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protein coding gene - pfh1 (SPBC887.14c) - mitochondrial 5' to 3' DNA helicase Pif1/Pfh1 OR nuclear 5' to 3' DNA helicase Pif1/Pfh1

Gene summary

Standard name
pfh1
Systematic ID
SPBC887.14c
Product
mitochondrial 5' to 3' DNA helicase Pif1/Pfh1 OR nuclear 5' to 3' DNA helicase Pif1/Pfh1
Organism
Schizosaccharomyces pombe (fission yeast)
Synonyms
pif1
UniProt ID
Q9UUA2
ORFeome ID
33/33H02
Characterisation status
biological role published
Feature type
mRNA gene
Genomic location
chromosome II: 3567593..3570476 reverse strand

Annotation

Comment

PBO:0004571 - localizes to DNA damage foci

References:

Complementation

PBO:0119952 - functionally complemented by human PIF1

References:

PBO:0004570 - functionally complemented by S. cerevisiae RRM3

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GO biological process

GO:0006310 - DNA recombination

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GO:0006281 - DNA repair

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GO:1902983 - DNA strand elongation involved in mitotic DNA replication

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GO:0043504 - mitochondrial DNA repair

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GO:1990426 - mitotic recombination-dependent replication fork processing

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GO:1903469 - removal of RNA primer involved in mitotic DNA replication

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GO:0031297 - replication fork processing

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GO:0071932 - replication fork reversal

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GO:0000723 - telomere maintenance

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GO cellular component

GO:0000785 - chromatin

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GO:0140445 - chromosome, telomeric repeat region

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GO:0005739 - mitochondrion

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GO:0043601 - nuclear replisome

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GO:0005730 - nucleolus

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GO:0005634 - nucleus

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GO:0033553 - rDNA heterochromatin

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GO:0035861 - site of double-strand break

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GO molecular function

GO:0043139 - 5'-3' DNA helicase activity

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GO:0033678 - 5'-3' DNA/RNA helicase activity

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GO:0005524 - ATP binding

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GO:0016887 - ATP hydrolysis activity

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GO:0061995 - ATP-dependent protein-DNA complex displacement activity

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GO:1990814 - DNA/DNA annealing activity

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GO:0070336 - flap-structured DNA binding

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GO:0051880 - G-quadruplex DNA binding

References:

GO:0160225 - G-quadruplex unwinding activity

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GO:0003723 - RNA binding

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GO:0017116 - single-stranded DNA helicase activity

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Modification

MOD:00046 - O-phospho-L-serine

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MOD:00048 - O4'-phospho-L-tyrosine

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MOD:00696 - phosphorylated residue

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Multi-locus phenotype

FYPO:0003084 - abolished replication fork arrest at mating-type locus

References:

Genotypes:

FYPO:0000229 - cut

References:

Genotypes:

FYPO:0001407 - decreased cell population growth on glucose carbon source

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Genotypes:

FYPO:0001355 - decreased vegetative cell population growth

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Genotypes:

FYPO:0002061 - inviable vegetative cell population

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Genotypes:

FYPO:0000256 - mutator

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Genotypes:

FYPO:0000957 - normal growth on methyl methanesulfonate

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Genotypes:

FYPO:0002687 - normal telomere length during vegetative growth

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Genotypes:

FYPO:0001357 - normal vegetative cell population growth

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Genotypes:

FYPO:0001098 - sensitive to 4-nitroquinoline N-oxide

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Genotypes:

FYPO:0002060 - viable vegetative cell population

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Genotypes:

Protein sequence feature

SO:0001808 - mitochondrial_targeting_signal

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Qualitative gene expression

PomGeneEx:0000012 - RNA level decreased

References:

PomGeneEx:0000011 - RNA level increased

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Quantitative gene expression

PBO:0006310 - protein level

References:

PBO:0011963 - RNA level

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Single locus phenotype

FYPO:0000059 - abnormal mitotic cell cycle

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Genotypes:

FYPO:0000444 - abnormal mitotic cell cycle arrest with replicated DNA

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Genotypes:

FYPO:0003818 - abolished 5'-3' DNA helicase activity

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Genotypes:

FYPO:0006649 - abolished 5'-3' DNA/RNA helicase activity

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Genotypes:

FYPO:0006651 - abolished ATP-dependent protein-DNA complex displacement activity

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Genotypes:

FYPO:0003674 - abolished ATPase activity

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Genotypes:

FYPO:0006655 - abolished G-quadruplex DNA unwinding

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Genotypes:

FYPO:0004337 - abolished protein localization to mitochondrion

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Genotypes:

FYPO:0003819 - decreased 5'-3' DNA helicase activity

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Genotypes:

FYPO:0006648 - decreased 5'-3' DNA/RNA helicase activity

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Genotypes:

FYPO:0001168 - decreased ATPase activity

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Genotypes:

FYPO:0000080 - decreased cell population growth at low temperature

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Genotypes:

FYPO:0006920 - decreased DNA recombination at mitotic DNA replication fork barriers

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Genotypes:

FYPO:0007005 - decreased DNA recombination downstream of mitotic DNA replication fork barriers

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Genotypes:

FYPO:0005439 - decreased DNA/DNA annealing activity

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Genotypes:

FYPO:0006656 - decreased G-quadruplex DNA unwinding

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Genotypes:

FYPO:0000470 - decreased mating type switching

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Genotypes:

FYPO:0004455 - decreased protein localization to nucleus

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Genotypes:

FYPO:0001514 - decreased protein localization to nucleus during vegetative growth

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Genotypes:

FYPO:0003925 - decreased rate of mitotic DNA replication elongation at highly transcribed RNA polymerase II genes

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Genotypes:

FYPO:0001916 - elongated mononucleate vegetative cell

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Genotypes:

FYPO:0002019 - elongated telomeres during vegetative growth

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Genotypes:

FYPO:0003924 - increased DNA damage at stalled replication fork

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Genotypes:

FYPO:0000167 - increased DNA recombination at mitotic DNA replication fork barriers

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Genotypes:

FYPO:0006652 - increased DNA/DNA annealing activity

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Genotypes:

FYPO:0005769 - increased histone H2A phosphorylation at G4 motif during vegetative growth

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Genotypes:

FYPO:0005770 - increased histone H2A phosphorylation at highly transcribed RNA polymerase II genes during vegetative growth

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Genotypes:

FYPO:0005771 - increased histone H2A phosphorylation at nucleosome-depleted regions during vegetative growth

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Genotypes:

FYPO:0002604 - increased histone H2A phosphorylation at rDNA during vegetative growth

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Genotypes:

FYPO:0005772 - increased histone H2A phosphorylation at tRNA genes during vegetative growth

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Genotypes:

FYPO:0003926 - increased number of converged replication forks

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Genotypes:

FYPO:0004815 - increased rDNA antisense siRNA level

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Genotypes:

FYPO:0003920 - increased replication fork arrest at mating-type locus

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Genotypes:

FYPO:0003921 - increased replication fork arrest at rDNA repeats

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Genotypes:

FYPO:0003922 - increased replication fork arrest at tRNA locus

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Genotypes:

FYPO:0005764 - increased replication fork pausing at G4 motif

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Genotypes:

FYPO:0005765 - increased replication fork pausing at highly transcribed RNA polymerase II genes

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Genotypes:

FYPO:0005766 - increased replication fork pausing at nucleosome-depleted regions

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Genotypes:

FYPO:0005768 - increased replication fork pausing at rDNA

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Genotypes:

FYPO:0005767 - increased replication fork pausing at tRNA genes

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Genotypes:

FYPO:0000314 - inviable after spore germination with elongated germ tube

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Genotypes:

FYPO:0003529 - inviable after spore germination, multiple cell divisions, cell cycle arrest in mitotic interphase, elongated cells

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Genotypes:

FYPO:0002262 - inviable after spore germination, multiple cell divisions, elongated cell

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Genotypes:

FYPO:0002061 - inviable vegetative cell population

References:

Genotypes:

FYPO:0004300 - normal ATPase activity

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Genotypes:

FYPO:0001929 - normal cell cycle regulation during cellular response to hydroxyurea

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Genotypes:

FYPO:0004787 - normal DNA/DNA annealing activity

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Genotypes:

FYPO:0006653 - normal flap-structured DNA binding

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Genotypes:

FYPO:0006654 - normal G-quadruplex DNA binding

References:

Genotypes:

FYPO:0004824 - normal rDNA copy number

References:

Genotypes:

FYPO:0001357 - normal vegetative cell population growth

References:

Genotypes:

FYPO:0000095 - sensitive to bleomycin

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Genotypes:

FYPO:0000088 - sensitive to hydroxyurea

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Genotypes:

FYPO:0000089 - sensitive to methyl methanesulfonate

References:

Genotypes:

FYPO:0002239 - shortened telomeres during vegetative growth

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Genotypes:

FYPO:0001234 - slow vegetative cell population growth

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Genotypes:

FYPO:0001492 - viable elongated vegetative cell

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Genotypes:

FYPO:0003612 - viable spore population

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Genotypes:

FYPO:0002060 - viable vegetative cell population

References:

Genotypes:

Subunit composition

PBO:0001467 - monomeric

References:

Taxonomic conservation

PBO:0011065 - conserved in eukaryotes

PBO:0011071 - conserved in eukaryotes only

PBO:0011064 - conserved in fungi

PBO:0011069 - conserved in metazoa

PBO:0011070 - conserved in vertebrates

PBO:0006222 - predominantly single copy (one to one)

Protein features

IDNameInterPro nameDB name
PF05970PIF1DNA_helicase_pif1-like_DEADPfam
PF21530Pif1_2B_domPif1-like_2B_domPfam
cd18037DEXSc_Pif1_likeCDD
cd18809SF1_C_RecDCDD
SM00382AAAAAA+_ATPaseSMART
G3DSA:3.40.50.300:FF:001226CATH-FunFam
G3DSA:3.40.50.300P-loop_NTPaseCATH-Gene3D
SSF52540P-loop_NTPaseSUPERFAMILY
PTHR47642PIF1_helicasePANTHER
MF_03176PIF1PIF1_RRM3_pfh1HAMAP
mobidb-lite-Disorderdisorder_predictionMobiDB-Disorder
mobidb-lite-Low-complexitydisorder_predictionMobiDB-Low-complexity
mobidb-lite-Polardisorder_predictionMobiDB-Polar

Orthologs

References / Literature

PMID:21511999 - Comparative functional genomics of the fission yeasts.
Rhind N et al. Science 2011 May 20;332(6032):930-6
PMID:39476757 - Characterization of Ksg1 protein kinase-dependent phosphoproteome in the fission yeast S. pombe.
Cipak L et al. Biochem Biophys Res Commun 2024 Oct 25;736:150895
PMID:23101633 - Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells.
Marguerat S et al. Cell 2012 Oct 26;151(3):671-83
PMID:12058079 - Schizosaccharomyces pombe pfh1+ encodes an essential 5' to 3' DNA helicase that is a member of the PIF1 subfamily of DNA helicases.
Zhou JQ et al. Mol Biol Cell 2002 Jun;13(6):2180-91
PMID:25720772 - Quantitative phosphoproteomics reveals pathways for coordination of cell growth and division by the conserved fission yeast kinase pom1.
Kettenbach AN et al. Mol Cell Proteomics 2015 May;14(5):1275-87
PMID:21712547 - Mitotic substrates of the kinase aurora with roles in chromatin regulation identified through quantitative phosphoproteomics of fission yeast.
Koch A et al. Sci Signal 2011 Jun 28;4(179):rs6
PMID:26041456 - RPA prevents G-rich structure formation at lagging-strand telomeres to allow maintenance of chromosome ends.
Audry J et al. EMBO J 2015 Jul 14;34(14):1942-58
PMID:15576681 - Genetics of lagging strand DNA synthesis and maturation in fission yeast: suppression analysis links the Dna2-Cdc24 complex to DNA polymerase delta.
Tanaka H et al. Nucleic Acids Res 2004;32(21):6367-77
PMID:12409464 - The fission yeast pfh1(+) gene encodes an essential 5' to 3' DNA helicase required for the completion of S-phase.
Tanaka H et al. Nucleic Acids Res 2002 Nov 01;30(21):4728-39
PMID:25303777 - The Pif1 family helicase Pfh1 facilitates telomere replication and has an RPA-dependent role during telomere lengthening.
McDonald KR et al. DNA Repair (Amst) 2014 Dec;24:80-86
PMID:19547744 - Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species.
Beltrao P et al. PLoS Biol 2009 Jun 16;7(6):e1000134
PMID:18257517 - Phosphoproteome analysis of fission yeast.
Wilson-Grady JT et al. J Proteome Res 2008 Mar;7(3):1088-97
PMID:28054200 - The functions of the multi-tasking Pfh1 Pif1 helicase.
Sabouri N Curr Genet 2017 Aug;63(4):621-626
PMID:22540037 - Predicting the fission yeast protein interaction network.
Pancaldi V et al. G3 (Bethesda) 2012 Apr;2(4):453-67
PMID:23628481 - A proteome-wide visual screen identifies fission yeast proteins localizing to DNA double-strand breaks.
Yu Y et al. DNA Repair (Amst) 2013 Jun 01;12(6):433-43
PMID:23697806 - A genome-wide resource of cell cycle and cell shape genes of fission yeast.
Hayles J et al. Open Biol 2013 May 22;3(5):130053
PMID:30053106 - The Pif1 signature motif of Pfh1 is necessary for both protein displacement and helicase unwinding activities, but is dispensable for strand-annealing activity.
Mohammad JB et al. Nucleic Acids Res 2018 Sep 19;46(16):8516-8531
PMID:30667359 - Factors affecting template switch recombination associated with restarted DNA replication.
Jalan M et al. Elife 2019 Jan 22;8
PMID:32692737 - CRL4Cdt2 ubiquitin ligase regulates Dna2 and Rad16 (XPF) nucleases by targeting Pxd1 for degradation.
Zhang JM et al. PLoS Genet 2020 Jul;16(7):e1008933
PMID:33313903 - Ribosome profiling reveals ribosome stalling on tryptophan codons and ribosome queuing upon oxidative stress in fission yeast.
Rubio A et al. Nucleic Acids Res 2021 Jan 11;49(1):383-399
PMID:36408920 - UniProt: the Universal Protein Knowledgebase in 2023.
UniProt Consortium Nucleic Acids Res 2023 Jan 06;51(D1):D523-D531
PMID:40015273 - A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with proteins and chromatin.
Skribbe M et al. Mol Cell 2025 Feb 19;
PMID:18388861 - Mus81 is essential for sister chromatid recombination at broken replication forks.
Roseaulin L et al. EMBO J 2008 May 07;27(9):1378-87
PMID:33823663 - A TOR (target of rapamycin) and nutritional phosphoproteome of fission yeast reveals novel targets in networks conserved in humans.
Halova L et al. Open Biol 2021 Apr;11(4):200405
PMID:19714215 - The fission yeast homeodomain protein Yox1p binds to MBF and confines MBF-dependent cell-cycle transcription to G1-S via negative feedback.
Aligianni S et al. PLoS Genet 2009 Aug;5(8):e1000626
GO_REF:0000033 - Annotation inferences using phylogenetic trees
PMID:27298342 - Identification of S-phase DNA damage-response targets in fission yeast reveals conservation of damage-response networks.
Willis NA et al. Proc Natl Acad Sci U S A 2016 Jun 28;113(26):E3676-85
PMID:22426534 - DNA replication through hard-to-replicate sites, including both highly transcribed RNA Pol II and Pol III genes, requires the S. pombe Pfh1 helicase.
Sabouri N et al. Genes Dev 2012 Mar 15;26(6):581-93
PMID:20473289 - Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe.
Kim DU et al. Nat Biotechnol 2010 Jun;28(6):617-623
PMID:15302919 - Genetic and biochemical analyses of Pfh1 DNA helicase function in fission yeast.
Ryu GH et al. Nucleic Acids Res 2004;32(14):4205-16
PMID:24763107 - Absolute proteome and phosphoproteome dynamics during the cell cycle of Schizosaccharomyces pombe (Fission Yeast).
Carpy A et al. Mol Cell Proteomics 2014 Aug;13(8):1925-36
PMID:25203555 - Fission yeast Pxd1 promotes proper DNA repair by activating Rad16XPF and inhibiting Dna2.
Zhang JM et al. PLoS Biol 2014 Sep;12(9):e1001946
PMID:22426535 - The DNA helicase Pfh1 promotes fork merging at replication termination sites to ensure genome stability.
Steinacher R et al. Genes Dev 2012 Mar 15;26(6):594-602
PMID:24875629 - Essential domains of Schizosaccharomyces pombe Rad8 required for DNA damage response.
Ding L et al. G3 (Bethesda) 2014 May 28;4(8):1373-84
PMID:25417108 - Dicer promotes transcription termination at sites of replication stress to maintain genome stability.
Castel SE et al. Cell 2014 Oct 23;159(3):572-83
GO_REF:0000104 - Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features.
PMID:27611590 - Pfh1 Is an Accessory Replicative Helicase that Interacts with the Replisome to Facilitate Fork Progression and Preserve Genome Integrity.
McDonald KR et al. PLoS Genet 2016 Sep;12(9):e1006238
PMID:29996109 - Quantitative Phosphoproteomics Reveals the Signaling Dynamics of Cell-Cycle Kinases in the Fission Yeast Schizosaccharomyces pombe.
Swaffer MP et al. Cell Rep 2018 Jul 10;24(2):503-514
PMID:22347400 - A genomewide screen for suppressors of Alu-mediated rearrangements reveals a role for PIF1.
Chisholm KM et al. PLoS One 2012;7(2):e30748
PMID:18725402 - The Schizosaccharomyces pombe Pfh1p DNA helicase is essential for the maintenance of nuclear and mitochondrial DNA.
Pinter SF et al. Mol Cell Biol 2008 Nov;28(21):6594-608
PMID:30726745 - Fission Yeast NDR/LATS Kinase Orb6 Regulates Exocytosis via Phosphorylation of the Exocyst Complex.
Tay YD et al. Cell Rep 2019 Feb 05;26(6):1654-1667.e7
PMID:16823372 - ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe.
Matsuyama A et al. Nat Biotechnol 2006 Jul;24(7):841-7
PMID:32093266 - Yeast Genome Maintenance by the Multifunctional PIF1 DNA Helicase Family.
Muellner J et al. Genes (Basel) 2020 Feb 20;11(2)
PMID:34228709 - Expression of the cancer-associated DNA polymerase ε P286R in fission yeast leads to translesion synthesis polymerase dependent hypermutation and defective DNA replication.
Soriano I et al. PLoS Genet 2021 Jul;17(7):e1009526
PMID:30321377 - Proteomic profiling and functional characterization of post-translational modifications of the fission yeast RNA exosome.
Telekawa C et al. Nucleic Acids Res 2018 Nov 30;46(21):11169-11183
GO_REF:0000024 - Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity.
PMID:26670050 - Regulation of mRNA Levels by Decay-Promoting Introns that Recruit the Exosome Specificity Factor Mmi1.
Kilchert C et al. Cell Rep 2015 Dec 22;13(11):2504-2515
PMID:25471935 - The essential Schizosaccharomyces pombe Pfh1 DNA helicase promotes fork movement past G-quadruplex motifs to prevent DNA damage.
Sabouri N et al. BMC Biol 2014 Dec 04;12:101
PMID:27185885 - 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.
Wallgren M et al. Nucleic Acids Res 2016 Jul 27;44(13):6213-31
PMID:22308326 - Tight coevolution of proliferating cell nuclear antigen (PCNA)-partner interaction networks in fungi leads to interspecies network incompatibility.
Zamir L et al. Proc Natl Acad Sci U S A 2012 Feb 14;109(7):E406-14