Structural basis of G-quadruplex unfolding by the DEAH/RHA helicase DHX36

• Published in: Nature (London) Vol. 558; no. 7710; pp. 465 - 469
• Main Authors: Chen, Michael C., Tippana, Ramreddy, Demeshkina, Natalia A., Murat, Pierre, Balasubramanian, Shankar, Myong, Sua, Ferré-D’Amaré, Adrian R.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01-06-2018; Nature Publishing Group
• Subjects: 631/337/1644; 631/45/607; 631/535/1266; 631/57/2265; Amino Acid Motifs; Animals; BASIC BIOLOGICAL SCIENCES; Cattle; Crystal pulling; Crystal structure; Crystallography, X-Ray; DEAD-box RNA Helicases - chemistry; DEAD-box RNA Helicases - genetics; DEAD-box RNA Helicases - metabolism; Deoxyribonucleic acid; Developmental biology; DNA; DNA - chemistry; DNA - metabolism; DNA helicase; Embryogenesis; Embryonic growth stage; Energy transfer; Enzymes; Fluorescence; Fluorescence Resonance Energy Transfer; G-Quadruplexes; Gene regulation; Guanine; Humanities and Social Sciences; Letter; Machinery; Models, Molecular; Molecular chains; multidisciplinary; Mutation; Nucleic Acid Denaturation; Nucleic acids; Observations; Peptides; Physiological aspects; Post-transcription; Protein folding; Purines; Ribonucleic acid; RNA; Science; Science (multidisciplinary); Single-molecule biophysics; Single-stranded DNA; X-ray crystallography; United States > US
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/s41586-018-0209-9

Guanine-rich nucleic acid sequences challenge the replication, transcription, and translation machinery by spontaneously folding into G-quadruplexes, the unfolding of which requires forces greater than most polymerases can exert
1
,
2
. Eukaryotic cells contain numerous helicases that can unfold G-quadruplexes
3
. The molecular basis of the recognition and unfolding of G-quadruplexes by helicases remains poorly understood. DHX36 (also known as RHAU and G4R1), a member of the DEAH/RHA family of helicases, binds both DNA and RNA G-quadruplexes with extremely high affinity
4
–
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, is consistently found bound to G-quadruplexes in cells
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,
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, and is a major source of G-quadruplex unfolding activity in HeLa cell lysates
6
. DHX36 is a multi-functional helicase that has been implicated in G-quadruplex-mediated transcriptional and post-transcriptional regulation, and is essential for heart development, haematopoiesis, and embryogenesis in mice
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–
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. Here we report the co-crystal structure of bovine DHX36 bound to a DNA with a G-quadruplex and a 3′ single-stranded DNA segment. We show that the N-terminal DHX36-specific motif folds into a DNA-binding-induced α-helix that, together with the OB-fold-like subdomain, selectively binds parallel G-quadruplexes. Comparison with unliganded and ATP-analogue-bound DHX36 structures, together with single-molecule fluorescence resonance energy transfer (FRET) analysis, suggests that G-quadruplex binding alone induces rearrangements of the helicase core; by pulling on the single-stranded DNA tail, these rearrangements drive G-quadruplex unfolding one residue at a time.
A mechanism for the unfolding of guanine-rich DNA ‘quadruplexes’ by helicases is suggested, based on the structure of a DNA-bound helicase.