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Biochemical analysis of Pfh1, the essential Pif1 family helicase in Schizosaccharomyces pombe
Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
2019 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
Abstract [en]

DNA stores the genetic information of all living organisms, and this information needs to be copied accurately and passed on to each daughter cell when a cell divides. However, the DNA replication machinery often meets obstacles in the genome that cause fork pausing and might result in DNA damage. DNA helicases are motor proteins that unwind duplex DNA structures using the energy from ATP hydrolysis. Helicases can also assist in replication fork progression by resolving obstacles that arise at hard-to-replicate sites such as tightly DNA-bound proteins, R-loops, and DNA secondary structures like G-quadruplexes (G4s). In this thesis, we focused on Schizosaccharomyces pombe DNA helicase Pfh1, which is localized in both the nucleus and the mitochondria and belongs to the evolutionary conserved Pif1 helicases. Pfh1 is an accessory replicative helicase, and the goal in this thesis was to gain a better mechanistic understanding of the role of nuclear Pfh1 (nPfh1). Our first aim was to elucidate the role of nPfh1 at G-quadruplex (G4) DNA. Aim two was to understand the function of nPfh1’s signature motif. Aim three was to characterize the role of nPfh1 in strand annealing.

Some G-rich sequences can form a four-stranded DNA structure called G4 DNA, and the S. pombe genome contains about 450 bioinformatically predicted G4 structures. We selected two of these sequences, one located in the ribosomal DNA region and one located in the telomeric DNA region, and showed that they form inter- and intramolecular G4 structures, respectively. Next, we established a method to express and purify recombinant nPfh1 and demonstrated that nPfh1 binds to and unwinds these structures. In addition, Pfh1 bound to both the ribosomal and telomeric DNA regions in vivo, suggesting that Pfh1 can bind and unwind G4 structures in vivo. The purified nPfh1 also unwound RNA/DNA more efficiently than DNA/DNA structures, suggesting that nPfh1 has the ability to unwind R-loops in vivo. nPfh1 also showed protein displacement activity, suggesting that it can remove tightly bound proteins from DNA. All of these properties of nPfh1 suggest that it is important for fork progression and for preserving genome integrity.

Furthermore, nPfh1 stimulated strand annealing, and this activity did not require ATP hydrolysis. The strand-annealing activity was higher for complementary DNA/DNA compared to RNA/DNA substrates and did not require a DNA overhang. Furthermore, by analyzing Pfh1 truncated variants we demonstrated that the N-terminus region of Pfh1 was mainly responsible for the strand-annealing activity, however the C-terminus region also possessed some strand-annealing activity. Point mutations in the Pif1 signature motif (SM) have been shown to be associated with an increased risk of breast cancer in humans and with inviable S. pombe cells. We purified several SM variants and found that the unwinding and protein displacement activities of nPfh1 were dependent on the SM, but not the strand-annealing activity, suggesting that the SM is important for functions that require ATP hydrolysis.

In conclusion, in this thesis we identified nPfh1 as a potent G4 unwinder, and this is the only G4 unwinder identified in S. pombe to date. We also provided detailed mechanistic insights into nPfh1 and its different domains, and this has enhanced our understanding of Pfh1’s role in maintaining genome integrity.

Ort, förlag, år, upplaga, sidor
Umeå: Umeå Universitet , 2019. , s. 38
Serie
Umeå University medical dissertations, ISSN 0346-6612 ; 2011
Nyckelord [en]
G4, Pfh1, Genome integrity, helicase
Nationell ämneskategori
Biokemi och molekylärbiologi
Forskningsämne
medicinsk biokemi
Identifikatorer
URN: urn:nbn:se:umu:diva-155477ISBN: 978-91-7855-020-3 (tryckt)OAI: oai:DiVA.org:umu-155477DiVA, id: diva2:1279948
Disputation
2019-02-15, KB:E3.01, Lilla Hörsalen, KBC-huset, Umeå, 13:00 (Engelska)
Opponent
Handledare
Forskningsfinansiär
Knut och Alice Wallenbergs StiftelseSvenska Sällskapet för Medicinsk Forskning (SSMF)Wenner-Gren StiftelsernaKempestiftelsernaVetenskapsrådetTillgänglig från: 2019-01-25 Skapad: 2019-01-17 Senast uppdaterad: 2019-01-23Bibliografiskt granskad
Delarbeten
1. G-rich telomeric and ribosomal DNA sequences from the fission yeast genome form stable G-quadruplex DNA structures in vitro and are unwound by the Pfh1 DNA helicase
Öppna denna publikation i ny flik eller fönster >>G-rich telomeric and ribosomal DNA sequences from the fission yeast genome form stable G-quadruplex DNA structures in vitro and are unwound by the Pfh1 DNA helicase
Visa övriga...
2016 (Engelska)Ingår i: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 44, nr 13, s. 6213-6231Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Certain guanine-rich sequences have an inherent propensity to form G-quadruplex (G4) structures. G4 structures are e.g. involved in telomere protection and gene regulation. However, they also constitute obstacles during replication if they remain unresolved. To overcome these threats to genome integrity, organisms harbor specialized G4 unwinding helicases. In Schizosaccharomyces pombe, one such candidate helicase is Pfh1, an evolutionarily conserved Pif1 homolog. Here, we addressed whether putative G4 sequences in S. pombe can adopt G4 structures and, if so, whether Pfh1 can resolve them. We tested two G4 sequences, derived from S. pombe ribosomal and telomeric DNA regions, and demonstrated that they form inter- and intramolecular G4 structures, respectively. Also, Pfh1 was enriched in vivo at the ribosomal G4 DNA and telomeric sites. The nuclear isoform of Pfh1 (nPfh1) unwound both types of structure, and although the G4-stabilizing compound Phen-DC3 significantly enhanced their stability, nPfh1 still resolved them efficiently. However, stable G4 structures significantly inhibited adenosine triphosphate hydrolysis by nPfh1. Because ribosomal and telomeric DNA contain putative G4 regions conserved from yeasts to humans, our studies support the important role of G4 structure formation in these regions and provide further evidence for a conserved role for Pif1 helicases in resolving G4 structures.

Ort, förlag, år, upplaga, sidor
Oxford University Press, 2016
Nationell ämneskategori
Biokemi och molekylärbiologi
Identifikatorer
urn:nbn:se:umu:diva-124639 (URN)10.1093/nar/gkw349 (DOI)000382999300021 ()27185885 (PubMedID)
Tillgänglig från: 2016-08-18 Skapad: 2016-08-18 Senast uppdaterad: 2019-01-22Bibliografiskt granskad
2. The Pif1 signature motif of Pfh1 is necessary for both protein displacement and helicase unwinding activities, but is dispensable for strand-annealing activity
Öppna denna publikation i ny flik eller fönster >>The Pif1 signature motif of Pfh1 is necessary for both protein displacement and helicase unwinding activities, but is dispensable for strand-annealing activity
2018 (Engelska)Ingår i: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 46, nr 16, s. 8516-8531Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Pfh1, the sole member of the Pif1 helicases in Schizosaccharomyces pombe, is multifunctional and essential for maintenance of both the nuclear and mitochondrial genomes. However, we lack mechanistic insights into the functions of Pfh1 and its different motifs. This paper is specifically concerned with the importance of the Pif1 signature motif (SM), a 23 amino acids motif unique to Pif1 helicases, because a single amino acid substitution in this motif is associated with increased risk of breast cancer in humans and inviability in S. pombe. Here we show that the nuclear isoform of Pfh1 (nPfh1) unwound RNA/DNA hybrids more efficiently than DNA/DNA, suggesting that Pfh1 resolves RNA/DNA structures like R-loops in vivo. In addition, nPfh1 displaced proteins from DNA and possessed strand-annealing activity. The unwinding and protein displacement activities were dependent on the SM because nPfh1 without a large portion of this motif (nPfh1-Δ21) or with the disease/inviability-linked mutation (nPfh1-L430P) lost these properties. Unexpectedly, both nPfh1-L430P and nPfh1-Δ21 still displayed binding to G-quadruplex DNA and demonstrated strand-annealing activity. Misregulated strand annealing and binding of nPfh1-L430P without unwinding are perhaps the reasons that cells expressing this allele are inviable.

Ort, förlag, år, upplaga, sidor
Oxford University Press, 2018
Nationell ämneskategori
Biokemi och molekylärbiologi
Identifikatorer
urn:nbn:se:umu:diva-151172 (URN)10.1093/nar/gky654 (DOI)000450950500040 ()30053106 (PubMedID)
Forskningsfinansiär
VetenskapsrådetKnut och Alice Wallenbergs Stiftelse
Tillgänglig från: 2018-08-29 Skapad: 2018-08-29 Senast uppdaterad: 2019-01-22Bibliografiskt granskad
3. Biochemical analysis of the strand annealing activity of the S. pombe Pif1 helicase
Öppna denna publikation i ny flik eller fönster >>Biochemical analysis of the strand annealing activity of the S. pombe Pif1 helicase
(Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
Abstract [en]

Pif1 helicases are evolutionary conserved and important for maintaining genome integrity. The S. pombe Pif1 helicase, Pfh1, unwinds DNA/DNA and RNA/DNA substrates and has both protein displacement and strand annealing activities. Here, we characterized the strand annealing properties of Pfh1. Although Pfh1 showed higher strand annealing activity on complementary oligonucleotides that produced DNA/DNA substrates, it could also anneal complementary RNA and DNA oligonucleotides. Strand annealing occurred in both the presence and absence of ATP, showing that binding of ATP does not inhibit strand annealing. Analysis of Pfh1 truncated mutants showed that the strand annealing activity of Pfh1 was primarily located on the N-terminus region, but that the C-terminus region also mediated some strand annealing activity. The N-terminus region was even more efficient than full-length Pfh1 to perform strand annealing, but in contrast to the full-length Pfh1, N-terminus Pfh1 was unable to stably bind single-stranded oligonucleotides. However, both proteins efficiently bound an intermolecular G-quadruplex DNA, showing that the N-terminus region can stably bind certain oligonucleotides, but not single-stranded oligonucleotides. These data suggest that the binding preference for single-stranded oligonucleotides is not the only important factor for Pfh1 to perform efficient strand annealing, but that other properties of the protein is also important for the annealing efficiency.

Nyckelord
Pfh1, Pif1, DNA helicase, Annealing
Nationell ämneskategori
Biokemi och molekylärbiologi
Forskningsämne
medicinsk biokemi
Identifikatorer
urn:nbn:se:umu:diva-155474 (URN)
Forskningsfinansiär
Knut och Alice Wallenbergs StiftelseSvenska Sällskapet för Medicinsk Forskning (SSMF)
Tillgänglig från: 2019-01-17 Skapad: 2019-01-17 Senast uppdaterad: 2019-01-22

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