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Article ; Online: Conditional Degrons for Controlling Protein Expression at the Protein Level.

Natsume, Toyoaki / Kanemaki, Masato T

2017 Volume 51, Page(s) 83–102

Abstract: The conditional depletion of a protein of interest (POI) is useful not only for loss-of-function studies, but also for the modulation of biological pathways. Technologies that work at the level of DNA, mRNA, and protein are available for temporal protein ...

Abstract	The conditional depletion of a protein of interest (POI) is useful not only for loss-of-function studies, but also for the modulation of biological pathways. Technologies that work at the level of DNA, mRNA, and protein are available for temporal protein depletion. Compared with technologies targeting the pretranslation steps, direct protein depletion (or protein knockdown approaches) is advantageous in terms of specificity, reversibility, and time required for depletion, which can be achieved by fusing a POI with a protein domain called a degron that induces rapid proteolysis of the fusion protein. Conditional degrons can be activated or inhibited by temperature, small molecules, light, or the expression of another protein. The conditional degron-based technologies currently available are described and discussed.
MeSH term(s)	Animals ; CRISPR-Cas Systems ; Gene Expression Regulation/drug effects ; Gene Expression Regulation/radiation effects ; Humans ; Integrases/genetics ; Integrases/metabolism ; Light ; Morpholinos/genetics ; Morpholinos/metabolism ; Plants/genetics ; Plants/metabolism ; Proteasome Endopeptidase Complex/metabolism ; Protein Biosynthesis/drug effects ; Protein Biosynthesis/radiation effects ; Protein Domains ; Protein Engineering ; Proteolysis/drug effects ; Proteolysis/radiation effects ; Proteomics/methods ; RNA, Small Interfering/genetics ; RNA, Small Interfering/metabolism ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Small Molecule Libraries/pharmacology
Chemical Substances	Morpholinos ; RNA, Small Interfering ; Recombinant Fusion Proteins ; Small Molecule Libraries ; Cre recombinase (EC 2.7.7.-) ; Integrases (EC 2.7.7.-) ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
Language	English
Publishing date	2017-11-24
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	207928-8
ISSN	1545-2948 ; 0066-4170 ; 0066-4197
ISSN (online)	1545-2948
ISSN	0066-4170 ; 0066-4197
DOI	10.1146/annurev-genet-120116-024656
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Article ; Online: Inducible Degradation of the Human SMC5/6 Complex Reveals an Essential Role Only during Interphase.

Venegas, Andrés Bueno / Natsume, Toyoaki / Kanemaki, Masato / Hickson, Ian D

Cell reports

2020 Volume 31, Issue 3, Page(s) 107533

Abstract: The cohesin- and condensin-related SMC5/6 complex has largely been studied in the context of DNA repair. Nevertheless, SMC5/6 has an undefined essential function even in the absence of cellular stress. Through the use of an auxin-inducible degradation ... ...

Abstract	The cohesin- and condensin-related SMC5/6 complex has largely been studied in the context of DNA repair. Nevertheless, SMC5/6 has an undefined essential function even in the absence of cellular stress. Through the use of an auxin-inducible degradation system for rapidly depleting subunits of the SMC5/6 complex, we show that SMC5/6 is essential for viability in cancer-derived and normal human cells. Impairment of SMC5/6 function is associated with spontaneous induction of DNA damage, p53 activation, cell-cycle arrest, and senescence, as well as an increased frequency of various mitotic chromosome segregation abnormalities. However, we show that this chromosome missegregation is apparent only when SMC5/6 function is impaired during the preceding S and G2 phases. In contrast, degradation of SMC5/6 immediately prior to mitotic entry has little or no impact on the fidelity of chromosome segregation, highlighting the importance of the complex during interphase in order to ensure faithful sister chromatid disjunction.
MeSH term(s)	Cell Cycle Proteins/genetics ; Cell Cycle Proteins/metabolism ; Cell Line ; Cell Proliferation/physiology ; Cell Survival/physiology ; Chromosomal Proteins, Non-Histone/genetics ; Chromosomal Proteins, Non-Histone/metabolism ; Chromosome Segregation ; Cyclin-Dependent Kinase Inhibitor p21/genetics ; Cyclin-Dependent Kinase Inhibitor p21/metabolism ; DNA Damage ; Genomic Instability ; HCT116 Cells ; Humans ; Interphase/physiology ; Tumor Suppressor Protein p53/genetics ; Tumor Suppressor Protein p53/metabolism
Chemical Substances	CDKN1A protein, human ; Cell Cycle Proteins ; Chromosomal Proteins, Non-Histone ; Cyclin-Dependent Kinase Inhibitor p21 ; SMC5 protein, human ; SMC6 protein, human ; TP53 protein, human ; Tumor Suppressor Protein p53
Language	English
Publishing date	2020-04-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2020.107533
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Article ; Online: AMBRA1 p.Gln30Arg Mutation, Identified in a Cowden Syndrome Family, Exhibits Hyperproliferative Potential in hTERT-RPE1 Cells.

Revathidevi, Sundaramoorthy / Hosomichi, Kazuyoshi / Natsume, Toyoaki / Nakaoka, Hirofumi / Fujito, Naoko T / Akatsuka, Hisako / Sato, Takehito / Munirajan, Arasambattu Kannan / Inoue, Ituro

International journal of molecular sciences

2022 Volume 23, Issue 19

Abstract: Cowden syndrome (CS) is a rare autosomal dominant disorder associated with multiple hamartomatous and neoplastic lesions in various organs. Most CS patients have been found to have germline mutations in ... ...

Abstract	Cowden syndrome (CS) is a rare autosomal dominant disorder associated with multiple hamartomatous and neoplastic lesions in various organs. Most CS patients have been found to have germline mutations in the
MeSH term(s)	Animals ; Beclin-1/genetics ; Germ-Line Mutation ; Hamartoma Syndrome, Multiple/complications ; Hamartoma Syndrome, Multiple/genetics ; Hamartoma Syndrome, Multiple/pathology ; Mutation ; PTEN Phosphohydrolase/genetics ; RNA-Directed DNA Polymerase/genetics ; Tensins/genetics ; Zebrafish/genetics
Chemical Substances	Beclin-1 ; Tensins ; RNA-Directed DNA Polymerase (EC 2.7.7.49) ; PTEN Phosphohydrolase (EC 3.1.3.67)
Language	English
Publishing date	2022-09-22
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms231911124
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Article ; Online: Chromosome oscillation promotes Aurora A-dependent Hec1 phosphorylation and mitotic fidelity.

Iemura, Kenji / Natsume, Toyoaki / Maehara, Kayoko / Kanemaki, Masato T / Tanaka, Kozo

The Journal of cell biology

2021 Volume 220, Issue 7

Abstract: Most cancer cells show chromosomal instability, a condition where chromosome missegregation occurs frequently. We found that chromosome oscillation, an iterative chromosome motion during metaphase, is attenuated in cancer cell lines. We also found that ... ...

Abstract	Most cancer cells show chromosomal instability, a condition where chromosome missegregation occurs frequently. We found that chromosome oscillation, an iterative chromosome motion during metaphase, is attenuated in cancer cell lines. We also found that metaphase phosphorylation of Hec1 at serine 55, which is mainly dependent on Aurora A on the spindle, is reduced in cancer cell lines. The Aurora A-dependent Hec1-S55 phosphorylation level was regulated by the chromosome oscillation amplitude and vice versa: Hec1-S55 and -S69 phosphorylation by Aurora A is required for efficient chromosome oscillation. Furthermore, enhancement of chromosome oscillation reduced the number of erroneous kinetochore-microtubule attachments and chromosome missegregation, whereas inhibition of Aurora A during metaphase increased such errors. We propose that Aurora A-mediated metaphase Hec1-S55 phosphorylation through chromosome oscillation, together with Hec1-S69 phosphorylation, ensures mitotic fidelity by eliminating erroneous kinetochore-microtubule attachments. Attenuated chromosome oscillation and the resulting reduced Hec1-S55 phosphorylation may be a cause of CIN in cancer cell lines.
MeSH term(s)	Aurora Kinase A/genetics ; Chromosome Segregation/genetics ; Chromosomes/genetics ; Cytoskeletal Proteins/genetics ; HeLa Cells ; Humans ; Kinetochores ; Microtubules/genetics ; Mitosis/genetics ; Phosphorylation/genetics ; Spindle Apparatus/genetics
Chemical Substances	Cytoskeletal Proteins ; NDC80 protein, human ; AURKA protein, human (EC 2.7.11.1) ; Aurora Kinase A (EC 2.7.11.1)
Language	English
Publishing date	2021-05-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218154-x
ISSN	1540-8140 ; 0021-9525
ISSN (online)	1540-8140
ISSN	0021-9525
DOI	10.1083/jcb.202006116
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Article ; Online: Inducible Degradation of the Human SMC5/6 Complex Reveals an Essential Role Only during Interphase

Andrés Bueno Venegas / Toyoaki Natsume / Masato Kanemaki / Ian D. Hickson

Cell Reports, Vol 31, Iss 3, Pp - (2020)

2020

Abstract: Summary: The cohesin- and condensin-related SMC5/6 complex has largely been studied in the context of DNA repair. Nevertheless, SMC5/6 has an undefined essential function even in the absence of cellular stress. Through the use of an auxin-inducible ... ...

Abstract	Summary: The cohesin- and condensin-related SMC5/6 complex has largely been studied in the context of DNA repair. Nevertheless, SMC5/6 has an undefined essential function even in the absence of cellular stress. Through the use of an auxin-inducible degradation system for rapidly depleting subunits of the SMC5/6 complex, we show that SMC5/6 is essential for viability in cancer-derived and normal human cells. Impairment of SMC5/6 function is associated with spontaneous induction of DNA damage, p53 activation, cell-cycle arrest, and senescence, as well as an increased frequency of various mitotic chromosome segregation abnormalities. However, we show that this chromosome missegregation is apparent only when SMC5/6 function is impaired during the preceding S and G2 phases. In contrast, degradation of SMC5/6 immediately prior to mitotic entry has little or no impact on the fidelity of chromosome segregation, highlighting the importance of the complex during interphase in order to ensure faithful sister chromatid disjunction. : Venegas et al. employ an auxin-inducible degron system for different subunits of the SMC5/6 complex to interrogate the short- and long-term effects of SMC5/6 impairment in human cells. Degradation of SMC5/6’s subunits at different cell cycle stages places the essential role of the complex during S phase.
Keywords	Biology (General) ; QH301-705.5
Subject code	571
Language	English
Publishing date	2020-04-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
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Article ; Online: TRAIP resolves DNA replication-transcription conflicts during the S-phase of unperturbed cells.

Scaramuzza, Shaun / Jones, Rebecca M / Sadurni, Martina Muste / Reynolds-Winczura, Alicja / Poovathumkadavil, Divyasree / Farrell, Abigail / Natsume, Toyoaki / Rojas, Patricia / Cuesta, Cyntia Fernandez / Kanemaki, Masato T / Saponaro, Marco / Gambus, Agnieszka

Nature communications

2023 Volume 14, Issue 1, Page(s) 5071

Abstract: Cell division is the basis for the propagation of life and requires accurate duplication of all genetic information. DNA damage created during replication (replication stress) is a major cause of cancer, premature aging and a spectrum of other human ... ...

Abstract	Cell division is the basis for the propagation of life and requires accurate duplication of all genetic information. DNA damage created during replication (replication stress) is a major cause of cancer, premature aging and a spectrum of other human disorders. Over the years, TRAIP E3 ubiquitin ligase has been shown to play a role in various cellular processes that govern genome integrity and faultless segregation. TRAIP is essential for cell viability, and mutations in TRAIP ubiquitin ligase activity lead to primordial dwarfism in patients. Here, we have determined the mechanism of inhibition of cell proliferation in TRAIP-depleted cells. We have taken advantage of the auxin induced degron system to rapidly degrade TRAIP within cells and to dissect the importance of various functions of TRAIP in different stages of the cell cycle. We conclude that upon rapid TRAIP degradation, specifically in S-phase, cells cease to proliferate, arrest in G2 stage of the cell cycle and undergo senescence. Our findings reveal that TRAIP works in S-phase to prevent DNA damage at transcription start sites, caused by replication-transcription conflicts.
MeSH term(s)	Humans ; S Phase/genetics ; Cell Division/genetics ; Cell Proliferation/genetics ; Cell Cycle ; Cell Survival ; Ubiquitin-Protein Ligases/genetics
Chemical Substances	TRAIP protein, human (EC 2.3.2.27) ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
Language	English
Publishing date	2023-08-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-40695-y
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Article ; Online: Generation of conditional auxin-inducible degron (AID) cells and tight control of degron-fused proteins using the degradation inhibitor auxinole.

Yesbolatova, Aisha / Natsume, Toyoaki / Hayashi, Ken-Ichiro / Kanemaki, Masato T

Methods (San Diego, Calif.)

2019 Volume 164-165, Page(s) 73–80

Abstract: Controlling protein expression using a degron is advantageous because the protein of interest can be rapidly depleted in a reversible manner. We pioneered the development of the auxin-inducible degron (AID) technology by transplanting a plant-specific ... ...

Abstract	Controlling protein expression using a degron is advantageous because the protein of interest can be rapidly depleted in a reversible manner. We pioneered the development of the auxin-inducible degron (AID) technology by transplanting a plant-specific degradation pathway to non-plant cells. In human cells expressing an E3 ligase component, OsTIR1, it is possible to degrade a degron-fused protein with a half-life of 15-45 min in the presence of the phytohormone auxin. We reported previously the generation of human HCT116 mutants in which the C terminus of endogenous proteins was fused with the degron by CRISPR-Cas9-based knock-in. Here, we show new plasmids for N-terminal tagging and describe a detailed protocol for the generation of AID mutants of human HCT116 and DLD1 cells. Moreover, we report the use of an OsTIR1 inhibitor, auxinole, to suppress leaky degradation of degron-fused proteins. The addition of auxinole is also useful for rapid re-expression after depletion of degron-fused proteins. These improvements enhance the utility of AID technology for studying protein function in living human cells.
MeSH term(s)	CRISPR-Cas Systems/genetics ; Cell Culture Techniques/methods ; Genetic Vectors/genetics ; HCT116 Cells ; Half-Life ; Humans ; Indoleacetic Acids/pharmacology ; Luminescent Proteins/genetics ; Luminescent Proteins/metabolism ; Plant Proteins/antagonists & inhibitors ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Plasmids/genetics ; Proteolysis/drug effects ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/metabolism ; Transfection/methods ; Ubiquitin-Protein Ligases/antagonists & inhibitors ; Ubiquitin-Protein Ligases/genetics ; Ubiquitin-Protein Ligases/metabolism
Chemical Substances	Indoleacetic Acids ; Luminescent Proteins ; Plant Proteins ; Recombinant Fusion Proteins ; alpha-(2,4-dimethylphenylethyl-2-oxo)indole-3-acetic acid ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
Language	English
Publishing date	2019-04-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1066584-5
ISSN	1095-9130 ; 1046-2023
ISSN (online)	1095-9130
ISSN	1046-2023
DOI	10.1016/j.ymeth.2019.04.010
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Article ; Online: Inflammation Flare and Radiation Necrosis Around a Stereotactic Radiotherapy-Pretreated Brain Metastasis Site After Nivolumab Treatment.

Furuta, Hiromi / Yoshida, Tatsuya / Natsume, Atsushi / Hida, Toyoaki / Yatabe, Yasushi

Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer

2018 Volume 13, Issue 12, Page(s) 1975–1978

MeSH term(s)	Antineoplastic Agents, Immunological/adverse effects ; Brain Neoplasms/drug therapy ; Brain Neoplasms/secondary ; Brain Neoplasms/surgery ; Humans ; Inflammation/etiology ; Inflammation/pathology ; Lung Neoplasms/drug therapy ; Lung Neoplasms/pathology ; Lung Neoplasms/surgery ; Male ; Middle Aged ; Necrosis ; Nivolumab/adverse effects ; Prognosis ; Radiation Injuries/etiology ; Radiation Injuries/pathology ; Radiosurgery/adverse effects
Chemical Substances	Antineoplastic Agents, Immunological ; Nivolumab (31YO63LBSN)
Language	English
Publishing date	2018-07-12
Publishing country	United States
Document type	Case Reports ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2432037-7
ISSN	1556-1380 ; 1556-0864
ISSN (online)	1556-1380
ISSN	1556-0864
DOI	10.1016/j.jtho.2018.07.005
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Zs.A 6664: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular ab Jg. 2022: Lesesaal (EG)
Zs.MO 652: Show issues

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Article ; Online: Global landscape of replicative DNA polymerase usage in the human genome

Eri Koyanagi / Yoko Kakimoto / Tamiko Minamisawa / Fumiya Yoshifuji / Toyoaki Natsume / Atsushi Higashitani / Tomoo Ogi / Antony M. Carr / Masato T. Kanemaki / Yasukazu Daigaku

Nature Communications, Vol 13, Iss 1, Pp 1-

2022 Volume 18

Abstract: Profiling of human DNA polymerase Polε and Polα demonstrates their roles in leading and lagging strand DNA synthesis, and their independent measures allowed accurate predictions of replication dynamics and effects of transcription. ...

Abstract	Profiling of human DNA polymerase Polε and Polα demonstrates their roles in leading and lagging strand DNA synthesis, and their independent measures allowed accurate predictions of replication dynamics and effects of transcription.
Keywords	Science ; Q
Language	English
Publishing date	2022-11-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
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Article ; Online: Dynein-Dynactin-NuMA clusters generate cortical spindle-pulling forces as a multi-arm ensemble.

Okumura, Masako / Natsume, Toyoaki / Kanemaki, Masato T / Kiyomitsu, Tomomi

eLife

2018 Volume 7

Abstract: To position the mitotic spindle within the cell, dynamic plus ends of astral microtubules are pulled by membrane-associated cortical force-generating machinery. However, in contrast to the chromosome-bound kinetochore structure, how the diffusion-prone ... ...

Abstract	To position the mitotic spindle within the cell, dynamic plus ends of astral microtubules are pulled by membrane-associated cortical force-generating machinery. However, in contrast to the chromosome-bound kinetochore structure, how the diffusion-prone cortical machinery is organized to generate large spindle-pulling forces remains poorly understood. Here, we develop a light-induced reconstitution system in human cells. We find that induced cortical targeting of NuMA, but not dynein, is sufficient for spindle pulling. This spindle-pulling activity requires dynein-dynactin recruitment by NuMA's N-terminal long arm, dynein-based astral microtubule gliding, and NuMA's direct microtubule-binding activities. Importantly, we demonstrate that cortical NuMA assembles specialized focal structures that cluster multiple force-generating modules to generate cooperative spindle-pulling forces. This clustering activity of NuMA is required for spindle positioning, but not for spindle-pole focusing. We propose that cortical Dynein-Dynactin-NuMA (DDN) clusters act as the core force-generating machinery that organizes a multi-arm ensemble reminiscent of the kinetochore.
MeSH term(s)	Amino Acid Motifs ; Amino Acid Sequence ; Antigens, Nuclear/chemistry ; Antigens, Nuclear/metabolism ; Cell Line ; Dynactin Complex/metabolism ; Dyneins/metabolism ; Humans ; Indoleacetic Acids/pharmacology ; Light ; Microtubules/drug effects ; Microtubules/metabolism ; Mutation/genetics ; Nuclear Matrix-Associated Proteins/chemistry ; Nuclear Matrix-Associated Proteins/metabolism ; Optogenetics ; Paclitaxel/pharmacology ; Phenotype ; Protein Domains ; Spindle Apparatus/metabolism
Chemical Substances	Antigens, Nuclear ; Dynactin Complex ; Indoleacetic Acids ; NUMA1 protein, human ; Nuclear Matrix-Associated Proteins ; Dyneins (EC 3.6.4.2) ; Paclitaxel (P88XT4IS4D)
Language	English
Publishing date	2018-05-31
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.36559
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