- 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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Abstract
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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
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