​Nara Institute of Science and Technology
Divison of Biological Science

Original Research papers

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56. Hata T, Ishiwata-Kimata Y, Kimata Y

Self-association status-dependent inactivation of the endoplasmic reticulum stress sensor Ire1 by C-terminal tagging with artificial peptides

Biosci. Biotechnol. Biochem. in press

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55. Hata T, Ishiwata-Kimata Y, Kimata Y

Induction of the unfolded protein response at high temperature in Saccharomyces cerevisiae

Int. J. Mol. Sci. Vol.23, 1669, 2022

https://pubmed.ncbi.nlm.nih.gov/35163590/
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54. Ishiwata-Kimata Y, Le QG, Kimata Y

Induction and aggravation of the endoplasmic-reticulum stress by membrane-lipid metabolic intermediate phosphatidyl-N-monomethylethanolamine

Front. Cell Dev. Biol. Vol.9, 743018, 2022

https://pubmed.ncbi.nlm.nih.gov/35071223/

 

53. Phuong TH, Ishiwata-Kimata Y, Nishi Y, Oguchi N, Takagi H, Kimata Y

"Aeration mitigates endoplasmic reticulum stress in Saccharomyces cerevisiae even without mitochondrial respiration."

Microb. Cell Vol.8, 77-86, 2021

https://pubmed.ncbi.nlm.nih.gov/33816593/

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52. Le QG, Ishiwata-Kimata Y, Phuong TH, Fukunaka S, Kohno K, Kimata Y

"The ADP-binding kinase region of Ire1 directly contributes to its responsiveness to endoplasmic reticulum stress."

Sci. Rep. Vol.11 4506, 2021

https://pubmed.ncbi.nlm.nih.gov/33627709/

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51. Fauzee YNBM, Taniguchi N, Ishiwata-Kimata Y, Takagi H, Kimata Y

"The unfolded protein response in Pichia pastoris without external stressing stimuli."

FEMS Yeast Res. Vol.20 foaa053, 2020

https://pubmed.ncbi.nlm.nih.gov/33775971/

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50. Tran DM, Ishiwata-Kimata Y, Mai TC, Kubo M, Kimata Y.

“The unfolded protein response alongside the diauxic shift of yeast cells and its involvement in mitochondria enlargement.”

Sci. Rep. Vol. 9 12780, 2019

https://www.ncbi.nlm.nih.gov/pubmed/31484935

 

49. Mai TC, Ishiwata-Kimata Y, Le QG, Kido H, Kimata Y.

“Dispersion of Endoplasmic Reticulum-associated Compartments by 4-phenyl Butyric Acid in Yeast Cells.”

Cell. Struct. Funct. Vol. 44, 173-182, 2019

https://www.ncbi.nlm.nih.gov/pubmed/31619600

 

48. Nguyen PTM, Ishiwata-Kimata Y, Kimata Y.

“Monitoring ADP/ATP ratio in yeast cells using the fluorescent-protein reporter PercevalHR.”

Biosci. Biotechnol. Biochem. Vol. 83, 824-828, 2019

https://www.ncbi.nlm.nih.gov/pubmed/30704350

 

47. Tran DM, Takagi H, Kimata Y.

“Categorization of endoplasmic reticulum stress as accumulation of unfolded proteins or membrane lipid aberrancy using yeast Ire1 mutants.”

Biosci. Biotechnol. Biochem. Vol. 83, 326-329, 2019

https://www.ncbi.nlm.nih.gov/pubmed/30319071

 

46. Mai TC, Munakata T, Tran DM, Takagi H, Kimata Y.

“A chimeric mutant analysis in yeast cells suggests BiP independent regulation of the mammalian endoplasmic reticulum-stress sensor IRE1α.”

Biosci. Biotechnol. Biochem. Vol. 82, 1527-1530, 2018

https://www.ncbi.nlm.nih.gov/pubmed/29806786

 

45. Mai CT, Le QG, Ishiwata-Kimata Y, Takagi H, Kohno K, Kimata Y.

“4-Phenylbutyrate suppresses the unfolded protein response without restoring protein folding in Saccharomyces cerevisiae.”

FEMS Yeast Res. Vol. 18, foy016, 2018

https://www.ncbi.nlm.nih.gov/pubmed/29452364

 

44. Itooka K, Takahashi K, Kimata Y, Izawa S.

“Cold atmospheric pressure plasma causes protein denaturation and endoplasmic reticulum stress in Saccharomyces cerevisiae.”

Appl. Microbiol. Biotechnol. Vol. 102, 2279-2288, 2018

https://www.ncbi.nlm.nih.gov/pubmed/29356871

 

43. Kawazoe N, Kimata Y, Izawa S.

“Acetic Acid Causes Endoplasmic Reticulum Stress and Induces the Unfolded Protein Response in Saccharomyces cerevisiae.”

Front. Microbiol. Vol. 8, 1192, 2017

https://www.ncbi.nlm.nih.gov/pubmed/28702017

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42. Le QG, Ishiwata-Kimata Y, Kohno K, Kimata Y.

“Cadmium impairs protein folding in the endoplasmic reticulum and induces the unfolded protein response.”

FEMS Yeast Res. Vol.16, fow049, 2016

https://www.ncbi.nlm.nih.gov/pubmed/27298227

 

41. Mathuranyanon R, Tsukamoto T, Takeuchi A, Ishiwata-Kimata Y, Tsuchiya Y, Kohno K, Kimata Y.

“Tight regulation of the unfolded protein sensor Ire1 by its intramolecularly antagonizing subdomain.”

J. Cell Sci. Vol.128, 1762-172, 2015

https://www.ncbi.nlm.nih.gov/pubmed/25770101

 

40. Mochizuki T, Kimata Y, Uemura S, Abe F.

“Retention of chimeric Tat2-Gap1 permease in the endoplasmic reticulum induces unfolded protein response in Saccharomyces cerevisiae.”

FEMS Yeast Res. Vol.15, fov044, 2015

https://www.ncbi.nlm.nih.gov/pubmed/26071436

 

39. Miyagawa D, Ishiwata-Kimata Y, Kohno K, Kimata Y

“Ethanol stress impairs protein folding in the endoplasmic reticulum and activates Ire1 in Saccharomyces cerevisiae.”

Biosci. Biotechnol. Biochem. Vol.78,1389-1391, 2014

https://www.ncbi.nlm.nih.gov/pubmed/25130742

 

38. Ishiwata-Kimata Y, Yamamoto YH, Takizawa K, Kohno K, Kimata Y

F-actin and a type-II myosin are required for efficient clustering of the ER stress sensor Ire1.

Cell Struct. Funct. Vol.38, 135-143. 2013

https://www.ncbi.nlm.nih.gov/pubmed/23666407

 

37. Ishiwata-Kimata Y, Promlek T, Kohno K, Kimata Y

“BiP-bound and nonclustered mode of Ire1 evokes a weak but sustained unfolded protein response.”

Genes Cells Vol.18, 288-301, 2013

https://www.ncbi.nlm.nih.gov/pubmed/23387983

 

36. Nguyen TSL, Kohno K, Kimata Y

“Zinc depletion activates the endoplasmic reticulum-stress sensor Ire1 via pleiotropic mechanisms.”

Biosci. Biotechnol. Biochem. Vol. 77, 1337-1339, 2013

https://www.ncbi.nlm.nih.gov/pubmed/23748779

 

35. Promlek T, Ishiwata-Kimata Y, Shido M, Sakuramoto M, Kohno K, Kimata Y

“Membrane aberrancy and unfolded aroteins activate the endoplasmic reticulum-stress sensor Ire1 by different manners.”

Mol. Biol. Cell Vol.22, 3520-3532, 2011

https://www.ncbi.nlm.nih.gov/pubmed/21775630

 

34. Yanagitani K, Kimata Y, Kadokura H, Kohno K

“Translational pausing ensures membrane targeting and cytoplasmic splicing of XBP1u mRNA.”

Science Vol.331, 586-589, 2011

https://www.ncbi.nlm.nih.gov/pubmed/21233347

 

33. Yamamoto YH, Kimura T, Momohara S, Takeuchi M, Tani T, Kimata Y, Kadokura H, Kohno K

“A novel ER J-protein DNAJB12 accelerates ER-associated degradation of membrane proteins including CFTR.”

Cell Struct. Funct. Vol.35, 107-116, 2010

https://www.ncbi.nlm.nih.gov/pubmed/21150129

 

32. Yanagitani K, Imagawa Y, Iwawaki T, Hosoda A, Saito M, Kimata Y, Kohno K

“Cotranslational targeting of XBP1 protein to the membrane promotes cytoplasmic splicing of its own mRNA.”

Mol. Cell Vol.34, 191-200, 2009

https://www.ncbi.nlm.nih.gov/pubmed/19394296

 

31. Oikawa D, Kimata Y, Kohno K, Iwawaki T

“Activation of mammalian IRE1alpha upon ER stress depends on dissociation of BiP rather than on direct interaction with unfolded proteins.”

Exp. Cell Res. Vol. 315, 2496-2504. 2009

https://www.ncbi.nlm.nih.gov/pubmed/19538957

 

30. Takeuchi M, Kimata Y, Kohno K

“Saccharomyces cerevisiae Rot1 Is an Essential Molecular Chaperone in the Endoplasmic Reticulum.”

Mol. Biol. Cell Vol.19, 3514-3525, 2008

https://www.ncbi.nlm.nih.gov/pubmed/18508919

 

29. Kimata Y, Ishiwata-Kimata Y, Ito T, Hirata A, Suzuki T, Oikawa D, Takeuchi M, Kohno K

“Two regulatory steps of ER-stress sensor Ire1 involving its cluster formation and interaction with unfolded proteins.”

J. Cell Biol. Vol.179, 75-86, 2007

https://www.ncbi.nlm.nih.gov/pubmed/17923530

 

28. Kimura Y, Saito M, Kimata Y, Kohno K

“Transgenic mice expressing a fully nontoxic diphtheria toxin mutant, not CRM197 mutant, acquire immune tolerance against diphtheria toxin.”

J. Biochem. Vol.142, 105-112, 2007

https://www.ncbi.nlm.nih.gov/pubmed/17522091

 

27. Oikawa D, Kimata Y, Kohno K

“Self-association and BiP dissociation are not sufficient for activation of the ER stress sensor Ire1.”

J. Cell Sci. Vol.120, 1681-1688, 2007

https://www.ncbi.nlm.nih.gov/pubmed/17452628

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26. Takeuchi M, Kimata Y, Hirata A, Oka M, Kohno K

“Saccharomyces cerevisiae Rot1p Is an ER-Localized Membrane Protein That May Function with BiP/Kar2p in Protein Folding.”

J. Biochem. Vol.139, 597-605, 2006

https://www.ncbi.nlm.nih.gov/pubmed/16567426

 

25. Kimata Y, Ishiwata-Kimata Y, Yamada S, Kohno K

“Yeast unfolded protein response pathway regulates expression of genes for anti-oxidative stress and for cell surface proteins.”

Genes Cells. Vol.11, 59-69, 2006

https://www.ncbi.nlm.nih.gov/pubmed/16371132

 

24. Oikawa D, Kimata Y, Takeuchi M, Kohno K

“An essential dimer-forming subregion of the endoplasmic reticulum stress sensor Ire1.”

Biochem J. Vol.391, 135-142, 2005

https://www.ncbi.nlm.nih.gov/pubmed/15954865

 

23. Kimata Y, Oikawa D, Shimizu Y, Ishiwata-Kimata Y, Kohno, K

“A role for BiP as an adjustor for the endoplasmic reticulum stress-sensing protein Ire1.”

J. Cell Biol. Vol.167, 445-456, 2004

https://www.ncbi.nlm.nih.gov/pubmed/15520230

 

22. Kimata Y, Kimata YI, Shimizu Y, Abe H, Farcasanu IC, Takeuchi M, Rose MD, Kohno K

“Genetic evidence for a role of BiP/Kar2 that regulates Ire1 in response to accumulation of unfolded proteins.”

Mol. Biol. Cell Vol.14, 2559-2569, 2003

https://www.ncbi.nlm.nih.gov/pubmed/12808051

 

21. Ohdate H, Lim CR, Kokubo T, Matsubara K, Kimata Y, Kohno K

“Impairment of the DNA binding activity of the TATA-binding protein renders the transcriptional function of Rvb2p/Tih2p, the yeast RuvB-like protein, essential for cell growth.”

J. Biol. Chem. Vol.278, 14647-14656, 2003

https://www.ncbi.nlm.nih.gov/pubmed/12576485

 

20. Hosoda A, Kimata Y, Tsuru A, Kohno K

“JPDI, a novel endoplasmic reticulum-resident protein containing both a BiP-interacting J-domain and thioredoxin-like motifs.”

J. Biol. Chem. Vol.278, 2669-2676 2003

https://www.ncbi.nlm.nih.gov/pubmed/12446677

 

19. Fujioka Y, Kimata Y, Nomaguchi K, Watanabe K, Kohno K

“Identification of a novel non-structural maintenance of chromosomes (SMC) component of the SMC5/SMC6 complex involved in DNA repair.”

J. Biol. Chem. Vol.277, 21585-21591, 2002

https://www.ncbi.nlm.nih.gov/pubmed/11927594

 

18. Okushima Y, Koizumi N, Yamaguchi Y, Kimata Y, Kohno K, Sano H

“Isolation and Characterization of a Putative Transducer of Endoplasmic Reticulum Stress in Oryza sativa.”

Plant Cell Physiol. Vol.43, 532-539, 2002

https://www.ncbi.nlm.nih.gov/pubmed/12040100

 

17. Koizumi N, Martinez I, Kimata Y, Kohno K, Sano H, Chrispeels MJ

“Molecular characterization of two Arabidopsis Ire1 homologs, endoplasmic reticulum located transmembrane protein kinases.”

Plant Physiol. Vol.127, 949-962, 2001

https://www.ncbi.nlm.nih.gov/pubmed/11706177

 

16. Saito M, Iwawaki T, Taya C, Yonekawa H, Noda M, Inui Y, Mekada E, Kimata Y, Tsuru A, Kohno K

“Diphtheria toxin receptor-mediated conditional and targeted cell ablation in transgenic mice.”

Nature Biotechnol. Vol.19, 746-750, 2001

https://www.ncbi.nlm.nih.gov/pubmed/11479567

 

15. Iwawaki T, Hosoda A, Okuda T, Kamigori Y, Nomura-Furuwatari C, Kimata Y, Tsuru A, Kohno K

“Translation control by ER transmembrane kinase/ribonuclease IRE1 under ER stress.”

Nature Cell Biol. Vol.3, 158-164, 2001

https://www.ncbi.nlm.nih.gov/pubmed/11175748

 

14. Kimata Y, Ooboki K, Nomura-Furuwatari C, Hosoda A, Tsuru A, Kohno K

“Identification of a novel mammalian endoplasmic reticulum-resident KDEL protein using an EST database motif search.”

Gene Vol.261, 321-327, 2000

https://www.ncbi.nlm.nih.gov/pubmed/11167020

 

13. Yoshizawa F, Miura Y, Tsurumaru K, Kimata Y, Yagasaki K, Funabiki R

“Elongation factor 2 in the liver and skeletal muscle of mice is decreased by starvation.”

Biosci. Biotechnol. Biochem. Vol.64, 2482-2485, 2000

https://www.ncbi.nlm.nih.gov/pubmed/11193422

 

12. Okamura K, Kimata Y, Higashio H, Tsuru A, Kohno K

“Dissociation of Kar2p/BiP from an endoplasmic reticulum sensory molecule, Ire1p, triggers unfolded protein response in yeast.”

Biochem. Biophys. Res. Commun. Vol.279, 445-450, 2000

https://www.ncbi.nlm.nih.gov/pubmed/11118306

 

11. Lim CR, Kimata Y, Ohdate H, Kokubo T, Kikuchi N, Horigome T, Kohno K

“The Saccharomyces cerevisiae RuvB-like protein, Tih2p is required for cell cycle progression.”

J. Biol. Chem. Vol.275, 22409-22417, 2000

https://www.ncbi.nlm.nih.gov/pubmed/10787406

 

10. Higashio H, Kimata Y, Kiriyama T, Hirata A, Kohno K

“Sfb2p, a yeast protein related to Sec24p, can function as a constituent of COPII coats required for vesicle budding from the endoplasmic reticulum.”

J. Biol. Chem. Vol.275, 17900-17908, 2000

https://www.ncbi.nlm.nih.gov/pubmed/10749860

 

9. Kimata Y, Higashio H, Kohno K

“Impaired proteasome function rescues thermosensitivity of yeast cells lacking the coatomer subunit epsilon-COP.”

J. Biol. Chem. Vol.275, 10655-10660, 2000

https://www.ncbi.nlm.nih.gov/pubmed/10744762

 

8. Kimata Y, Lim CR, Kiriyama T, Nara A, Hirata A, Kohno K

“Mutation of the yeast epsilon-COP gene ANU2 causes abnormal nuclear morphology and defects in intracellular vesicular transport.”

Cell Struct. Funct. Vol.24, 197-208, 1999

https://www.ncbi.nlm.nih.gov/pubmed/10532354

 

7. Oka M, Nakai M, Endo T, Lim CR, Kimata Y, Kohno K

“Loss of Hsp70-Hsp40 chaperone activity causes abnormal nuclear distribution and aberrant microtubule formation in M-phase of Saccharomyces cerevisiae.”

J. Biol. Chem. Vol.273, 29727-29737, 1998

https://www.ncbi.nlm.nih.gov/pubmed/9792686

 

6. Kimata Y, Iwaki M, Lim CR, Kohno K

“A novel mutation which enhances the fluorescence of green fluorescent protein at high temperatures.”

Biochem. Biophys. Res. Commun. Vol.232, 69-73, 1997

https://www.ncbi.nlm.nih.gov/pubmed/9125154

 

5. Oka M, Kimata Y, Mori K, Kohno K

“Saccharomyces cerevisiae KAR2 (BiP) gene expression is induced by loss of cytosolic HSP70/Ssa1p through a heat shock element-mediated pathway.”

J. Biochem. Vol.121, 578-584, 1997

https://www.ncbi.nlm.nih.gov/pubmed/9133628

 

4. Lim CR, Kimata Y, Oka M, Nomaguchi K, Kohno K

“Thermosensitivity of green fluorescent protein fluorescence utilized to reveal novel nuclear-like compartments in a mutant nucleoporin NSP1.” 

J. Biochem. Vol.118, 13-17 1995

https://www.ncbi.nlm.nih.gov/pubmed/8537302

 

3. Kimata Y, Kohno K

“Elongation factor 2 mutants deficient in diphthamide formation show temperature-sensitive cell growth.”

J. Biol. Chem. Vol.269, 13497-134501 1994

https://www.ncbi.nlm.nih.gov/pubmed/8175783

 

2. Kimata Y, Harashima S, Kohno K

“Expression of non-ADP-ribosylatable, diphtheria toxin-resistant elongation factor 2 in Saccharomyces cerevisiae.”

Biochem. Biophys. Res. Commun. Vol.191, 1145-1151 1993

https://www.ncbi.nlm.nih.gov/pubmed/8466491

 

1. Masui M, Tsuchida K, Kimata Y, Ozaki S

“Epoxidation catalyzed by manganese(III) tetraphenylporphyrin chloride using dioxygen activated by a novel system containing N-hydroxyphthalimide and styrene.”

Chem. Pharm. Bull. Vol.35, 3078-3081, 1987

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Reviews and Book Chapters

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8. Le QG, Kimata Y.

"Multiple ways for stress sensing and regulation of the endoplasmic reticulum-stress sensors."

Cell Struct. Funct. In press

https://pubmed.ncbi.nlm.nih.gov/33775971/

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7. Ishiwata-Kimata Y, Le QG, Kimata Y.

“Stress-sensing and regulatory mechanism of the endoplasmic-stress sensors Ire1 and PERK.”

Endoplasmic Reticulum Stress in Diseases Vol. 5, 1-10, 2018

https://www.degruyter.com/view/j/ersc.2018.5.issue-1/ersc-2018-0001/ersc-2018-0001.xml

 

6. Tran DM, Kimata Y.

“The unfolded protein response of yeast Saccharomyces cerevisiae and other organisms.”

Plant Morphology Vol. 30, 15-24, 2018

https://www.jstage.jst.go.jp/article/plmorphol/30/1/30_15/_article/-char/en

 

5. Kimata Y, Nguyen PTM, Kohno K

“Response and cytoprotective mechanisms against proteotoxic stress in yeast and fungi.”

in Stress Response Mechanisms in Fungi -Theoretical and Practical Aspects- (Book) pp. 161-188, Springer

https://www.springer.com/gp/book/9783030006822

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4. Oikawa D, Kimata Y

“Experimental approaches for elucidation of stress-sensing mechanisms of the Ire1 family proteins.”

Methods Enzymol. Vol.490, 195-216, 2011

 

3. Kimata Y, Kohno K

“Endoplasmic reticulum stress-sensing mechanisms in yeast and mammalian cellsh

Curr. Opp. Cell. Biol. Vol.23, 135-142, 2011

https://www.ncbi.nlm.nih.gov/pubmed/21093243

 

2. Takeuchi M, Kimata Y, Kohno K

“Causal links between protein folding in the ER and events along the secretory pathway.”

Autophagy Vol.2, 323-324, 2006

https://www.ncbi.nlm.nih.gov/pubmed/16874095

 

1. Kimata Y, Lim CR, Kohno K

“S147P green fluorescent protein: a less thermosensitive green fluorescent protein variant.”

Methods Enzymol. Vol.302, 373-378, 1999

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