163
  5. Jackson RJ, Hellen CUT and Pestova TV (2010) The mechanism of eukaryotic translation initiation and principles of its regulation. Nat Rev Mol Cell Biol 11, 113-127 https://doi.org/10.1038/nrm2838
  6. Jankowsky A, Guenther UP and Jankowsky E (2011) The RNA helicase database. Nucleic Acids Res 39, D338-D341
  7. Valiente-Echeverria F, Hermoso MA and Soto-Rifo R (2015) RNA helicase DDX3: at the crossroad of viral replication and antiviral immunity. Rev Med Virol 25, 286-299 https://doi.org/10.1002/rmv.1845
  8. Soto-Rifo R and Ohlmann T (2013) The role of the DEAD-box RNA helicase DDX3 in mRNA metabolism. Wiley interdisciplinary reviews. RNA 4, 369-385
  9. Mo J, Liang H, Su C et al (2021) DDX3X: structure, physiologic functions and cancer. Mol Cancer 20, 38 https://doi.org/10.1186/s12943-021-01325-7
  10. Kellaris G, Khan K, Baig SM et al (2018) A hypomorphic inherited pathogenic variant in DDX3X causes male intellectual disability with additional neurodevelopmental and neurodegenerative features. Hum Genomics 12, 11 https://doi.org/10.1186/s40246-018-0141-y
  11. 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
  12. Kim YS, Lee SG, Park SH and Song K (2001) Gene structure of the human DDX3 and chromosome mapping of its related sequences. Mol Cell 12, 209-214 https://doi.org/10.1016/S1097-2765(03)00269-7
  13. Park SH, Lee SG, Kim Y and Song K (1998) Assignment1 of a human putative RNA helicase gene, DDX3, to human X chromosome bands p11.3→p11.23. Cytogenet Genome Res 81, 178-179 https://doi.org/10.1159/000015022
  14. Lahn BT and Page DC (1997) Functional coherence of the human Y chromosome. Science 278, 675-680 https://doi.org/10.1126/science.278.5338.675
  15. Foresta C, Ferlin A and Moro E (2000) Deletion and expression analysis of AZFa genes on the human Y chromosome revealed a major role for DBY in male infertility. Hum Mol Genet 9, 1161-1169 https://doi.org/10.1093/hmg/9.8.1161
  16. Venkataramanan S, Gadek M, Calviello L, Wilkins K and Floor S (2021) DDX3X and DDX3Y are redundant in protein synthesis. RNA 27, rna.078926.121
  17. 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
  18. Hogbom M, Collins R, Berg S van den et al (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
  19. Valentin-Vega YA, Wang YD, Parker M et al (2016) Cancer-associated DDX3X mutations drive stress granule assembly and impair global translation. Sci Rep 6, 25996 https://doi.org/10.1038/srep25996
  20. Valentini M and Linder P (2020) RNA remodeling proteins, methods and protocols. Methods Mol Biol 2209, 17-34 https://doi.org/10.1007/978-1-0716-0935-4_2
  21. Brennan R, Haap-Hoff A, Gu L et al (2018) Investigating nucleo-cytoplasmic shuttling of the human DEAD-box helicase DDX3. Eur J Cell Biol 97, 501-511 https://doi.org/10.1016/j.ejcb.2018.08.001
  22. Yedavalli, VSRK, Neuveut C, Chi YH, Kleiman L and Jeang KT (2004) Requirement of DDX3 DEAD box RNA helicase for HIV-1 Rev-RRE export function. Cell 119, 381-392 https://doi.org/10.1016/j.cell.2004.09.029
  23. Lai MC, Lee YHW and Tarn WY (2008) The DEAD-box RNA helicase DDX3 associates with export messenger ribonucleoproteins as well as tip-associated protein and participates in translational control. Mol Biol Cell 19, 3847-3858 https://doi.org/10.1091/mbc.E07-12-1264
  24. Shih JW, Tsai TY, Chao CH and Lee YHW (2008) Candidate tumor suppressor DDX3 RNA helicase specifically represses cap-dependent translation by acting as an eIF4E inhibitory protein. Oncogene 27, 700-714 https://doi.org/10.1038/sj.onc.1210687
  25. Oh S, Flynn RA, Floor SN et al (2016) Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress. Oncotarget 7, 28169-28182 https://doi.org/10.18632/oncotarget.8612
  26. Floor SN, Condon KJ, Sharma D, Jankowsky E and Doudna JA (2016) 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
  27. Epling LB, Grace CR, Lowe BR, Partridge JF and Enemark EJ (2015) Cancer-associated mutants of RNA helicase DDX3X are defective in RNA-stimulated ATP hydrolysis. J Mol Biol 427, 1779-1796 https://doi.org/10.1016/j.jmb.2015.02.015
  28. 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
  29. Hernandez-Diaz T, Valiente-Echeverria F and Soto-Rifo R (2021) RNA helicase DDX3: a double-edged sword for viral replication and immune signaling. Microorganisms 9, 1206 https://doi.org/10.3390/microorganisms9061206
  30. Schroder M (2011) Viruses and the human DEAD-box helicase DDX3: inhibition or exploitation? Biochem Soc Trans 39, 679-683 https://doi.org/10.1042/BST0390679
  31. Soto-Rifo R, Rubilar PS, Limousin T et al (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
  32. Darnell RB (2010) HITS-CLIP: panoramic views of protein-RNA regulation in living cells. Wiley interdisciplinary reviews. RNA 1, 266-286
  33. Guenther UP, Weinberg DE, Zubradt MM 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
  34. Calviello L, Venkataramanan S, Rogowski KJ et al (2021) DDX3 depletion represses translation of mRNAs with complex 5' UTRs. Nucleic Acids Res 49, 5336-5350 https://doi.org/10.1093/nar/gkab287
  35. Jankowsky E and Guenther UP (2018) A helicase links upstream ORFs and RNA structure. Curr Genet 65, 453-456 https://doi.org/10.1007/s00294-018-0911-z
  36. Ingolia NT, Ghaemmaghami S, Newman JRS and Weissman JS (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science (New York, NY) 324, 218-223 https://doi.org/10.1126/science.1168978
  37. Ingolia NT (2014) Ribosome profiling: new views of translation, from single codons to genome scale. Nat Rev Genet 15, 205-213 https://doi.org/10.1038/nrg3645
  38. Padmanabhan PK, Ferreira GR, Zghidi-Abouzid O et al (2021) Genetic depletion of the RNA helicase DDX3 leads to impaired elongation of translating ribosomes triggering co-translational quality control of newly synthesized polypeptides. Nucleic Acids Res 49, 9459-9478 https://doi.org/10.1093/nar/gkab667
  39. Lennox AL, Hoye ML, Jiang R et al (2020) Pathogenic DDX3X mutations impair RNA metabolism and neurogenesis during fetal cortical development. Neuron 106, 404-420.e8 https://doi.org/10.1016/j.neuron.2020.01.042
  40. Robichaud N, Sonenberg N, Ruggero D and Schneider RJ (2019) Translational control in cancer. Cold Spring Harb Perspect Biol 11, a032896 https://doi.org/10.1101/cshperspect.a032896
  41. Sherman MY and Qian SB (2013) Less is more: improving proteostasis by translation slow down. Trends Biochem Sci 38, 585-591 https://doi.org/10.1016/j.tibs.2013.09.003
  42. Liu B and Qian SB (2014) Translational reprogramming in cellular stress response. Wiley interdisciplinary reviews. RNA 5, 301-305
  43. Conn CS and Qian SB (2013) Nutrient signaling in protein homeostasis: an increase in quantity at the expense of quality. Sci Signal 6, ra24-ra24
  44. Ojha J, Secreto CR, Rabe KG et al (2014) Identification of recurrent truncated DDX3X mutations in chronic lymphocytic leukaemia. Br J Haematol 169, 445-448 https://doi.org/10.1111/bjh.13211
  45. Phung B, Ciesla M, Sanna A et al (2019) The X-linked DDX3X RNA helicase dictates translation reprogramming and metastasis in melanoma. Cell Rep 27, 3573-3586.e7 https://doi.org/10.1016/j.celrep.2019.05.069
  46. Jiang L, Gu ZH, Yan ZX et al (2015) Exome sequencing identifies somatic mutations of DDX3X in natural killer/T-cell lymphoma. Nat Genet 47, 1061-1066 https://doi.org/10.1038/ng.3358
  47. Brandimarte L, Starza RL, Gianfelici V et al (2014) DDX3X-MLLT10 fusion in adults with NOTCH1 positive T-cell acute lymphoblastic leukemia. Haematologica 99, 64-66 https://doi.org/10.3324/haematol.2013.101725
  48. Northcott PA, Jones DTW, Kool M et al (2012) Medulloblastomics: the end of the beginning. Nat Rev Cancer 12, 818-834 https://doi.org/10.1038/nrc3410
  49. Kool M, Jones DTW, Jager N et al (2014) Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition. Cancer Cell 25, 393-405 https://doi.org/10.1016/j.ccr.2014.02.004
  50. Patmore DM, Jassim A, Nathan E et al (2020) DDX3X suppresses the susceptibility of hindbrain lineages to medulloblastoma. Dev Cell 54, 455-470.e5 https://doi.org/10.1016/j.devcel.2020.05.027
  51. Schuller AP and Green R (2018) Roadblocks and resolutions in eukaryotic translation. Nat Rev Mol Cell Biol 19, 526-541 https://doi.org/10.1038/s41580-018-0011-4
  52. Mayr C (2017) Regulation by 3'-untranslated regions. Annu Rev Genet 51, 171-194 https://doi.org/10.1146/annurev-genet-120116-024704
  53. Kwok CK and Merrick CJ (2017) G-quadruplexes: prediction, characterization, and biological application. Trends in Biotechnol 35, 997-1013 https://doi.org/10.1016/j.tibtech.2017.06.012
  54. Wolfe AL, Singh K, Zhong Y et al (2014) RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer. Nature 513, 65-70 https://doi.org/10.1038/nature13485
  55. Rogers GW, Richter NJ and Merrick WC (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
  56. Saxton RA and Sabatini DM (2017) mTOR signaling in growth, metabolism, and disease. Cell 168, 960-976 https://doi.org/10.1016/j.cell.2017.02.004
  57. Thoreen CC, Chantranupong L, Keys HR et al (2012) A unifying model for mTORC1-mediated regulation of mRNA translation. Nature 485, 109-113 https://doi.org/10.1038/nature11083
  58. Elfakess R, Sinvani H, Haimov O et al (2011) Unique translation initiation of mRNAs-containing TISU element. Nucleic Acids Res 39, 7598-7609 https://doi.org/10.1093/nar/gkr484
  59. Yueh A and Schneider RJ (2000) Translation by ribosome shunting on adenovirus and hsp70 mRNAs facilitated by complementarity to 18S rRNA. Genes Dev 14, 414-421 https://doi.org/10.1101/gad.14.4.414
  60. Haimov O, Sinvani H, Martin F et al (2017) Efficient and accurate translation initiation directed by TISU involves RPS3 and RPS10e binding and differential eukaryotic initiation factor 1A regulation. Mol Cell Biol 37, e00150-17
  61. Sinvani H, Haimov O, Svitkin Y et al (2015) Translational tolerance of mitochondrial genes to metabolic energy stress involves TISU and eIF1-eIF4GI cooperation in start codon selection. Cell Metab 21, 479-492 https://doi.org/10.1016/j.cmet.2015.02.010
  62. Koh DC, Edelman GM and Mauro VP (2013) Physical evidence supporting a ribosomal shunting mechanism of translation initiation for BACE1 mRNA. Translation 1, e24400 https://doi.org/10.4161/trla.24400
  63. Nicholson J, Jevons SJ, Groselj B et al (2017) E3 ligase cIAP2 mediates downregulation of MRE11 and radiosensitization in response to HDAC inhibition in bladder cancer. Cancer Res 77, 3027-3039 https://doi.org/10.1158/0008-5472.CAN-16-3232
  64. Yamamoto H, Unbehaun A and Spahn CMT (2017) Ribosomal chamber music: toward an understanding of IRES mechanisms. Trends Biochem Sci 42, 655-668 https://doi.org/10.1016/j.tibs.2017.06.002
  65. Meyer KD and Jaffrey SR (2017) Rethinking m6A readers, writers, and erasers. Annu Rev Cell Dev Biol 33, 319-342 https://doi.org/10.1146/annurev-cellbio-100616-060758
  66. Meyer KD, Saletore Y, Zumbo P et al (2012) Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons. Cell 149, 1635-1646 https://doi.org/10.1016/j.cell.2012.05.003
  67. Meyer KD, Patil DP, Zhou J et al (2015) 5' UTR m(6)A promotes cap-independent translation. Cell 163, 999-1010 https://doi.org/10.1016/j.cell.2015.10.012
  68. Zhou J, Wan J, Gao X et al (2015) Dynamic m(6)A mRNA methylation directs translational control of heat shock response. Nature 526, 591-594 https://doi.org/10.1038/nature15377
  69. Coots RA, Liu XM, Mao Y et al (2017) m6A facilitates eIF4F-independent mRNA translation. Mol Cell 68, 504-514. e7 https://doi.org/10.1016/j.molcel.2017.10.002
  70. Calvo SE, Pagliarini DJ and Mootha VK (2009) Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans. Proc Natl Acad Sci U S A 106, 7507-7512 https://doi.org/10.1073/pnas.0810916106
  71. Protter DSW and Parker R (2016) Principles and properties of stress granules. Trends Cell Biol 26, 668-679 https://doi.org/10.1016/j.tcb.2016.05.004
  72. Gao X, Wan J, Liu B et al (2015) Quantitative profiling of initiating ribosomes in vivo. Nat Methods 12, 147-153 https://doi.org/10.1038/nmeth.3208
  73. Wortel IMN, Meer LT van der, Kilberg MS and Leeuwen FN van (2017) Surviving stress: modulation of ATF4-mediated stress responses in normal and malignant cells. Trends in Endocrinol Metab 28, 794-806 https://doi.org/10.1016/j.tem.2017.07.003
  74. Chuang RY, Weaver PL, Liu Z and Chang TH (1997) Requirement of the DEAD-Box protein Ded1p for messenger RNA translation. Science 275, 1468-1471 https://doi.org/10.1126/science.275.5305.1468
  75. Cruz J de la, Iost I, Kressler D and Linder P (1997) The p20 and Ded1 proteins have antagonistic roles in eIF4Edependent translation in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 94, 5201-5206 https://doi.org/10.1073/pnas.94.10.5201
  76. 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
  77. Lee CS, Dias AP, Jedrychowski M et al (2008) Human DDX3 functions in translation and interacts with the translation initiation factor eIF3. Nucleic Acids Res 36, 4708-4718 https://doi.org/10.1093/nar/gkn454
  78. Geissler R, Golbik RP and Behrens SE (2012) The DEAD-box helicase DDX3 supports the assembly of functional 80S ribosomes. Nucleic Acids Res 40, 4998-5011 https://doi.org/10.1093/nar/gks070
  79. Yan KKP, Obi I and Sabouri N (2021) The RGG domain in the C-terminus of the DEAD box helicases Dbp2 and Ded1 is necessary for G-quadruplex destabilization. Nucleic Acids Res 49, 8339-8354 https://doi.org/10.1093/nar/gkab620
  80. Comyn SA, Chan GT and Mayor T (2014) False start: Cotranslational protein ubiquitination and cytosolic protein quality control. J Proteomics 100, 92-101 https://doi.org/10.1016/j.jprot.2013.08.005
  81. Wang F, Durfee LA and Huibregtse JM (2013) A co-translational ubiquitination pathway for quality control of misfolded proteins. Mol Cell 50, 368-378 https://doi.org/10.1016/j.molcel.2013.03.009
  82. Duttler S, Pechmann S and Frydman J (2013) Principles of cotranslational ubiquitination and quality control at the ribosome. Mol Cell 50, 379-393 https://doi.org/10.1016/j.molcel.2013.03.010
  83. Cheng W, Wang S, Zhang Z et al (2019) CRISPR-Cas9 screens identify the RNA helicase DDX3X as a repressor of C9ORF72 (GGGGCC)n repeat-associated Non-AUG translation. Neuron 104, 885-898.e8 https://doi.org/10.1016/j.neuron.2019.09.003
  84. DeJesus-Hernandez M, Mackenzie IR, Boeve BF et al (2011) Expanded GGGGCC hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p-linked FTD and ALS. Neuron 72, 245-256 https://doi.org/10.1016/j.neuron.2011.09.011
  85. Renton AE, Majounie E, Waite A et al (2011) A hexa-nucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-linked ALS-FTD. Neuron 72, 257-268 https://doi.org/10.1016/j.neuron.2011.09.010
  86. Cleary JD, Pattamatta A and Ranum LPW (2018) Repeat-associated non-ATG (RAN) translation. J Biol Chem 293, 16127-16141 https://doi.org/10.1074/jbc.R118.003237
  87. Shih JW, Wang WT, Tsai TY et al (2012) Critical roles of RNA helicase DDX3 and its interactions with eIF4E/PABP1 in stress granule assembly and stress response. Bio Chem J 441, 119-129
  88. Soto-Rifo R, Rubilar PS and Ohlmann T (2013) The DEAD-box helicase DDX3 substitutes for the cap-binding protein eIF4E to promote compartmentalized translation initiation of the HIV-1 genomic RNA. Nucleic Acids Res 41, 6286-6299 https://doi.org/10.1093/nar/gkt306
  89. Gilks N, Kedersha N, Ayodele M et al (2004) Stress granule assembly is mediated by prion-like aggregation of TIA-1. Mol Biol Cell 15, 5383-5398 https://doi.org/10.1091/mbc.E04-08-0715
  90. Tourriere H, Chebli K, Zekri L et al (2003) The RasGAP-associated endoribonuclease G3BP assembles stress granules. J Cell Biol 160, 823-831 https://doi.org/10.1083/jcb.200212128
  91. Corbet GA and Parker R (2020) RNP granule formation: lessons from P-bodies and stress granules. Cold Spring Harb Symp Quant Biol 84, 040329
  92. Samir P, Kesavardhana S, Patmore DM et al (2019) DDX3X acts as a live-or-die checkpoint in stressed cells by regulating NLRP3 inflammasome. Nature 573, 590-594 https://doi.org/10.1038/s41586-019-1551-2
  93. Shi J, Gao W and Shao F (2017) Pyroptosis: gasdermin-mediated programmed necrotic cell death. Trends in Biochem Sci 42, 245-254 https://doi.org/10.1016/j.tibs.2016.10.004
  94. Saito M, Hess D, Eglinger J et al (2019) Acetylation of intrinsically disordered regions regulates phase separation. Nat Chem Biol 15, 51-61 https://doi.org/10.1038/s41589-018-0180-7
  95. Zhou HX, Nguemaha V, Mazarakos K and Qin S (2018) Why do disordered and structured proteins behave differently in phase separation? Trends Biochem Sci 43, 499-516 https://doi.org/10.1016/j.tibs.2018.03.007
  96. Courchaine EM, Lu A and Neugebauer KM (2016) Droplet organelles? EMBO J 35, 1603-1612 https://doi.org/10.15252/embj.201593517
  97. Martin F, Menetret JF, Simonetti A et al (2016) Ribo-somal 18S rRNA base pairs with mRNA during eukaryotic translation initiation. Nat Commun 7, 12622. https://doi.org/10.1038/ncomms12622
  98. Iserman C, Altamirano CD, Jegers C et al (2020) Condensation of Ded1p promotes a translational switch from housekeeping to stress protein production. Cell 181, 818-831.e19 https://doi.org/10.1016/j.cell.2020.04.009
  99. Adjibade P, St-Sauveur VG, Bergeman J et al (2017) DDX3 regulates endoplasmic reticulum stress-induced ATF4 expression. Sci Rep 7, 13832 https://doi.org/10.1038/s41598-017-14262-7
  100. Voss MRH van, Diest PJ van and Raman V (2017) Targeting RNA helicases in cancer: the translation trap. Biochimica et biophysica acta. Rev Cancer 1868, 510-520