Senataxin: A Putative RNA: DNA Helicase Mutated in ALS4—Emerging Mechanisms of Genome Stability in Motor Neurons

Requirement for Three Novel Protein Complexes in the Absence of the Sgs1 DNA Helicase in Saccharomyces cerevisiae

Genetics ◽

10.1093/genetics/157.1.103 ◽

2001 ◽

Vol 157 (1) ◽

pp. 103-118 ◽

Cited By ~ 16

Author(s):

Janet R Mullen ◽

Vivek Kaliraman ◽

Samer S Ibrahim ◽

Steven J Brill

Keyword(s):

Saccharomyces Cerevisiae ◽

Genome Stability ◽

Protein Complexes ◽

Ring Finger ◽

Dna Helicase ◽

Open Reading Frames ◽

Temperature Sensitive ◽

Restrictive Temperature ◽

Dna Helicases ◽

Cell Extracts

Abstract The Saccharomyces cerevisiae Sgs1 protein is a member of the RecQ family of DNA helicases and is required for genome stability, but not cell viability. To identify proteins that function in the absence of Sgs1, a synthetic-lethal screen was performed. We obtained mutations in six complementation groups that we refer to as SLX genes. Most of the SLX genes encode uncharacterized open reading frames that are conserved in other species. None of these genes is required for viability and all SLX null mutations are synthetically lethal with mutations in TOP3, encoding the SGS1-interacting DNA topoisomerase. Analysis of the null mutants identified a pair of genes in each of three phenotypic classes. Mutations in MMS4 (SLX2) and SLX3 generate identical phenotypes, including weak UV and strong MMS hypersensitivity, complete loss of sporulation, and synthetic growth defects with mutations in TOP1. Mms4 and Slx3 proteins coimmunoprecipitate from cell extracts, suggesting that they function in a complex. Mutations in SLX5 and SLX8 generate hydroxyurea sensitivity, reduced sporulation efficiency, and a slow-growth phenotype characterized by heterogeneous colony morphology. The Slx5 and Slx8 proteins contain RING finger domains and coimmunoprecipitate from cell extracts. The SLX1 and SLX4 genes are required for viability in the presence of an sgs1 temperature-sensitive allele at the restrictive temperature and Slx1 and Slx4 proteins are similarly associated in cell extracts. We propose that the MMS4/SLX3, SLX5/8, and SLX1/4 gene pairs encode heterodimeric complexes and speculate that these complexes are required to resolve recombination intermediates that arise in response to DNA damage, during meiosis, and in the absence of SGS1/TOP3.

The Main Role of Srs2 in DNA Repair Depends on Its Helicase Activity, Rather than on Its Interactions with PCNA or Rad51

mBio ◽

10.1128/mbio.01192-18 ◽

2018 ◽

Vol 9 (4) ◽

Cited By ~ 5

Author(s):

Alex Bronstein ◽

Lihi Gershon ◽

Gilad Grinberg ◽

Elisa Alonso-Perez ◽

Martin Kupiec

Keyword(s):

Dna Damage ◽

Dna Replication ◽

Genome Stability ◽

Dna Helicase ◽

Main Role ◽

Helicase Domain ◽

Helicase Activity ◽

C Terminus ◽

Srs2 Helicase

ABSTRACTHomologous recombination (HR) is a mechanism that repairs a variety of DNA lesions. Under certain circumstances, however, HR can generate intermediates that can interfere with other cellular processes such as DNA transcription or replication. Cells have therefore developed pathways that abolish undesirable HR intermediates. TheSaccharomyces cerevisiaeyeast Srs2 helicase has a major role in one of these pathways. Srs2 also works during DNA replication and interacts with the clamp PCNA. The relative importance of Srs2’s helicase activity, Rad51 removal function, and PCNA interaction in genome stability remains unclear. We created a newSRS2allele [srs2(1-850)] that lacks the whole C terminus, containing the interaction site for Rad51 and PCNA and interactions with many other proteins. Thus, the new allele encodes an Srs2 protein bearing only the activity of the DNA helicase. We find that the interactions of Srs2 with Rad51 and PCNA are dispensable for the main role of Srs2 in the repair of DNA damage in vegetative cells and for proper completion of meiosis. On the other hand, it has been shown that in cells impaired for the DNA damage tolerance (DDT) pathways, Srs2 generates toxic intermediates that lead to DNA damage sensitivity; we show that this negative Srs2 activity requires the C terminus of Srs2. Dissection of the genetic interactions of thesrs2(1-850) allele suggest a role for Srs2’s helicase activity in sister chromatid cohesion. Our results also indicate that Srs2’s function becomes more central in diploid cells.IMPORTANCEHomologous recombination (HR) is a key mechanism that repairs damaged DNA. However, this process has to be tightly regulated; failure to regulate it can lead to genome instability. The Srs2 helicase is considered a regulator of HR; it was shown to be able to evict the recombinase Rad51 from DNA. Cells lacking Srs2 exhibit sensitivity to DNA-damaging agents, and in some cases, they display defects in DNA replication. The relative roles of the helicase and Rad51 removal activities of Srs2 in genome stability remain unclear. To address this question, we created a new Srs2 mutant which has only the DNA helicase domain. Our study shows that only the DNA helicase domain is needed to deal with DNA damage and assist in DNA replication during vegetative growth and in meiosis. Thus, our findings shift the view on the role of Srs2 in the maintenance of genome integrity.

Nol12 is a multifunctional endonuclease at the nexus of RNA and DNA metabolism

10.1101/043935 ◽

2016 ◽

Cited By ~ 1

Author(s):

Daniel D Scott ◽

Christian Trahan ◽

Pierre-Joachim Zindy ◽

Lisbeth-Carolina Aguilar ◽

Marc Delubac ◽

...

Keyword(s):

Ribosome Biogenesis ◽

Genome Stability ◽

Oxidative Dna Damage ◽

Damage Identification ◽

Alternative Pathway ◽

Rna Metabolism ◽

Small Subunit ◽

Dna Helicase ◽

P Bodies ◽

Dna Maintenance

Endo- and exonucleases are major contributors to RNA metabolism through their diverse roles in maturation and turnover of different species of RNA as well as transcription. Recent data suggests RNA nucleases also affect genome stability programs and act along DNA repair pathways. Here, we describe Nol12 as a multifunctional RNA/DNA endonuclease found in different subcellular compartments - the nucleoplasm, where it co-localizes with the RNA/DNA helicase Dhx9 and paraspeckles, nucleoli as well as GW/P-bodies. We show that Nol12 is required for a key step in ribosomal RNA processing, separating large and small subunit precursors at site 2, rerouting ribosome biogenesis via an alternative pathway in its absence to ensure ribosome production. Furthermore, loss of Nol12 results in increased oxidized DNA levels followed by a rapid p53-independent ATR-Chk1-mediated apoptotic response, suggesting a role for Nol12 in the prevention or resolution of oxidative DNA damage. Identification of a complex Nol12 interactome, which includes NONO, Dhx9 and DNA-PK, further supports its diverse functions in RNA metabolism and DNA maintenance, establishing Nol12 as a multifunctional endonuclease.

HeterozygousRTEL1mutations are associated with familial pulmonary fibrosis

European Respiratory Journal ◽

10.1183/09031936.00040115 ◽

2015 ◽

Vol 46 (2) ◽

pp. 474-485 ◽

Cited By ~ 85

Author(s):

Caroline Kannengiesser ◽

Raphael Borie ◽

Christelle Ménard ◽

Marion Réocreux ◽

Patrick Nitschké ◽

...

Keyword(s):

Pulmonary Fibrosis ◽

Genome Stability ◽

Dna Helicase ◽

Telomere Maintenance ◽

Candidate Gene Approach ◽

Autosomal Dominant Trait ◽

Telomere Shortening ◽

Telomere Elongation ◽

Whole Exome ◽

Familial Pulmonary Fibrosis

Pulmonary fibrosis is a fatal disease with progressive loss of respiratory function. Defective telomere maintenance leading to telomere shortening is a cause of pulmonary fibrosis, as mutations in the telomerase component genesTERT(reverse transcriptase) andTERC(RNA component) are found in 15% of familial pulmonary fibrosis (FPF) cases. However, so far, about 85% of FPF remain genetically uncharacterised.Here, in order to identify new genetic causes of FPF, we performed whole-exome sequencing, with a candidate-gene approach, of 47 affected subjects from 35 families with FPF withoutTERTandTERCmutations.We identified heterozygous mutations in regulator of telomere elongation helicase 1 (RTEL1) in four families. RTEL1 is a DNA helicase with roles in DNA replication, genome stability, DNA repair and telomere maintenance. The heterozygousRTEL1mutations segregated as an autosomal dominant trait in FPF, and were predicted by structural analyses to severely affect the function and/or stability of RTEL1. In agreement with this,RTEL1-mutated patients exhibited short telomeres in comparison with age-matched controls.Our results provide evidence that heterozygousRTEL1mutations are responsible for FPF and, thereby, extend the clinical spectrum of RTEL1 deficiency. Thus,RTEL1enlarges the number of telomere-associated genes implicated in FPF.

Control of Translocations between Highly Diverged Genes by Sgs1, the Saccharomyces cerevisiae Homolog of the Bloom'sSyndrome Protein

Molecular and Cellular Biology ◽

10.1128/mcb.00161-06 ◽

2006 ◽

Vol 26 (14) ◽

pp. 5406-5420 ◽

Cited By ~ 52

Author(s):

Kristina H. Schmidt ◽

Joann Wu ◽

Richard D. Kolodner

Keyword(s):

Saccharomyces Cerevisiae ◽

Dna Sequences ◽

Genome Stability ◽

Dna Helicase ◽

Telomere Maintenance ◽

Template Switching ◽

Checkpoint Kinase ◽

Genes Encoding ◽

Atm Protein ◽

Break Induced Replication

ABSTRACT Sgs1 is a RecQ family DNA helicase required for genome stability in Saccharomyces cerevisiae whose human homologs BLM, WRN, and RECQL4 are mutated in Bloom's, Werner, and Rothmund Thomson syndromes, respectively. Sgs1 and mismatch repair (MMR) are inhibitors of recombination between similar but divergent (homeologous) DNA sequences. Here we show that SGS1, but not MMR, is critical for suppressing spontaneous, recurring translocations between diverged genes in cells with mutations in the genes encoding the checkpoint proteins Mec3, Rad24, Rad9, or Rfc5, the chromatin assembly factors Cac1 or Asf1, and the DNA helicase Rrm3. The S-phase checkpoint kinase and telomere maintenance factor Tel1, a homolog of the human ataxia telangiectasia (ATM) protein, prevents these translocations, whereas the checkpoint kinase Mec1, a homolog of the human ATM-related protein, and the Rad53 checkpoint kinase are not required. The translocation structures observed suggest involvement of a dicentric intermediate and break-induced replication with multiple cycles of DNA template switching.

Human Pif1 helicase is a G-quadruplex DNA-binding protein with G-quadruplex DNA-unwinding activity

Biochemical Journal ◽

10.1042/bj20100612 ◽

2010 ◽

Vol 430 (1) ◽

pp. 119-128 ◽

Cited By ~ 98

Author(s):

Cyril M. Sanders

Keyword(s):

Dna Binding ◽

Dna Sequences ◽

Genome Stability ◽

Dna Helicase ◽

Dna Unwinding ◽

Helicase Domain ◽

Quadruplex Dna ◽

G4 Dna ◽

G Quadruplex ◽

Pif1 Helicase

Pif1 proteins are helicases that in yeast are implicated in the maintenance of genome stability. One activity of Saccharomyces cerevisiae Pif1 is to stabilize DNA sequences that could otherwise form deleterious G4 (G-quadruplex) structures by acting as a G4 resolvase. The present study shows that human Pif1 (hPif1, nuclear form) is a G4 DNA-binding and resolvase protein and that these activities are properties of the conserved helicase domain (amino acids 206–620 of 641, hPifHD). hPif1 preferentially bound synthetic G4 DNA relative to ssDNA (single-stranded DNA), dsDNA (double-stranded DNA) and a partially single-stranded duplex DNA helicase substrate. G4 DNA unwinding, but not binding, required an extended (>10 nucleotide) 5′ ssDNA tail, and in competition assays, G4 DNA was an ineffective suppressor of helicase activity compared with ssDNA. These results suggest a distinction between the determinants of G4 DNA binding and the ssDNA interactions required for helicase action and that hPif1 may act on G4 substrates by binding alone or as a resolvase. Human Pif1 could therefore have a role in processing G4 structures that arise in the single-stranded nucleic acid intermediates formed during DNA replication and gene expression.

RecQ-like helicases: the DNA replication checkpoint connection

Journal of Cell Science ◽

10.1242/jcs.113.15.2641 ◽

2000 ◽

Vol 113 (15) ◽

pp. 2641-2646 ◽

Cited By ~ 1

Author(s):

C. Frei ◽

S.M. Gasser

Keyword(s):

Escherichia Coli ◽

Dna Replication ◽

Normal Cell ◽

Genome Stability ◽

Dna Helicase ◽

S Phase ◽

Replication Checkpoint ◽

Dna Replication Checkpoint ◽

Coherent Picture ◽

Stability Results

The eukaryotic homologues of the Escherichia coli RecQ DNA helicase play conserved roles in the maintenance of genome stability. Results obtained in yeast and mammalian systems are beginning to form a coherent picture about what these helicases do to ensure normal cell division and why humans who lack these enzymes are cancer prone. Recent data suggest that the yeast enzyme Sgs1p, as well as two human homologues, which are encoded by the Bloom's and Werner's syndrome genes, function during DNA replication and possibly in a replication checkpoint specific to S phase.

Bloom syndrome DNA helicase deficiency is associated with oxidative stress and mitochondrial network changes

Scientific Reports ◽

10.1038/s41598-021-81075-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Veena Subramanian ◽

Brian Rodemoyer ◽

Vivek Shastri ◽

Lene J. Rasmussen ◽

Claus Desler ◽

...

Keyword(s):

Oxidative Stress ◽

Genome Stability ◽

Genome Instability ◽

Genetic Disorder ◽

Mitochondrial Fission ◽

Cyclin B1 ◽

Bloom Syndrome ◽

Dna Helicase ◽

G1 Phase ◽

Stress Dependent

AbstractBloom Syndrome (BS; OMIM #210900; ORPHA #125) is a rare genetic disorder that is associated with growth deficits, compromised immune system, insulin resistance, genome instability and extraordinary predisposition to cancer. Most efforts thus far have focused on understanding the role of the Bloom syndrome DNA helicase BLM as a recombination factor in maintaining genome stability and suppressing cancer. Here, we observed increased levels of reactive oxygen species (ROS) and DNA base damage in BLM-deficient cells, as well as oxidative-stress-dependent reduction in DNA replication speed. BLM-deficient cells exhibited increased mitochondrial mass, upregulation of mitochondrial transcription factor A (TFAM), higher ATP levels and increased respiratory reserve capacity. Cyclin B1, which acts in complex with cyclin-dependent kinase CDK1 to regulate mitotic entry and associated mitochondrial fission by phosphorylating mitochondrial fission protein Drp1, fails to be fully degraded in BLM-deficient cells and shows unscheduled expression in G1 phase cells. This failure to degrade cyclin B1 is accompanied by increased levels and persistent activation of Drp1 throughout mitosis and into G1 phase as well as mitochondrial fragmentation. This study identifies mitochondria-associated abnormalities in Bloom syndrome patient-derived and BLM-knockout cells and we discuss how these abnormalities may contribute to Bloom syndrome.

The DNA helicase Pfh1 promotes fork merging at replication termination sites to ensure genome stability

Genes & Development ◽

10.1101/gad.184663.111 ◽

2012 ◽

Vol 26 (6) ◽

pp. 594-602 ◽

Cited By ~ 47

Author(s):

R. Steinacher ◽

F. Osman ◽

J. Z. Dalgaard ◽

A. Lorenz ◽

M. C. Whitby

Keyword(s):

Genome Stability ◽

Dna Helicase

The WYL domain of the PIF1 helicase from the thermophilic bacteriumThermotoga elfiiis an accessory single-stranded DNA binding module

10.1101/163188 ◽

2017 ◽

Author(s):

Nicholas M. Andis ◽

Christopher W. Sausen ◽

Ashna Alladin ◽

Matthew L. Bochman

Keyword(s):

Unknown Function ◽

Genome Stability ◽

Dna Helicase ◽

Thermophilic Bacterium ◽

Helicase Domain ◽

Single Stranded Dna ◽

Ssdna Binding ◽

Pif1 Helicase

ABSTRACTPIF1 family helicases are conserved from bacteria to man. With the exception of the well-studied yeast PIF1 helicases (e.g., ScPif1 and ScRrm3), however, very little is known about how these enzymes help maintain genome stability. Indeed, we lack a basic understanding of the protein domains found N- and C-terminal to the characteristic central PIF1 helicase domain in these proteins. Here, using chimeric constructs, we show that the ScPif1 and ScRrm3 helicase domains are interchangeable and that the N-terminus of ScRrm3 is important for its functionin vivo. This suggests that PIF1 family helicases evolved functional modules fused to a generic motor domain. To investigate this hypothesis, we characterized the biochemical activities of the PIF1 helicase from the thermophilic bacteriumThermotoga elfii(TePif1), which contains a C-terminal WYL domain of unknown function. Like helicases from other thermophiles, recombinant TePif1 was easily prepared, thermostablein vitro, and displayed activities similar to its eukaryotic homologs. We also found that the WYL domain was necessary for high-affinity single-stranded DNA (ssDNA) binding and affected both ATPase and helicase activities. Deleting the WYL domain from TePif1 or mutating conserved residues in the predicted ssDNA binding site uncoupled ATPase activity and DNA unwinding, leading to higher rates of ATP hydrolysis but less efficient DNA helicase activity. Our findings suggest that the domains of unknown function found in eukaryotic PIF1 helicases may also confer functional specificity and additional activities to these enzymes, which should be investigated in future work.