- Effects of the loss of mismatch repair genes on single-strand annealing between divergent sequences in Saccharomyces cerevisiae
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Ye-Seul Lim , Ju-Hee Choi , Kyu-Jin Ahn , Min-Ku Kim , Sung-Ho Bae
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J. Microbiol. 2021;59(4):401-409. Published online March 29, 2021
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DOI: https://doi.org/10.1007/s12275-021-1076-x
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 Abstract
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Eukaryotic genomes contain many duplicated genes closely
located with each other, such as the hexose transporter (HXT)
genes in Saccharomyces cerevisiae. They can potentially recombine
via single-strand annealing (SSA) pathway. SSA between
highly divergent sequences generates heteroduplex
DNA intermediates with many mismatches, which can be
corrected by mismatch repair (MMR), resulting in recombinant
sequences with a single junction point. In this report,
we demonstrate that SSA between HXT1 and HXT4 genes
in MMR-deficient yeast cells produces recombinant genes
with multiple-junctions resulting from alternating HXT1 and
HXT4 tracts. The mutations in MMR genes had differential
effects on SSA frequencies; msh6Δ mutation significantly
stimulated SSA events, whereas msh2Δ and msh3Δ slightly
suppressed it. We set up an assay that can identify a pair of
recombinant genes derived from a single heteroduplex DNA.
As a result, the recombinant genes with multiple-junctions
were found to accompany genes with single-junctions. Based
on the results presented here, a model was proposed to generate
multiple-junctions in SSA pathway involving an alternative
short-patch repair system.
- Analyses of DNA double-strand break repair pathways in tandem arrays of HXT genes of Saccharomyces cerevisiae
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Ju-Hee Choi , Ye-Seul Lim , Min-Ku Kim , Sung-Ho Bae
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J. Microbiol. 2020;58(11):957-966. Published online October 30, 2020
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DOI: https://doi.org/10.1007/s12275-020-0461-1
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360
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4
Web of Science
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4
Crossref
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Abstract
PDF
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Eukaryotic genomes contain numerous homologous repeat
sequences including redundant genes with divergent homology
that can be potential recombination targets. Recombination
between divergent sequences is rare but poses a substantial
threat to genome stability. The hexose transporter
(HXT) gene family shares high sequence similarities at both
protein and DNA levels, and some members are placed close
together in tandem arrays. In this study, we show that spontaneous
interstitial deletions occur at significantly high rates
in HXT gene clusters, resulting in chimeric HXT sequences
that contain a single junction point. We also observed that
DNA double-strand breaks created between HXT genes produce
primarily interstitial deletions, whereas internal cleavage
of the HXT gene resulted in gene conversions as well as deletion
products. Interestingly, interstitial deletions were less constrained
by sequence divergence than gene conversion. Moreover,
recombination-defective mutations differentially affected
the survival frequency. Mutations that impair single-strand
annealing (SSA) pathway greatly reduced the survival frequency
by 10–1,000-fold, whereas disruption of Rad51-dependent
homologous recombination exhibited only modest reduction.
Our results indicate that recombination in the tandemly
repeated HXT genes occurs primarily via SSA pathway.
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Citations
Citations to this article as recorded by  - Deletion of IRC19 Causes Defects in DNA Double-Strand Break Repair Pathways in Saccharomyces cerevisiae
Ju-Hee Choi, Oyungoo Bayarmagnai, Sung-Ho Bae
Journal of Microbiology.2024; 62(9): 749. CrossRef - A novel CRISPR/Cas9 system with high genomic editing efficiency and recyclable auxotrophic selective marker for multiple-step metabolic rewriting in Pichia pastoris
Xiang Wang, Yi Li, Zhehao Jin, Xiangjian Liu, Xiang Gao, Shuyuan Guo, Tao Yu
Synthetic and Systems Biotechnology.2023; 8(3): 445. CrossRef - Enhancing Homologous Recombination Efficiency in Pichia pastoris for Multiplex Genome Integration Using Short Homology Arms
Jucan Gao, Cuifang Ye, Jintao Cheng, Lihong Jiang, Xinghao Yuan, Jiazhang Lian
ACS Synthetic Biology.2022; 11(2): 547. CrossRef - Effects of the loss of mismatch repair genes on single-strand annealing between divergent sequences in Saccharomyces cerevisiae
Ye-Seul Lim, Ju-Hee Choi, Kyu-Jin Ahn, Min-Ku Kim, Sung-Ho Bae
Journal of Microbiology.2021; 59(4): 401. CrossRef
- Hrq1 Facilitates Nucleotide Excision Repair of DNA Damage Induced by 4-Nitroquinoline-1-Oxide and Cisplatin in Saccharomyces cerevisiae
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Do-Hee Choi , Moon-Hee Min , Min-Ji Kim , Rina Lee , Sung-Hun Kwon , Sung-Ho Bae
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J. Microbiol. 2014;52(4):292-298. Published online March 29, 2014
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DOI: https://doi.org/10.1007/s12275-014-4018-z
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342
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15
Crossref
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Abstract
PDF
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Hrq1 helicase is a novel member of the RecQ family. Among the five human RecQ helicases, Hrq1 is most homologous to RECQL4 and is conserved in fungal genomes. Recent genetic and biochemical studies have shown that it is a functional
gene, involved in the maintenance of genome stability. To better define the roles of Hrq1 in yeast cells, we investigated genetic interactions between HRQ1 and several DNA repair genes. Based on DNA damage sensitivities induced by 4-nitroquinoline-
1-oxide (4-NQO) or cisplatin, RAD4 was found to be epistatic to HRQ1. On the other hand, mutant strains defective in either homologous recombination (HR) or postreplication repair (PRR) became more sensitive by additional deletion of HRQ1, indicating that HRQ1 functions in the RAD4-dependent nucleotide excision repair (NER) pathway independent of HR or PRR. In support of this, yeast twohybrid
analysis showed that Hrq1 interacted with Rad4, which was enhanced by DNA damage. Overexpression of Hrq1K318A helicase-deficient protein rendered mutant cells more sensitive to 4-NQO and cisplatin, suggesting that helicase activity is required for the proper function of Hrq1 in NER.
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Citations
Citations to this article as recorded by - Metabolomics Combined with Physiology and Transcriptomics Reveal the Response of Samsoniella hepiali to Key Metabolic Pathways and Its Degradation Mechanism during Subculture
Hui He, Zhengfei Cao, Tao Wang, Chuyu Tang, Yuling Li, Xiuzhang Li
Antioxidants.2024; 13(7): 780. CrossRef - Yeast Ribonucleotide Reductase Is a Direct Target of the Proteasome and Provides Hyper Resistance to the Carcinogen 4-NQO
Daria S. Spasskaya, Kirill A. Kulagin, Evgenia N. Grineva, Pamila J. Osipova, Svetlana V. Poddubko, Julia A. Bubis, Elizaveta M. Kazakova, Tomiris T. Kusainova, Vladimir A. Gorshkov, Frank Kjeldsen, Vadim L. Karpov, Irina A. Tarasova, Dmitry S. Karpov
Journal of Fungi.2023; 9(3): 351. CrossRef - Hrq1/RECQL4 regulation is critical for preventing aberrant recombination during DNA intrastrand crosslink repair and is upregulated in breast cancer
Thong T. Luong, Zheqi Li, Nolan Priedigkeit, Phoebe S. Parker, Stefanie Böhm, Kyle Rapchak, Adrian V. Lee, Kara A. Bernstein, Dmitry A. Gordenin
PLOS Genetics.2022; 18(9): e1010122. CrossRef - A skipping rope translocation mechanism in a widespread family of DNA repair helicases
Johann J Roske, Sunbin Liu, Bernhard Loll, Ursula Neu, Markus C Wahl
Nucleic Acids Research.2021; 49(1): 504. CrossRef - Role and Regulation of the RECQL4 Family during Genomic Integrity Maintenance
Thong T. Luong, Kara A. Bernstein
Genes.2021; 12(12): 1919. CrossRef - Zuo1 supports G4 structure formation and directs repair toward nucleotide excision repair
Alessio De Magis, Silvia Götz, Mona Hajikazemi, Enikő Fekete-Szücs, Marco Caterino, Stefan Juranek, Katrin Paeschke
Nature Communications.2020;[Epub] CrossRef - The Genetic and Physical Interactomes of theSaccharomyces cerevisiaeHrq1 Helicase
Cody M Rogers, Elsbeth Sanders, Phoebe A Nguyen, Whitney Smith-Kinnaman, Amber L Mosley, Matthew L Bochman
G3 Genes|Genomes|Genetics.2020; 10(12): 4347. CrossRef - Maintenance of Yeast Genome Integrity by RecQ Family DNA Helicases
Sonia Vidushi Gupta, Kristina Hildegard Schmidt
Genes.2020; 11(2): 205. CrossRef - Analyses of DNA double-strand break repair pathways in tandem arrays of HXT genes of Saccharomyces cerevisiae
Ju-Hee Choi, Ye-Seul Lim, Min-Ku Kim, Sung-Ho Bae
Journal of Microbiology.2020; 58(11): 957. CrossRef - DNA Helicases as Safekeepers of Genome Stability in Plants
Annika Dorn, Holger Puchta
Genes.2019; 10(12): 1028. CrossRef - The RecQ‐like helicase HRQ1 is involved in DNA crosslink repair in Arabidopsis in a common pathway with the Fanconi anemia‐associated nuclease FAN1 and the postreplicative repair ATPase RAD5A
Sarah Röhrig, Annika Dorn, Janina Enderle, Angelina Schindele, Natalie J. Herrmann, Alexander Knoll, Holger Puchta
New Phytologist.2018; 218(4): 1478. CrossRef - Yeast Hrq1 shares structural and functional homology with the disease-linked human RecQ4 helicase
Cody M. Rogers, Joseph Che-Yen Wang, Hiroki Noguchi, Tsuyoshi Imasaki, Yuichiro Takagi, Matthew L. Bochman
Nucleic Acids Research.2017; 45(9): 5217. CrossRef - Interaction of RECQ4 and MCM10 is important for efficient DNA replication origin firing in human cells
Maciej Kliszczak, Hana Sedlackova, Ganesha P. Pitchai, Werner W. Streicher, Lumir Krejci, Ian D. Hickson
Oncotarget.2015; 6(38): 40464. CrossRef - DNA repair defects ascribed to pby1 are caused by disruption of Holliday junction resolvase Mus81-Mms4
Gizem Ölmezer, Dominique Klein, Ulrich Rass
DNA Repair.2015; 33: 17. CrossRef - Characterization of Hrq1-Rad14 Interaction in Saccharomyces cerevisiae
Moon-Hee Min, Min-Ji Kim, You-Jin Choi, Min-Ju You, Uy-Ra Kim, Hyo-Bin An, Chae-Hyun Kim, Chae-Yeon Kwon, Sung-Ho Bae
The Korean Journal of Microbiology.2014; 50(2): 95. CrossRef
- Hrq1 Functions Independently of Sgs1 to Preserve Genome Integrity in Saccharomyces cerevisiae
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Do-Hee Choi , Rina Lee , Sung-Hun Kwon , Sung-Ho Bae
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J. Microbiol. 2013;51(1):105-112. Published online March 2, 2013
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DOI: https://doi.org/10.1007/s12275-013-3048-2
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268
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0
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18
Crossref
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Abstract
PDF
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Maintenance of genome stability in eukaryotes involves a number of conserved proteins, including RecQ helicases, which play multiple roles at various steps in homologous recombination and DNA repair pathways. Sgs1 has been described as the only RecQ helicase in lower eukaryotes. However, recent studies revealed the presence of a second RecQ helicase, Hrq1, which is most homologous to human RECQL4. Here we show that hrq1Δ mutation resulted in increased mitotic recombination and spontaneous mutation in Saccharomyces cerevisiae, and sgs1Δ mutation had additive effects on the phenotypes of hrq1Δ. We also observed that the hrq1Δ mutant was sensitive to 4-nitroquinoline 1-oxide and cisplatin, which was not complemented by overexpression of Sgs1. In addition, the hrq1Δ sgs1Δ double mutant displayed synthetic growth defect as well as a shortened chronological life span compared with the respective single mutants. Analysis of the type of age-dependent Canr mutations revealed that only point mutations were found in hrq1Δ, whereas significant numbers of gross deletion mutations were found in sgs1Δ. Our results suggest that Hrq1 is involved in recombination and DNA repair pathways in S. cerevisiae independent of Sgs1.
-
Citations
Citations to this article as recorded by - Deletion of IRC19 Causes Defects in DNA Double-Strand Break Repair Pathways in Saccharomyces cerevisiae
Ju-Hee Choi, Oyungoo Bayarmagnai, Sung-Ho Bae
Journal of Microbiology.2024; 62(9): 749. CrossRef - Systematic analysis of changes across different developmental stages of the mushroom Sarcomyxa edulis
Chao Duan, Lan Yao, Jian-Hua Lv, Chuan-Wen Jia, Feng-hua Tian, Chang-Tian Li
Gene.2022; 824: 146450. CrossRef - Human RecQ Helicases in DNA Double-Strand Break Repair
Huiming Lu, Anthony J. Davis
Frontiers in Cell and Developmental Biology.2021;[Epub] CrossRef - Effects of the loss of mismatch repair genes on single-strand annealing between divergent sequences in Saccharomyces cerevisiae
Ye-Seul Lim, Ju-Hee Choi, Kyu-Jin Ahn, Min-Ku Kim, Sung-Ho Bae
Journal of Microbiology.2021; 59(4): 401. CrossRef - Analyses of DNA double-strand break repair pathways in tandem arrays of HXT genes of Saccharomyces cerevisiae
Ju-Hee Choi, Ye-Seul Lim, Min-Ku Kim, Sung-Ho Bae
Journal of Microbiology.2020; 58(11): 957. CrossRef - The Genetic and Physical Interactomes of theSaccharomyces cerevisiaeHrq1 Helicase
Cody M Rogers, Elsbeth Sanders, Phoebe A Nguyen, Whitney Smith-Kinnaman, Amber L Mosley, Matthew L Bochman
G3 Genes|Genomes|Genetics.2020; 10(12): 4347. CrossRef - Maintenance of Yeast Genome Integrity by RecQ Family DNA Helicases
Sonia Vidushi Gupta, Kristina Hildegard Schmidt
Genes.2020; 11(2): 205. CrossRef - The nature of meiotic chromosome dynamics and recombination in budding yeast
Soogil Hong, Jeong Hwan Joo, Hyeseon Yun, Keunpil Kim
Journal of Microbiology.2019; 57(4): 221. CrossRef - Ku complex suppresses recombination in the absence of MRX activity during budding yeast meiosis
Hyeseon Yun, Keunpil Kim
BMB Reports.2019; 52(10): 607. CrossRef - The RecQ‐like helicase HRQ1 is involved in DNA crosslink repair in Arabidopsis in a common pathway with the Fanconi anemia‐associated nuclease FAN1 and the postreplicative repair ATPase RAD5A
Sarah Röhrig, Annika Dorn, Janina Enderle, Angelina Schindele, Natalie J. Herrmann, Alexander Knoll, Holger Puchta
New Phytologist.2018; 218(4): 1478. CrossRef - Disruption of SUMO-targeted ubiquitin ligases Slx5–Slx8/RNF4 alters RecQ-like helicase Sgs1/BLM localization in yeast and human cells
Stefanie Böhm, Michael Joseph Mihalevic, Morgan Alexandra Casal, Kara Anne Bernstein
DNA Repair.2015; 26: 1. CrossRef - Interaction of RECQ4 and MCM10 is important for efficient DNA replication origin firing in human cells
Maciej Kliszczak, Hana Sedlackova, Ganesha P. Pitchai, Werner W. Streicher, Lumir Krejci, Ian D. Hickson
Oncotarget.2015; 6(38): 40464. CrossRef - Hrq1 facilitates nucleotide excision repair of DNA damage induced by 4-nitroquinoline-1-oxide and cisplatin in Saccharomyces cerevisiae
Do-Hee Choi, Moon-Hee Min, Min-Ji Kim, Rina Lee, Sung-Hun Kwon, Sung-Ho Bae
Journal of Microbiology.2014; 52(4): 292. CrossRef - Conditional Genetic Interactions ofRTT107,SLX4, andHRQ1Reveal Dynamic Networks upon DNA Damage inS. cerevisiae
Grace P Leung, Maria J Aristizabal, Nevan J Krogan, Michael S Kobor
G3 Genes|Genomes|Genetics.2014; 4(6): 1059. CrossRef - Characterization of the Caenorhabditis elegans HIM-6/BLM Helicase: Unwinding Recombination Intermediates
Hana Jung, Jin A Lee, Seoyoon Choi, Hyunwoo Lee, Byungchan Ahn, Michael Lichten
PLoS ONE.2014; 9(7): e102402. CrossRef - Characterization of Hrq1-Rad14 Interaction in Saccharomyces cerevisiae
Moon-Hee Min, Min-Ji Kim, You-Jin Choi, Min-Ju You, Uy-Ra Kim, Hyo-Bin An, Chae-Hyun Kim, Chae-Yeon Kwon, Sung-Ho Bae
The Korean Journal of Microbiology.2014; 50(2): 95. CrossRef - The intrinsically disordered amino-terminal region of human RecQL4: multiple DNA-binding domains confer annealing, strand exchange and G4 DNA binding
Heidi Keller, Kristin Kiosze, Juliane Sachsenweger, Sebastian Haumann, Oliver Ohlenschläger, Tarmo Nuutinen, Juhani E. Syväoja, Matthias Görlach, Frank Grosse, Helmut Pospiech
Nucleic Acids Research.2014; 42(20): 12614. CrossRef - Human RecQ Helicases in DNA Repair, Recombination, and Replication
Deborah L. Croteau, Venkateswarlu Popuri, Patricia L. Opresko, Vilhelm A. Bohr
Annual Review of Biochemistry.2014; 83(1): 519. CrossRef
- Saccharomyces cerevisiae Cmr1 Protein Preferentially Binds to UV-Damaged DNA In Vitro
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Do-Hee Choi , Sung-Hun Kwon , Joon-Ho Kim , Sung-Ho Bae
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J. Microbiol. 2012;50(1):112-118. Published online February 27, 2012
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DOI: https://doi.org/10.1007/s12275-012-1597-4
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246
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10
Crossref
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Abstract
PDF
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DNA metabolic processes such as DNA replication, recombination,
and repair are fundamentally important for the
maintenance of genome integrity and cell viability. Although
a large number of proteins involved in these pathways have
been extensively studied, many proteins still remain to be
identified. In this study, we isolated DNA-binding proteins
from Saccharomyces cerevisiae using DNA-cellulose columns.
By analyzing the proteins using mass spectrometry, an uncharacterized
protein, Cmr1/YDL156W, was identified. Cmr1
showed sequence homology to human Damaged-DNA binding
protein 2 in its C-terminal WD40 repeats. Consistent
with this finding, the purified recombinant Cmr1 protein
was found to be intrinsically associated with DNA-binding
activity and exhibited higher affinity to UV-damaged DNA
substrates. Chromatin isolation experiments revealed that
Cmr1 localized in both the chromatin and supernatant
fractions, and the level of Cmr1 in the chromatin fraction
increased when yeast cells were irradiated with UV. These
results
suggest that Cmr1 may be involved in DNA-damage
responses in yeast.
-
Citations
Citations to this article as recorded by - An integrated structural model of the DNA damage-responsive H3K4me3 binding WDR76:SPIN1 complex with the nucleosome
Xingyu Liu, Ying Zhang, Zhihui Wen, Yan Hao, Charles A.S. Banks, Joseph Cesare, Saikat Bhattacharya, Shreyas Arvindekar, Jeffrey J. Lange, Yixuan Xie, Benjamin A. Garcia, Brian D. Slaughter, Jay R. Unruh, Shruthi Viswanath, Laurence Florens, Jerry L. Work
Proceedings of the National Academy of Sciences.2024;[Epub] CrossRef - Histone H4 dosage modulates DNA damage response in the pathogenic yeast Candida glabrata via homologous recombination pathway
Kundan Kumar, Romila Moirangthem, Rupinder Kaur, Michael Freitag
PLOS Genetics.2020; 16(3): e1008620. CrossRef - Genome Wide Analysis of WD40 Proteins in Saccharomyces cerevisiae and Their Orthologs in Candida albicans
Buddhi Prakash Jain
The Protein Journal.2019; 38(1): 58. CrossRef - Biochemical Reduction of the Topology of the Diverse WDR76 Protein Interactome
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Journal of Proteome Research.2019; 18(9): 3479. CrossRef - Mte1 interacts with Mph1 and promotes crossover recombination and telomere maintenance
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Genes & Development.2016; 30(6): 700. CrossRef - Recruitment of Saccharomyces cerevisiae Cmr1/Ydl156w to Coding Regions Promotes Transcription Genome Wide
Jeffery W. Jones, Priyanka Singh, Chhabi K. Govind, Sukesh R. Bhaumik
PLOS ONE.2016; 11(2): e0148897. CrossRef - Cmr1/WDR76 defines a nuclear genotoxic stress body linking genome integrity and protein quality control
Irene Gallina, Camilla Colding, Peter Henriksen, Petra Beli, Kyosuke Nakamura, Judith Offman, David P. Mathiasen, Sonia Silva, Eva Hoffmann, Anja Groth, Chunaram Choudhary, Michael Lisby
Nature Communications.2015;[Epub] CrossRef - Compartment‐specific aggregases direct distinct nuclear and cytoplasmic aggregate deposition
Stephanie BM Miller, Chi‐Ting Ho, Juliane Winkler, Maria Khokhrina, Annett Neuner, Mohamed YH Mohamed, D Lys Guilbride, Karsten Richter, Michael Lisby, Elmar Schiebel, Axel Mogk, Bernd Bukau
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Basel Abu-Jamous, Rui Fa, David J. Roberts, Asoke K. Nandi
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Johnny M. Tkach, Askar Yimit, Anna Y. Lee, Michael Riffle, Michael Costanzo, Daniel Jaschob, Jason A. Hendry, Jiongwen Ou, Jason Moffat, Charles Boone, Trisha N. Davis, Corey Nislow, Grant W. Brown
Nature Cell Biology.2012; 14(9): 966. CrossRef
- The Mutation of a Novel Saccharomyces cerevisiae SRL4 Gene Rescues the Lethality of rad53 and lcd1 Mutations by Modulating dNTP Levels
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Do-Hee Choi , Young-Mi Oh , Sung-Hun Kwon , Sung-Ho Bae
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J. Microbiol. 2008;46(1):75-80.
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DOI: https://doi.org/10.1007/s12275-008-0013-6
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295
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0
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5
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Abstract
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The SRL4 (YPL033C) gene was initially identified by the screening of Saccharomyces cerevisiae genes that play a role in DNA metabolism and/or genome stability using the SOS system of Escherichia coli. In this study, we found that the srl4Δ; mutant cells were resistant to the chemicals that inhibit nucleotide metabolism and evidenced higher dNTP levels than were observed in the wild-type cells in the presence of hydroxyurea. The mutant cells also showed a significantly faster growth rate and higher dNTP levels at low temperature (16 oC) than were observed in the wild-type cells, whereas we detected no differences in the growth rate at 30oC. Furthermore, srl4Δ was shown to suppress the lethality of mutations of the essential S phase checkpoint genes, RAD53 and LCD1. These results indicate that SRL4 may be involved in the regulation of dNTP production by its function as a negative regulator of ribonucleotide reductase.
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Citations
Citations to this article as recorded by - Peroxisomal Compartmentalization of the Methylerythritol-4-phosphate Pathway Alleviates Cellular Stress and Enhances Geraniol Production in Saccharomyces cerevisiae
Jerome R. Lon, Xuemei Zhao, Gulkiz Mamatrixat, Zhoukang Zhuang, Zhehao Jin, Tao Yu, Jufang Wang, Hongting Tang
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Do-Hee Choi, Sung-Hun Kwon, Joon-Ho Kim, Sung-Ho Bae
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Dong-Uk Kim, Jacqueline Hayles, Dongsup Kim, Valerie Wood, Han-Oh Park, Misun Won, Hyang-Sook Yoo, Trevor Duhig, Miyoung Nam, Georgia Palmer, Sangjo Han, Linda Jeffery, Seung-Tae Baek, Hyemi Lee, Young Sam Shim, Minho Lee, Lila Kim, Kyung-Sun Heo, Eun Joo
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