start-ver=1.4
cd-journal=joma
no-vol=9
cd-vols=
no-issue=
article-no=
start-page=8866
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2019
dt-pub=2019620
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Yeast screening system reveals the inhibitory mechanism of cancer cell proliferation by benzyl isothiocyanate through down-regulation of Mis12
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Benzyl isothiocyanate (BITC) is a naturally-occurring isothiocyanate derived from cruciferous vegetables. BITC has been reported to inhibit the proliferation of various cancer cells, which is believed to be important for the inhibition of tumorigenesis. However, the detailed mechanisms of action remain unclear. In this study, we employed a budding yeast Saccharomyces cerevisiae as a model organism for screening. Twelve genes including MTW1 were identified as the overexpression suppressors for the antiproliferative effect of BITC using the genome-wide multi-copy plasmid collection for S. cerevisiae. Overexpression of the kinetochore protein Mtw1 counteracts the antiproliferative effect of BITC in yeast. The inhibitory effect of BITC on the proliferation of human colon cancer HCT-116 cells was consistently suppressed by the overexpression of Mis12, a human orthologue of Mtw1, and enhanced by the knockdown of Mis12. We also found that BITC increased the phosphorylated and ubiquitinated Mis12 level with consequent reduction of Mis12, suggesting that BITC degrades Mis12 through an ubiquitin-proteasome system. Furthermore, cell cycle analysis showed that the change in the Mis12 level affected the cell cycle distribution and the sensitivity to the BITC-induced apoptosis. These results provide evidence that BITC suppresses cell proliferation through the post-transcriptional regulation of the kinetochore protein Mis12.
en-copyright=
kn-copyright=

en-aut-name=Abe-KanohNaomi
en-aut-sei=Abe-Kanoh
en-aut-mei=Naomi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=KunisueNarumi
en-aut-sei=Kunisue
en-aut-mei=Narumi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=MyojinTakumi
en-aut-sei=Myojin
en-aut-mei=Takumi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=ChinoAyako
en-aut-sei=Chino
en-aut-mei=Ayako
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

en-aut-name=MunemasaShintaro
en-aut-sei=Munemasa
en-aut-mei=Shintaro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=

en-aut-name=MurataYoshiyuki
en-aut-sei=Murata
en-aut-mei=Yoshiyuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=

en-aut-name=SatohAyano
en-aut-sei=Satoh
en-aut-mei=Ayano
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=

en-aut-name=MoriyaHisao
en-aut-sei=Moriya
en-aut-mei=Hisao
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=

en-aut-name=NakamuraYoshimasa
en-aut-sei=Nakamura
en-aut-mei=Yoshimasa
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=

affil-num=1
en-affil=Graduate School of Environmental and Life Science, Okayama University
kn-affil=

affil-num=2
en-affil=Graduate School of Environmental and Life Science, Okayama University
kn-affil=

affil-num=3
en-affil=Graduate School of Environmental and Life Science, Okayama University
kn-affil=

affil-num=4
en-affil=Research Core for Interdisciplinary Sciences, Okayama University
kn-affil=

affil-num=5
en-affil=Graduate School of Environmental and Life Science, Okayama University
kn-affil=

affil-num=6
en-affil=Graduate School of Environmental and Life Science, Okayama University
kn-affil=

affil-num=7
en-affil= Graduate School of Natural Science and Technology, Okayama University
kn-affil=

affil-num=8
en-affil=Research Core for Interdisciplinary Sciences, Okayama University
kn-affil=

affil-num=9
en-affil=Graduate School of Environmental and Life Science, Okayama University, Okayama
kn-affil=
END

start-ver=1.4
cd-journal=joma
no-vol=109
cd-vols=
no-issue=
article-no=
start-page=7
end-page=11
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2020
dt-pub=20200201
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=Mathematical analysis of copy number variation of 2 μ-based plasmids in yeast cells
kn-title=酵母2μプラスミドのコピー数変動の数理的解析
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract= 　Plasmids with the 2 μ plasmid origin are commonly-used in the genetic engineering of the budding yeast Saccharomyces cerevisiae. Intracellular copy numbers of 2 μ plasmids are different depending on the genes inserted into the plasmids. This difference is thought to occur from the difference in the growth efficiency （fitness） produced by the positive- and negative-selection biases of genes inserted in the plasmid. In this study, we made a mathematical model based on this assumption. Computational simulations of the model validated that copy numbers of the plasmids are rapidly settled depending on the fitness created by the gene on the plasmid. The copy number of a plasmid only contains a bias to keep the plasmid in a single copy became average 20copies per cell when the plasmid is randomly distributed, suggesting that no positive distribution mechanism is required for a plasmid to become multicopy.
en-copyright=
kn-copyright=

en-aut-name=SaekiNozomu
en-aut-sei=Saeki
en-aut-mei=Nozomu
kn-aut-name=佐伯望
kn-aut-sei=佐伯
kn-aut-mei=望
aut-affil-num=1
ORCID=

en-aut-name=MoriyaHisao
en-aut-sei=Moriya
en-aut-mei=Hisao
kn-aut-name=守屋央朗
kn-aut-sei=守屋
kn-aut-mei=央朗
aut-affil-num=2
ORCID=

affil-num=1
en-affil=Graduate School of Environmental and Life Science, Okayama University)
kn-affil=岡山大学大学院　環境生命科学研究科

affil-num=2
en-affil= Research Core for Interdisciplinary Sciences, Okayama University
kn-affil=異分野融合先端研究コア
en-keyword=yeast
kn-keyword=yeast
en-keyword=2 μ plasmid
kn-keyword=2 μ plasmid
en-keyword=mathematical model
kn-keyword=mathematical model
END

start-ver=1.4
cd-journal=joma
no-vol=7
cd-vols=
no-issue=2
article-no=
start-page=121
end-page=132
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2020
dt-pub=20200514
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=The expression level and cytotoxicity of green fluorescent protein are modulated by an additional N-terminal sequence
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Nucleotide and amino acid sequences at the N-terminus affect the expression level and cytotoxicity of proteins; however, their effects are not fully understood yet. Here, N-terminal 30 nucleotide/10 amino acid (N10) sequences that affect the expression level and cytotoxicity of a green fluorescent protein were systematically isolated in the budding yeast Saccharomyces cerevisiae. The expression per gene (EPG) and gene copy number limit (CNL) relationships were examined to assess the effects of the N10 sequence. The isolated N10 nucleotide sequences suggested that codon optimality is the major determinant of the protein expression level. A higher number of hydrophobic or cysteine residues in the N10 sequence seemed to increase the cytotoxicity of the protein. Therefore, a high frequency of specific amino acid residues in the outside of the main tertiary structure of proteins might not be preferable.
en-copyright=
kn-copyright=

en-aut-name=MoriyaHisao
en-aut-sei=Moriya
en-aut-mei=Hisao
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

affil-num=1
en-affil=Graduate School of Environmental and Life Sciences, Research Core for Interdisciplinary Sciences, Okayama University
kn-affil=
en-keyword=green fluorescent protein
kn-keyword=green fluorescent protein
en-keyword=overexpression
kn-keyword=overexpression
en-keyword=expression limit
kn-keyword=expression limit
en-keyword=expression level
kn-keyword=expression level
en-keyword=protein cytotoxicity
kn-keyword=protein cytotoxicity
END

start-ver=1.4
cd-journal=joma
no-vol=
cd-vols=
no-issue=
article-no=
start-page=
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2020
dt-pub=20200603
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Comparative Gene Analysis Focused on Silica Cell Wall Formation: Identification of Diatom-Specific SET Domain Protein Methyltransferases
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Silica cell walls of diatoms have attracted attention as a source of nanostructured functional materials and have immense potential for a variety of applications. Previous studies of silica cell wall formation have identified numerous involved proteins, but most of these proteins are species-specific and are not conserved among diatoms. However, because the basic process of diatom cell wall formation is common to all diatom species, ubiquitous proteins and molecules will reveal the mechanisms of cell wall formation. In this study, we assembled de novo transcriptomes of three diatom species, Nitzschia palea, Achnanthes kuwaitensis, and Pseudoleyanella lunata, and compared protein-coding genes of five genome-sequenced diatom species. These analyses revealed a number of diatom-specific genes that encode putative endoplasmic reticulum-targeting proteins. Significant numbers of these proteins showed homology to silicanin-1, which is a conserved diatom protein that reportedly contributes to cell wall formation. These proteins also included a previously unrecognized SET domain protein methyltransferase family that may regulate functions of cell wall formation-related proteins and long-chain polyamines. Proteomic analysis of cell wall-associated proteins in N. palea identified a protein that is also encoded by one of the diatom-specific genes. Expression analysis showed that candidate genes were upregulated in response to silicon, suggesting that these genes play roles in silica cell wall formation. These candidate genes can facilitate further investigations of silica cell wall formation in diatoms.
en-copyright=
kn-copyright=

en-aut-name=NemotoMichiko
en-aut-sei=Nemoto
en-aut-mei=Michiko
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=IwakiSayako
en-aut-sei=Iwaki
en-aut-mei=Sayako
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=MoriyaHisao
en-aut-sei=Moriya
en-aut-mei=Hisao
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=MondenYuki
en-aut-sei=Monden
en-aut-mei=Yuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

en-aut-name=TamuraTakashi
en-aut-sei=Tamura
en-aut-mei=Takashi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=

en-aut-name=InagakiKenji
en-aut-sei=Inagaki
en-aut-mei=Kenji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=

en-aut-name=MayamaShigeki
en-aut-sei=Mayama
en-aut-mei=Shigeki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=

en-aut-name=ObuseKiori
en-aut-sei=Obuse
en-aut-mei=Kiori
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=

affil-num=1
en-affil=Graduate School of Environmental and Life Science, Okayama University
kn-affil=

affil-num=2
en-affil=Graduate School of Environmental and Life Science, Okayama University
kn-affil=

affil-num=3
en-affil=Graduate School of Environmental and Life Science, Okayama University
kn-affil=

affil-num=4
en-affil=Graduate School of Environmental and Life Science, Okayama University
kn-affil=

affil-num=5
en-affil=Graduate School of Environmental and Life Science, Okayama University
kn-affil=

affil-num=6
en-affil=Graduate School of Environmental and Life Science, Okayama University
kn-affil=

affil-num=7
en-affil=Department of Biology, Tokyo Gakugei University
kn-affil=

affil-num=8
en-affil=Graduate School of Environmental and Life Science, Okayama University
kn-affil=
en-keyword=Biomineralization
kn-keyword=Biomineralization
en-keyword=Diatom
kn-keyword=Diatom
en-keyword=Silica
kn-keyword=Silica
en-keyword=Transcriptome
kn-keyword=Transcriptome
en-keyword=Proteome
kn-keyword=Proteome
END

start-ver=1.4
cd-journal=joma
no-vol=10
cd-vols=
no-issue=1
article-no=
start-page=9500
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2020
dt-pub=20200611
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=N-terminal deletion of Swi3 created by the deletion of a dubious ORF YJL175W mitigates protein burden effect in S. cerevisiae
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Extreme overproduction of gratuitous proteins can overload cellular protein production resources, leading to growth defects, a phenomenon known as the protein burden/cost effect. Genetic screening in the budding yeast Saccharomyces cerevisiae has isolated several dubious ORFs whose deletions mitigated the protein burden effect, but individual characterization thereof has yet to be delineated. We found that deletion of the YJL175W ORF yielded an N-terminal deletion of Swi3, a subunit of the SWI/SNF chromatin remodeling complex, and partial loss of function of Swi3. The deletion mutant showed a reduction in transcription of genes encoding highly expressed, secreted proteins and an overall reduction in translation. Mutations in the chromatin remodeling complex could thus mitigate the protein burden effect, likely by reallocating residual cellular resources used to overproduce proteins. This cellular state might also be related to cancer cells, as they frequently harbor mutations in the SWI/SNF complex.
en-copyright=
kn-copyright=

en-aut-name=SaekiNozomu
en-aut-sei=Saeki
en-aut-mei=Nozomu
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=EguchiYuichi
en-aut-sei=Eguchi
en-aut-mei=Yuichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=KintakaReiko
en-aut-sei=Kintaka
en-aut-mei=Reiko
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=MakanaeKoji
en-aut-sei=Makanae
en-aut-mei=Koji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

en-aut-name=ShichinoYuichi
en-aut-sei=Shichino
en-aut-mei=Yuichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=

en-aut-name=IwasakiShintaro
en-aut-sei=Iwasaki
en-aut-mei=Shintaro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=

en-aut-name=KannoManabu
en-aut-sei=Kanno
en-aut-mei=Manabu
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=

en-aut-name=KimuraNobutada
en-aut-sei=Kimura
en-aut-mei=Nobutada
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=

en-aut-name=MoriyaHisao
en-aut-sei=Moriya
en-aut-mei=Hisao
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=

affil-num=1
en-affil=Graduate School of Environmental and Life Science, Okayama University
kn-affil=

affil-num=2
en-affil=Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University
kn-affil=

affil-num=3
en-affil=Donnelly Center for Cellular and Biomolecular Research, Department of Medical Genetics, University of Toronto
kn-affil=

affil-num=4
en-affil=Graduate School of Environmental and Life Science, Okayama University
kn-affil=

affil-num=5
en-affil=RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research
kn-affil=

affil-num=6
en-affil=RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research
kn-affil=

affil-num=7
en-affil=Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology
kn-affil=

affil-num=8
en-affil=Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology
kn-affil=

affil-num=9
en-affil=Research Core for Interdisciplinary Sciences, Okayama University
kn-affil=
en-keyword=Cell growth
kn-keyword=Cell growth
en-keyword=Gene expression
kn-keyword=Gene expression
en-keyword=Gene regulation
kn-keyword=Gene regulation
END

start-ver=1.4
cd-journal=joma
no-vol=10
cd-vols=
no-issue=1
article-no=
start-page=4798
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2020
dt-pub=20200316
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Development of an experimental method of systematically estimating protein expression limits in HEK293 cells
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Protein overexpression sometimes causes cellular defects, although the underlying mechanism is still unknown. A protein's expression limit, which triggers cellular defects, is a useful indication of the underlying mechanism. In this study, we developed an experimental method of estimating the expression limits of target proteins in the human embryonic kidney cell line HEK293 by measuring the proteins' expression levels in cells that survived after the high-copy introduction of plasmid DNA by which the proteins were expressed under a strong cytomegalovirus promoter. The expression limits of nonfluorescent target proteins were indirectly estimated by measuring the levels of green fluorescent protein (GFP) connected to the target proteins with the self-cleaving sequence P2A. The expression limit of a model GFP was similar to 5.0% of the total protein, and sustained GFP overexpression caused cell death. The expression limits of GFPs with mitochondria-targeting signals and endoplasmic reticulum localization signals were 1.6% and 0.38%, respectively. The expression limits of four proteins involved in vesicular trafficking were far lower compared to a red fluorescent protein. The protein expression limit estimation method developed will be valuable for defining toxic proteins and consequences of protein overexpression.
en-copyright=
kn-copyright=

en-aut-name=MoriYoshihiro
en-aut-sei=Mori
en-aut-mei=Yoshihiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=YoshidaYuki
en-aut-sei=Yoshida
en-aut-mei=Yuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=SatohAyano
en-aut-sei=Satoh
en-aut-mei=Ayano
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=MoriyaHisao
en-aut-sei=Moriya
en-aut-mei=Hisao
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

affil-num=1
en-affil=Graduate School of Natural Science and Technology, Okayama University
kn-affil=

affil-num=2
en-affil=Sony Computer Science Laboratories
kn-affil=

affil-num=3
en-affil=Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University
kn-affil=

affil-num=4
en-affil=Research Core for Interdisciplinary Sciences, Okayama University
kn-affil=
en-keyword=Biological techniques
kn-keyword=Biological techniques
en-keyword=Cell biology
kn-keyword=Cell biology
en-keyword=Gene expression analysis
kn-keyword=Gene expression analysis
en-keyword=Molecular biology
kn-keyword=Molecular biology
en-keyword=Protein translocation
kn-keyword=Protein translocation
en-keyword=Protein transport
kn-keyword=Protein transport
END

start-ver=1.4
cd-journal=joma
no-vol=16
cd-vols=
no-issue=10
article-no=
start-page=e1009091
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2020
dt-pub=20201028
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Exploring the Complexity of Protein-Level Dosage Compensation that Fine-Tunes Stoichiometry of Multiprotein Complexes
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Proper control of gene expression levels upon various perturbations is a fundamental aspect of cellular robustness. Protein-level dosage compensation is one mechanism buffering perturbations to stoichiometry of multiprotein complexes through accelerated proteolysis of unassembled subunits. Although N-terminal acetylation- and ubiquitin-mediated proteasomal degradation by the Ac/N-end rule pathway enables selective compensation of excess subunits, it is unclear how widespread this pathway contributes to stoichiometry control. Here we report that dosage compensation depends only partially on the Ac/N-end rule pathway. Our analysis of genetic interactions between 18 subunits and 12 quality control factors in budding yeast demonstrated that multiple E3 ubiquitin ligases and N-acetyltransferases are involved in dosage compensation. We find that N-acetyltransferases-mediated compensation is not simply predictable from N-terminal sequence despite their sequence specificity for N-acetylation. We also find that the compensation of Pop3 and Bet4 is due in large part to a minor N-acetyltransferase NatD. Furthermore, canonical NatD substrates histone H2A/H4 were compensated even in its absence, suggesting N-acetylation-independent stoichiometry control. Our study reveals the complexity and robustness of the stoichiometry control system. Author summary Quality control of multiprotein complexes is important for maintaining homeostasis in cellular systems that are based on functional complexes. Proper stoichiometry of multiprotein complexes is achieved by the balance between protein synthesis and degradation. Recent studies showed that translation efficiency tends to scale with stoichiometry of their subunits. On the other hand, although protein N-terminal acetylation- and ubiquitin-mediated proteolysis pathway is involved in selective degradation of excess subunits, it is unclear how widespread this pathway contributes to stoichiometry control due to the lack of a systematic investigation using endogenous proteins. To better understand the landscape of the stoichiometry control system, we examined genetic interactions between 18 subunits and 12 quality control factors (E3 ubiquitin ligases and N-acetyltransferases), in total 114 combinations. Our data suggest that N-acetyltransferases are partially responsible for stoichiometry control and that N-acetylation-independent pathway is also involved in selective degradation of excess subunits. Therefore, this study reveals the complexity and robustness of the stoichiometry control system. Further dissection of this complexity will help to understand the mechanisms buffering gene expression perturbations and shaping proteome stoichiometry.
en-copyright=
kn-copyright=

en-aut-name=IshikawaKoji
en-aut-sei=Ishikawa
en-aut-mei=Koji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=IshiharaAkari
en-aut-sei=Ishihara
en-aut-mei=Akari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=MoriyaHisao
en-aut-sei=Moriya
en-aut-mei=Hisao
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

affil-num=1
en-affil=Research Core for Interdisciplinary Sciences, Okayama University
kn-affil=

affil-num=2
en-affil=Course of Agrochemical Bioscience, Faculty of Agriculture, Okayama University
kn-affil=

affil-num=3
en-affil= Research Core for Interdisciplinary Sciences, Okayama University
kn-affil=
END

start-ver=1.4
cd-journal=joma
no-vol=9
cd-vols=
no-issue=
article-no=
start-page=e54080
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2020
dt-pub=20201104
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Genetic profiling of protein burden and nuclear export overload
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Overproduction (op) of proteins triggers cellular defects. One of the consequences of overproduction is the protein burden/cost, which is produced by an overloading of the protein synthesis process. However, the physiology of cells under a protein burden is not well characterized. We performed genetic profiling of protein burden by systematic analysis of genetic interactions between GFP-op, surveying both deletion and temperature-sensitive mutants in budding yeast. We also performed genetic profiling in cells with overproduction of triple-GFP (tGFP), and the nuclear export signal-containing tGFP (NES-tGFP). The mutants specifically interacted with GFP-op were suggestive of unexpected connections between actin-related processes like polarization and the protein burden, which was supported by morphological analysis. The tGFP-op interactions suggested that this protein probe overloads the proteasome, whereas those that interacted with NES-tGFP involved genes encoding components of the nuclear export process, providing a resource for further analysis of the protein burden and nuclear export overload.
en-copyright=
kn-copyright=

en-aut-name=KintakaReiko
en-aut-sei=Kintaka
en-aut-mei=Reiko
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=MakanaeKoji
en-aut-sei=Makanae
en-aut-mei=Koji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=NambaShotaro
en-aut-sei=Namba
en-aut-mei=Shotaro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=KatoHisaaki
en-aut-sei=Kato
en-aut-mei=Hisaaki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

en-aut-name=KitoKeiji
en-aut-sei=Kito
en-aut-mei=Keiji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=

en-aut-name=OhnukiShinsuke
en-aut-sei=Ohnuki
en-aut-mei=Shinsuke
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=

en-aut-name=OhyaYoshikazu
en-aut-sei=Ohya
en-aut-mei=Yoshikazu
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=

en-aut-name=AndrewsBrenda J.
en-aut-sei=Andrews
en-aut-mei=Brenda J.
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=

en-aut-name=BooneCharles
en-aut-sei=Boone
en-aut-mei=Charles
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=

en-aut-name=MoriyaHisao
en-aut-sei=Moriya
en-aut-mei=Hisao
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=10
ORCID=

affil-num=1
en-affil=Donnelly Center for Cellular and Biomolecular Research, Department of Medical Genetics, University of Toronto
kn-affil=

affil-num=2
en-affil=Research Core for Interdisciplinary Sciences, Okayama University
kn-affil=

affil-num=3
en-affil=Matching Program Course, Okayama University
kn-affil=

affil-num=4
en-affil=School of Environmental and Life Science, Okayama University
kn-affil=

affil-num=5
en-affil=Department of Life Sciences, School of Agriculture, Meiji University
kn-affil=

affil-num=6
en-affil=Graduate School of Frontier Sciences, University of Tokyo
kn-affil=

affil-num=7
en-affil=Graduate School of Frontier Sciences, University of Tokyo
kn-affil=

affil-num=8
en-affil=Donnelly Center for Cellular and Biomolecular Research, Department of Medical Genetics, University of Toronto
kn-affil=

affil-num=9
en-affil=Donnelly Center for Cellular and Biomolecular Research, Department of Medical Genetics, University of Toronto
kn-affil=

affil-num=10
en-affil=Research Core for Interdisciplinary Sciences, Okayama University
kn-affil=
END

start-ver=1.4
cd-journal=joma
no-vol=12
cd-vols=
no-issue=6
article-no=
start-page=jkac106
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2022
dt-pub=20220429
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Massive expression of cysteine-containing proteins causes abnormal elongation of yeast cells by perturbing the proteasome
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=The enhanced green fluorescent protein (EGFP) is considered to be a harmless protein because the critical expression level that causes growth defects is higher than that of other proteins. Here, we found that overexpression of EGFP, but not a glycolytic protein Gpm1, triggered the cell elongation phenotype in the budding yeast Saccharomyces cerevisiae. By the morphological analysis of the cell overexpressing fluorescent protein and glycolytic enzyme variants, we revealed that cysteine content was associated with the cell elongation phenotype. The abnormal cell morphology triggered by overexpression of EGFP was also observed in the fission yeast Schizosaccharomyces pombe. Overexpression of cysteine-containing protein was toxic, especially at high-temperature, while the toxicity could be modulated by additional protein characteristics. Investigation of protein aggregate formation, morphological abnormalities in mutants, and transcriptomic changes that occur upon overexpression of EGFP variants suggested that perturbation of the proteasome by the exposed cysteine of the overexpressed protein causes cell elongation. Overexpression of proteins with relatively low folding properties, such as EGFP, was also found to promote the formation of SHOTA (Seventy kDa Heat shock protein-containing, Overexpression-Triggered Aggregates), an intracellular aggregate that incorporates Hsp70/Ssa1, which induces a heat shock response, while it was unrelated to cell elongation. Evolutionary analysis of duplicated genes showed that cysteine toxicity may be an evolutionary bias to exclude cysteine from highly expressed proteins. The overexpression of cysteine-less moxGFP, the least toxic protein revealed in this study, would be a good model system to understand the physiological state of protein burden triggered by ultimate overexpression of harmless proteins.
en-copyright=
kn-copyright=

en-aut-name=NambaShotaro
en-aut-sei=Namba
en-aut-mei=Shotaro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=KatoHisaaki
en-aut-sei=Kato
en-aut-mei=Hisaaki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=ShigenobuShuji
en-aut-sei=Shigenobu
en-aut-mei=Shuji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=MakinoTakashi
en-aut-sei=Makino
en-aut-mei=Takashi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

en-aut-name=MoriyaHisao
en-aut-sei=Moriya
en-aut-mei=Hisao
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=

affil-num=1
en-affil=Graduate School of Environmental and Life Sciences, Okayama University
kn-affil=

affil-num=2
en-affil=Graduate School of Environmental and Life Sciences, Okayama University
kn-affil=

affil-num=3
en-affil=National Institute for Basic Biology
kn-affil=

affil-num=4
en-affil=Graduate School of Life Sciences, Tohoku University
kn-affil=

affil-num=5
en-affil=Graduate School of Environmental and Life Sciences, Okayama University
kn-affil=
en-keyword=yeast
kn-keyword=yeast
en-keyword=fluorescent protein
kn-keyword=fluorescent protein
en-keyword=cytotoxicity
kn-keyword=cytotoxicity
en-keyword=protein burden
kn-keyword=protein burden
en-keyword=heat shock response
kn-keyword=heat shock response
en-keyword=morphology
kn-keyword=morphology
en-keyword=proteasome
kn-keyword=proteasome
END

start-ver=1.4
cd-journal=joma
no-vol=19
cd-vols=
no-issue=4
article-no=
start-page=e1010732
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2023
dt-pub=20230428
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Overexpression profiling reveals cellular requirements in the context of genetic backgrounds and environments
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Overexpression can help life adapt to stressful environments, making an examination of overexpressed genes valuable for understanding stress tolerance mechanisms. However, a systematic study of genes whose overexpression is functionally adaptive (GOFAs) under stress has yet to be conducted. We developed a new overexpression profiling method and systematically identified GOFAs in Saccharomyces cerevisiae under stress (heat, salt, and oxidative). Our results show that adaptive overexpression compensates for deficiencies and increases fitness under stress, like calcium under salt stress. We also investigated the impact of different genetic backgrounds on GOFAs, which varied among three S. cerevisiae strains reflecting differing calcium and potassium requirements for salt stress tolerance. Our study of a knockout collection also suggested that calcium prevents mitochondrial outbursts under salt stress. Mitochondria-enhancing GOFAs were only adaptive when adequate calcium was available and non-adaptive when calcium was deficient, supporting this idea. Our findings indicate that adaptive overexpression meets the cell's needs for maximizing the organism's adaptive capacity in the given environment and genetic context. Author summaryThe study aimed to investigate how overexpression of genes can aid organisms in adapting to stress. The researchers utilized a new method to identify genes in yeast that demonstrated functional adaptability when overexpressed under stress such as heat, salt, and oxidative stress. The results indicated that overexpressing specific genes, like calcium, during salt stress could counteract deficiencies and improve the organism's ability to withstand stress. The study also examined the effect of different genetic backgrounds on these genes and discovered that the impact differed among various yeast strains. Additionally, the study revealed that calcium could play a key role in adapting to salt stress by preventing mitochondrial outbursts. These findings suggest that overexpressing certain genes can help the organism maximize its adaptability to stress in a given environment and genetic context.
en-copyright=
kn-copyright=

en-aut-name=SaekiNozomu
en-aut-sei=Saeki
en-aut-mei=Nozomu
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=YamamotoChie
en-aut-sei=Yamamoto
en-aut-mei=Chie
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=EguchiYuichi
en-aut-sei=Eguchi
en-aut-mei=Yuichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=SekitoTakayuki
en-aut-sei=Sekito
en-aut-mei=Takayuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

en-aut-name=ShigenobuShuji
en-aut-sei=Shigenobu
en-aut-mei=Shuji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=

en-aut-name=YoshimuraMami
en-aut-sei=Yoshimura
en-aut-mei=Mami
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=

en-aut-name=YashirodaYoko
en-aut-sei=Yashiroda
en-aut-mei=Yoko
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=

en-aut-name=BooneCharles
en-aut-sei=Boone
en-aut-mei=Charles
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=

en-aut-name=MoriyaHisao
en-aut-sei=Moriya
en-aut-mei=Hisao
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=

affil-num=1
en-affil=Graduate School of Environmental and Life Science, Okayama University
kn-affil=

affil-num=2
en-affil=Graduate School of Environmental and Life Science, Okayama University
kn-affil=

affil-num=3
en-affil=Biomedical Business Center, RICOH Futures BU
kn-affil=

affil-num=4
en-affil=Graduate School of Agriculture, Ehime University
kn-affil=

affil-num=5
en-affil=National Institute for Basic Biology
kn-affil=

affil-num=6
en-affil=RIKEN Center for Sustainable Resource Science
kn-affil=

affil-num=7
en-affil=RIKEN Center for Sustainable Resource Science
kn-affil=

affil-num=8
en-affil=RIKEN Center for Sustainable Resource Science
kn-affil=

affil-num=9
en-affil=Faculty of Environmental, Life, Natural Science and Technology, Okayama University
kn-affil=
END

start-ver=1.4
cd-journal=joma
no-vol=677
cd-vols=
no-issue=
article-no=
start-page=1
end-page=5
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2023
dt-pub=20231015
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Demonstration of iodide-dependent UVA-triggered growth inhibition in Saccharomyces cerevisiae cells and identification of its suppressive molecules
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Upon white light illumination, the growth of the budding yeast Saccharomyces cerevisiae was extremely impaired only in the presence of iodide ions, but not fluoride, chloride and bromide ions. Action spectroscopy revealed that the maximum wavelength of the light is around at 373 nm, corresponding to the UVA region. Using a genetic approach, several genes, including OPY1, HEM1, and PAU11, were identified as suppressors of this growth inhibition. This iodide-dependent UVA-triggered growth inhibition method, along with its suppressive molecules, would be beneficial for understanding cell growth processes in eukaryotes and can be utilized for medium sterilization using UVA light.
en-copyright=
kn-copyright=

en-aut-name=OnoRyota
en-aut-sei=Ono
en-aut-mei=Ryota
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=SaekiNozomu
en-aut-sei=Saeki
en-aut-mei=Nozomu
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=KojimaKeiichi
en-aut-sei=Kojima
en-aut-mei=Keiichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=MoriyaHisao
en-aut-sei=Moriya
en-aut-mei=Hisao
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

en-aut-name=SudoYuki
en-aut-sei=Sudo
en-aut-mei=Yuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=

affil-num=1
en-affil=Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
kn-affil=

affil-num=2
en-affil=Research Core for Interdisciplinary Sciences, Okayama University
kn-affil=

affil-num=3
en-affil=Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
kn-affil=

affil-num=4
en-affil=Research Core for Interdisciplinary Sciences, Okayama University
kn-affil=

affil-num=5
en-affil=Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
kn-affil=
en-keyword=UVA
kn-keyword=UVA
en-keyword=Saccharomyces cerevisiae
kn-keyword=Saccharomyces cerevisiae
en-keyword=Iodide
kn-keyword=Iodide
en-keyword=Growth inhibition
kn-keyword=Growth inhibition
en-keyword=Suppressive molecule
kn-keyword=Suppressive molecule
END

start-ver=1.4
cd-journal=joma
no-vol=113
cd-vols=
no-issue=
article-no=
start-page=1
end-page=6
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2024
dt-pub=20240201
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=Evaluator of adaptability of S. cerevisiae to grape juice using the oversxpression profiling ADOPT method
kn-title=過剰発現プロファイリングADOPT法を用いたS.cerevisiaeのワイン醸造用ブドウ果汁への適応性評価
en-subtitle=
kn-subtitle=
en-abstract=筆者らは最近，過剰発現プロファイリングADOPT 法を開発した．ADOPT 法では，出芽酵母Saccharomyces cerevisiae ゲノムのほとんどの遺伝子をそれぞれ過剰発現する酵母株を混合・競合培養し，その過程で濃縮されてきた株が過剰発現している遺伝子を体系的に同定する．さらに同定された遺伝子をたよりに，S. cerevisiae の与えられた条件での増殖に必要だが欠落しているボトルネック因子を明らかにできる．これまでの研究では，実験室で人為的に構築したストレス環境でのボトルネックの同定を行ってきたが，本研究では産業上のボトルネックを明らかにできるかをワイン醸造用のブドウ果汁を例として検証した．通常のワイン醸造に用いられる亜硫酸添加ブドウ果汁でのADOPT 実験は，亜硫酸ポンプSSU1とその転写因子FZF1の過剰発現株が強く濃縮された．SSU1機能の強化はワイン用酵母の馴養でも起きることが知られていることから，産業上のボトルネックを探索する際にもADOPT が有効であることが示された．一方，亜硫酸添加のないブドウ果汁ではADOPT で強く濃縮された遺伝子は見られず，ブドウ果汁はS. cerevisiae の増殖にとってボトルネックの少ないバランスのとれた培地であることが示唆された．
kn-abstract=The authors have recently developed the overexpression profiling ADOPT method. In the ADOPT method, yeast strains overexpressing most of the genes in the budding yeast Saccharomyces cerevisiae genome are mixed and competitively cultured, and the genes overexpressed in the enriched strains are systematically identified. Furthermore, the identified genes can be used to identify bottleneck factors that are necessary but lacking for growth of S. cerevisiae under given conditions. In our previous studies, we have identified bottlenecks in artificially created stress environments in the laboratory, but in this study, we used grape juice for winemaking as an example to see if industrial bottlenecks can be identified. ADOPT experiments with sulfite-added grape juice used in conventional winemaking resulted in a strong enrichment of strains overexpressing the sulfite pump SSU1 and its transcription factor FZF1. Since enhancement of SSU1 function is known to occur in wine yeast acclimation, ADOPT was also shown to be useful in the search for industrial bottlenecks. On the other hand, no genes were strongly enriched by ADOPT in grape juice without sulfite addition, suggesting that grape juice is a balanced medium with few bottlenecks for S. cerevisiae growth.
en-copyright=
kn-copyright=

en-aut-name=MoriyaHisao
en-aut-sei=Moriya
en-aut-mei=Hisao
kn-aut-name=守屋央朗
kn-aut-sei=守屋
kn-aut-mei=央朗
aut-affil-num=1
ORCID=

en-aut-name=OnoChiyuki Kohata 
en-aut-sei=Ono
en-aut-mei=Chiyuki Kohata 
kn-aut-name=小野千由貴
kn-aut-sei=小野
kn-aut-mei=千由貴
aut-affil-num=2
ORCID=

affil-num=1
en-affil=Course of Agrochemical Bioscience
kn-affil=農芸化学コース

affil-num=2
en-affil=Course of Agrochemical Bioscience
kn-affil=農芸化学コース
en-keyword=yeast
kn-keyword=yeast
en-keyword=S. cerevisiae
kn-keyword=S. cerevisiae
en-keyword=overexpression
kn-keyword=overexpression
en-keyword=wine making
kn-keyword=wine making
END