RecQ and Fe-S helicases have unique roles in DNA metabolism dictated by their unwinding directionality, substrate specificity, and protein interactions

Abstract

Helicases are molecular motors that play central roles in nucleic acid metabolism. Mutations in genes encoding DNA helicases of the RecQ and iron-sulfur (Fe-S) helicase families are linked to hereditary disorders characterized by chromosomal instabilities, highlighting the importance of these enzymes. Moreover, mono-allelic RecQ and Fe-S helicase mutations are associated with a broad spectrum of cancers. This review will discuss and contrast the specialized molecular functions and biological roles of RecQ and Fe-S helicases in DNA repair, the replication stress response, and the regulation of gene expression, laying a foundation for continued research in these important areas of study.

Keywords: DNA replication and recombination; DNA synthesis and repair; cancer; genetic disease; genome integrity; helicase.

Figure 1. Human DNA helicases of the RecQ and Fe–S families

Shown is an alignment of the RecQ (A) and Fe–S (B) human DNA helicases with their conserved ATPase/helicase domain consisting of two RecA folds. Auxiliary domains and selected protein interaction domains are also shown. (A) WRN is unique in that it has a proof-reading exonuclease domain. All the human RecQ helicases possess a Zn²⁺-binding domain, with RECQL4’s being distinct from the others. The RQC domain in RECQL1, WRN, and BLM mediates DNA-binding and protein interactions. A KIX domain in RECQL5 mediates interaction with RNA polymerase II. The Sld2 domain in RECQL4 shares homology to the yeast DNA replication initiator protein Sld2. (B) XPD and RTEL1 interact with the p44 subunit of TFIIH and PCNA, respectively, via regions in the C-terminus. FANCJ contains a C-terminal domain that upon phosphorylation at Ser-990 binds to the BRCT domain of BRCA1. See the text for details. BLM, Bloom’s syndrome helicase; BRCT, BRCA1 C-terminus; FANCJ, Fanconi Anemia Group J helicase; HRDC, helicase RNase D-like C-terminal; KIX, kinase-inducible; PCNA, proliferating cell nuclear antigen; RQC, RecQ C-terminal; RTEL1, regulator of telomere helicase; TFIIH, transcription factor IIH; WRN, Werner syndrome helicase-nuclease; XPD, Xeroderma pigmentosum Group D.

Figure 2. Various genomic processes are facilitated by the action of RecQ or Fe–S DNA helicases during DNA replication or repair

Replication and DNA repair are two areas which involve helicases of the human RecQ (WRN, BLM, RECQL1, RECQL4, and RECQL5) and Fe–S (FANCJ, RTEL1, XPD, and DDX11) families to act on unique structures in nucleic acid metabolism. Some of the prominent DNA structural intermediates of the pathways are shown. RecQ and Fe–S helicases are implicated in the regulation of HR repair of DSBs and remodeling of stalled replication forks via their helicase or branch-migration activities on multi-stranded DNA structures. BLM is a prominent player in DNA end-resection (an early event in HR repair), as well as the dissolution of double HJs that arise during HR or replication fork convergence. Certain RecQ and Fe–S helicases are believed to resolve unusual DNA structures such as G-quadruplexes or telomeric D-loops to preserve genomic stability during replication and at chromosome ends. WRN, BLM, and DDX11 interact with the structure-specific nuclease FEN-1 that is implicated in Okazaki fragment processing. XPD, together with the DNA helicase XPB (not shown), resides in the TFIIH complex and is implicated in NER and transcription. RECQL5, via its interaction with RNA polymerase II, resolves conflicts between the replisome and the transcription complex. RECQL4 is unique among the RecQ helicases to be found in the mitochondria where it is proposed to facilitate replication of the organelle’s circular genome through its interaction with mitochondrial replisome proteins. See the text for details. RNA Pol, RNA polymerase II.

Figure 3. Models for the involvement of RecQ and Fe–S helicases at replication forks

(A) WRN facilitates lagging strand synthesis and maturation by co-ordinate unwinding of 5′ flaps and interacting with pol δ and FEN-1 to stimulate DNA synthesis and cleave flaps to allow ligation of Okazaki fragments, respectively. (B) RTEL1 interacts with the replication clamp PCNA to ensure processive DNA synthesis by pol ε and pol δ (not shown) and telomere stability. (C and D) The Fe–S helicase FANCJ collaborates with the RecQ helicases WRN or BLM (C) or the translesion polymerase REV1 (D) to allow smooth DNA synthesis through G4-forming DNA sequences, which is important for normal epigenetic modifications of the nuclear genome. (E) RECQL5 displaces RAD51 from DNA to enable cleavage of stalled forks by the structure-specific nuclease MUS81 (anchored by the SLX4 scaffold protein), an event that is important during early mitosis to allow chromosome segregation. (F) RECQL1 restores the replication fork in a manner that is negatively regulated by PARP-1 to allow replication restart. See the text for details.

Figure 4. Models for the involvement of RecQ and Fe–S helicases in homologous recombinational repair and telomere maintenance

(A and B) RecQ (RECQL5 and BLM) and Fe–S (FANCJ) helicases are proposed to regulate HR repair of DSBs by catalytically removing the major strand exchange protein RAD51 from single-stranded DNA overhangs. This may serve to suppress inappropriate recombination events or help to mature recombinant DNA molecules to allow HR to proceed. (C and D) RECQL1 and RTEL1 or FANCJ act upon three-stranded D-loop structures via branch-migration or helicase activity, respectively, to suppress inadvertent HR, thereby preventing inadvertent and dead-end toxic DNA intermediates. (E) WRN or BLM promotes HR repair by branch-migrating four-stranded HJ intermediates. See the text for details. (F) The shelterin proteins TRF1 and TRF2 negatively regulates WRN’s 3′–5′ exonuclease activity at chromosome ends to maintain telomeric stability at the T-loop structure. (G) TRF2 recruits RTEL1 to T-loops to promote DNA unwinding to enable replication or DNA repair of telomere repeats. (H and I) WRN [and possibly BLM (not shown)] or RTEL1 resolves telomeric G4 DNA structures to allow normal DNA synthesis or repair of telomeric G-rich DNA.