# Human Helicase DDX5 is Hijacked by SARS-CoV‑2 Nsp13 Helicase to Enhance RNA Unwinding

**Authors:** Giovanni Barra, Alessia Ruggiero, Valeria Napolitano, Camilla Lodola, Massimiliano Secchi, Maria Michela Pallotta, Viviana Benincasa, Francesco Leone, Giovanni Maga, Rita Berisio

PMC · DOI: 10.1021/acsomega.5c04271 · 2025-07-31

## TL;DR

The study reveals that the human protein DDX5 interacts with SARS-CoV-2's Nsp13 helicase to enhance RNA unwinding, a key step in viral replication.

## Contribution

The paper identifies a novel synergistic interaction between DDX5 and SARS-CoV-2 Nsp13 helicase that enhances RNA unwinding.

## Key findings

- DDX5 binds to SARS-CoV-2 Nsp13 helicase with nanomolar affinity.
- The RecA1 domain of DDX5 mediates the interaction with Nsp13 and weakly inhibits their synergistic RNA unwinding.
- DDX5 and Nsp13 work together to unwind RNA, likely aiding early stages of SARS-CoV-2 infection.

## Abstract

DEAD-box protein (DDX) 5 plays important roles in multiple
aspects
of cellular processes that require modulation of the RNA structure.
Alongside the canonical role in RNA metabolism, numerous studies have
demonstrated that DDX5 influences viral infections by directly interacting
with viral proteins. However, the precise functional role of DDX5
during viral infection remains largely unclear. Here, we explore the
previously undiscovered ability of DDX5 to interact and synergize
with the Nsp13 helicase of SARS-CoV-2. We show that DDX5 exhibits
a nanomolar binding affinity to Nsp13. Also, by dissecting DDX5 in
its individual domains, we show that the Nsp13–DDX5 interaction
is mediated by the RecA1 domain of DDX5. Importantly, we show that
DDX5 and Nsp13 synergize in unwinding double-stranded RNA. Consistent
with its ability to bind Nsp13, the RecA1 domain of DDX5 acts as a
weak inhibitor of the synergic action of the two helicases in the
RNA unwinding process. Modeling of the DDX5–Nsp13 complex provides
a plausible explanation for the synergic action of the two helicases,
in a mechanism that is likely instrumental in the early stage of infection,
when the concentration of Nsp13 is still low.

## Linked entities

- **Proteins:** DDX5 (DEAD-box helicase 5), NSP1-3 (nonstructural protein 1-3), AKR1C3 (aldo-keto reductase family 1 member C3), RECA1 (recA DNA recombination family protein)
- **Diseases:** SARS-CoV-2 (MONDO:0100096)

## Full-text entities

- **Genes:** EWSR1 (EWS RNA binding protein 1) [NCBI Gene 2130] {aka EWS, EWS-FLI1}, RAD51 (RAD51 recombinase) [NCBI Gene 5888] {aka BRCC5, FANCR, HRAD51, HsRad51, HsT16930, MRMV2}, DNAH8 (dynein axonemal heavy chain 8) [NCBI Gene 1769] {aka ATPase, SPGF46, hdhc9}, USP13 (ubiquitin specific peptidase 13) [NCBI Gene 8975] {aka ISOT3, IsoT-3}, DDX1 (DEAD-box helicase 1) [NCBI Gene 1653] {aka DBP-RB, TSLIG6, UKVH5d}, PRUNE1 (prune exopolyphosphatase 1) [NCBI Gene 58497] {aka DRES-17, DRES17, H-PRUNE, HTCD37, NMIHBA, PRUNE}, DDX5 (DEAD-box helicase 5) [NCBI Gene 1655] {aka G17P1, HLR1, HUMP68, p68}, DDX3X (DEAD-box helicase 3 X-linked) [NCBI Gene 1654] {aka CAP-Rf, DBX, DDX14, DDX3, HLP2, MRX102}, DHX30 (DExH-box helicase 30) [NCBI Gene 22907] {aka DDX30, NEDMIAL, RETCOR}, N (nucleocapsid phosphoprotein) [NCBI Gene 43740575], DDX21 (DExD-box helicase 21) [NCBI Gene 9188] {aka GUA, GURDB, II/Gu, RH, RH II/Gu, RH-II/GU}, SF1 (splicing factor 1) [NCBI Gene 7536] {aka BBP, D11S636, MBBP, ZCCHC25, ZFM1, ZNF162}, AKR1C3 (aldo-keto reductase family 1 member C3) [NCBI Gene 8644] {aka DD3, DDX, HA1753, HAKRB, HAKRe, HSD17B5}, IFNA1 (interferon alpha 1) [NCBI Gene 3439] {aka IFL, IFN, IFN-ALPHA, IFN-alphaD, IFNA13, IFNA@}, DHX9 (DExH-box helicase 9) [NCBI Gene 1660] {aka DDX9, LKP, MRD75, NDH2, NDHII, RHA}, NFKB1 (nuclear factor kappa B subunit 1) [NCBI Gene 4790] {aka CVID12, EBP-1, KBF1, NF-kB, NF-kB1, NF-kappa-B1}, DHX58 (DExH-box helicase 58) [NCBI Gene 79132] {aka D11LGP2, D11lgp2e, LGP2, RLR-3}, ORF1ab (ORF1a polyprotein;ORF1ab polyprotein) [NCBI Gene 43740578], HFM1 (helicase for meiosis 1) [NCBI Gene 164045] {aka MER3, POF9, SEC63D1, Si-11, Si-11-6, helicase}
- **Diseases:** SARS-CoV-2 infection (MESH:D000086382), viral infection (MESH:D014777), tumorigenesis (MESH:D063646), infection (MESH:D007239), Dengue (MESH:D003715), inflammation (MESH:D007249), Infectious Diseases (MESH:D003141), neurodegeneration (MESH:D019636), Infectious Bronchitis Virus (IBV)-CoV (MESH:D018352), CD (MESH:D003424)
- **Chemicals:** zinc (MESH:D015032), nucleotide (MESH:D009711), KOH (MESH:C029943), ethanolamine (MESH:D019856), EDC (MESH:C024565), oligonucleotides (MESH:D009841), NaCl (MESH:D012965), NH4Ac (-), DTT (MESH:D004229), IPTG (MESH:D007544), Sulfo-NHS (MESH:C465543), polyacrylamide (MESH:C016679), SDS (MESH:D012967), FAM (MESH:C031179), Tween 20 (MESH:D011136), N6-methyladenosine (MESH:C010223), ATP (MESH:D000255), KCl (MESH:D011189), HEPES (MESH:D006531), glycerol (MESH:D005990), PBS (MESH:D007854), sodium phosphate (MESH:C018279), MgCl2 (MESH:D015636), His (MESH:D006639)
- **Species:** Severe acute respiratory syndrome coronavirus 2 (no rank) [taxon 2697049], Severe acute respiratory syndrome-related coronavirus (no rank) [taxon 694009], Myxoma virus (no rank) [taxon 10273], Human immunodeficiency virus 1 (no rank) [taxon 11676], Homo sapiens (human, species) [taxon 9606], Porcine reproductive and respiratory syndrome virus (no rank) [taxon 28344]
- **Cell lines:** 13 — Homo sapiens (Human), Childhood T acute lymphoblastic leukemia, Cancer cell line (CVCL_1081), BL21(DE3) — Mus musculus (Mouse), Hybridoma (CVCL_B7HM), Nsp13 — Chlorocebus pygerythrus (Vervet monkey), Spontaneously immortalized cell line (CVCL_HA70)

## Figures

9 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12355267/full.md

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Source: https://tomesphere.com/paper/PMC12355267