Shiomi Lab. - Publications

Publications

原著論文

29. Relationship between the Rod complex and peptidoglycan structure in Escherichia coli

Ago R, Tahara YO, Yamaguchi H, Saito M, Ito W, Yamasaki K, Kasai T, Okamoto S, Chikada T, Oshima T, Osaka I, Miyata M, Niki H, Shiomi D.

MicrobiologyOpen 2023 October: 12 e1385. DOI: 10.1002/mbo3.1385

28. D-amino Acids Ameliorate Experimental Colitis and Cholangitis by Inhibiting Growth of Proteobacteria: Potential Therapeutic Role in Inflammatory Bowel Disease

Umeda S, Sujino T, Miyamoto K, Yoshimatsu Y, Harada Y, Nishiyama K, Aoto Y, Adachi K, Hayashi N, Amafuji K, Moritoki N, Shibata S, Sasaki N, Mita M, Tanemoto S, Ono K, Mikami Y, Sasabe J, Takabayashi K, Hosoe N, Suzuki T, Sato T, Atarashi K, Teratani T, Ogata H, Nakamoto N, Shiomi D, Ashida H, Kanai T.

Cell Mol Gastroenterol Hepatol. 2023 Aug 9:S2352-345X(23)00148-0. doi: 10.1016/j.jcmgh.2023.08.002.

27. Direct observation of conversion from walled cells to wall-deficient L-form and vice versa in Escherichia coli indicates the essentiality of the outer membrane for proliferation of L-form cells

Chikada T, Kanai T, Hayashi M, Kasai T, Oshima T, and Shiomi D.

Frontiers in Microbiology 2021 March; 12: 1-15.doi: 10.3389/fmicb.2021.645965

26. Alteration of membrane fluidity or phospholipid composition perturbs rotation of MreB complexes in Escherichia coli

Kurita K, Kato F, and Shiomi, D.

Frontiers in Molecular Biosciences 2020 Nov; 7:1-9. doi: 10.3389/fmolb.2020.582660

25. Division‐site localization of RodZ is required for efficient Z ring formation in Escherichia coli.

Yoshii Y, Niki H, and Shiomi, D.

Molecular Microbiology 2019 May;111(5):1229-1244. doi: 10.1111/mmi.14217.

PMID: 30742332

24. Relation between rotation of MreB actin and cell width of Escherichia coli.

Kurita K, Shin R, Tabei T, and Shiomi, D

Genes to Cells 2019 Mar;24(3):259-265. doi: 10.1111/gtc.12667.

PMID: 30597729

23. The periplasmic disordered domain of RodZ promotes its self-interaction in Escherichia coli.

Ikebe R, Kuwabara Y, Chikada T, Niki H, and Shiomi, D

Genes to Cells 2018 Apr;23(4):307-317. doi: 10.1111/gtc.12572. Epub 2018 Feb 26.

PMID: 29480545

22. ARC6-mediated Z ring-like structure formation of prokaryote-descended chloroplast FtsZ in Escherichia coli.

Irieda H, and Shiomi, D.

Sci Rep. 2017 Jun 14;7(1):3492. doi: 10.1038/s41598-017-03698-6.

PMID: 28615720

21. Exclusion of assembled MreB by anionic phospholipids at cell poles confers cell polarity for bidirectional growth.

Kawazura T, Matsumoto K, Kojima K, Kato F, Kanai T, Niki H, and Shiomi, D

Molecular Microbiology 2017 May;104(3):472-486. doi: 10.1111/mmi.13639.

（Faculty of 1000 でrecommendされました）

20. Rapid, precise quantification of bacterial cellular dimensions across a genomic-scale knockout library.

Ursell T†, Lee TK†, Shiomi, D, Shi H, Tropini C, Monds RD, Colavin A, Billings G, Bhaya-Grossman I, Broxton M, Huang BE, Niki H, and Huang KC.

BMC Biology 2017 Feb 21;15(1):17. doi: 10.1186/s12915-017-0348-8.

19. A mutation in the promoter region of zipA, a component of the divisome, suppresses the shape defect of RodZ-deficient cells.

Shiomi, D, and Niki H.

MicrobiologyOpen 2013 Oct; 2(5):798-810

18. Mutations in cell elongation genes mreB, mrdA and mrdB suppress the shape defect of RodZ-deficient cells.

Shiomi, D, Toyoda A, Aizu T, Ejima F, Fujiyama A, Shini T, Kohara Y, and Niki H.

Mol Microbiol. 2013 Mar;87(5):1029-44. doi: 10.1111/mmi.12148.

17. A mutation of ispA that is involved in isoprenoid biogenesis can improve growth of Escherichia coli at low temperatures.

Shiomi, D, and Niki H.

Microbiol Immunol. 2011 Dec;55(12):885-8. doi: 10.1111/j.1348-0421.2011.00391.x.

16. Visualization of bacteriophage P1 infection by cryo-electron tomography of tiny Escherichia coli.

Liu J, Chen CY, Shiomi, D, Niki H, and Margolin W.

Virology. 2011 Sep 1;417(2):304-11. doi: 10.1016/j.virol.2011.06.005.

15. Identification of Escherichia coli ZapC (YcbW) as a component of the division apparatus that binds and bundles FtsZ polymers.

Hale CA, Shiomi, D, Liu B, Bernhardt TG, Margolin W, Niki H, and de Boer PA.

J Bacteriol. 2011 Mar;193(6):1393-404. doi: 10.1128/JB.01245-10.

14. Determination of bacterial rod shape by a novel cytoskeletal membrane protein.

Shiomi, D, Sakai M, and Niki H.

EMBO J. 2008 Dec 3;27(23):3081-91. doi: 10.1038/emboj.2008.234.

13. Compensation for the loss of the conserved membrane targeting sequence of FtsA provides new insights into its function.

Shiomi, D, and Margolin W.

Mol Microbiol. 2008 Feb;67(3):558-69. doi: 10.1111/j.1365-2958.2007.06085.x.

12. Dimerization or oligomerization of the actin-like FtsA protein enhances the integrity of the cytokinetic Z ring.

Shiomi, D, and Margolin W.

Mol Microbiol. 2007 Dec;66(6):1396-415.

11. An altered FtsA can compensate for the loss of essential cell division protein FtsN in Escherichia coli.

Bernard CS*, Sadasivam M*, Shiomi, D*, and Margolin W. *equal contributions to this work

Mol Microbiol. 2007 Jun;64(5):1289-305.

10. The ftsA* gain-of-function allele of Escherichia coli and its effects on the stability and dynamics of the Z ring.

Geissler B, Shiomi, D, and Margolin W.

Microbiology. 2007 Mar;153(Pt 3):814-25.

9. The C-terminal domain of MinC inhibits assembly of the Z ring in Escherichia coli.

Shiomi, D, and Margolin W.

J Bacteriol. 2007 Jan;189(1):236-43.

8. Helical distribution of the bacterial chemoreceptor via colocalization with the Sec protein translocation machinery.

Shiomi, D, Yoshimoto M, Homma M, and Kawagishi I.

Mol Microbiol. 2006 May;60(4):894-906.

7. Stabilization of polar localization of a chemoreceptor via its covalent modifications and its communication with a different chemoreceptor.

Shiomi, D, Banno S, Homma M, and Kawagishi I.

J Bacteriol. 2005 Nov;187(22):7647-54.

6. Targeting of the chemotaxis methylesterase/deamidase CheB to the polar receptor-kinase cluster in an Escherichia coli cell.

Banno S, Shiomi, D, Homma M, and Kawagishi I.

Mol Microbiol. 2004 Aug;53(4):1051-63.

5. Simultaneous measurement of sensor-protein dynamics and motility of a single cell by on-chip microcultivation system.

Inoue I, Shiomi, D, Kawagishi I, and Yasuda K.

J Nanobiotechnology. 2004 Apr 30;2(1):4.

4. Attractant binding alters arrangement of chemoreceptor dimers within its cluster at a cell pole.

Homma M, Shiomi, D, Homma M, and Kawagishi I.

Proc Natl Acad Sci U S A. 2004 Mar 9;101(10):3462-7.

3. Intragenic suppressors of a mutation in the aspartate chemoreceptor gene that abolishes binding of the receptor to methyltransferase.

Shiomi, D, Homma M, and Kawagishi I.

Microbiology. 2002 Oct;148(Pt 10):3265-75.

2. Dual recognition of the bacterial chemoreceptor by chemotaxis-specific domains of the CheR methyltransferase.

Shiomi, D, Zhulin IB, Homma M, and Kawagishi I.

J Biol Chem. 2002 Nov 1;277(44):42325-33.

1. The aspartate chemoreceptor Tar is effectively methylated by binding to the methyltransferase mainly through hydrophobic interaction.

Shiomi, D, Okumura H, Homma M, and Kawagishi I.

Mol Microbiol. 2000 Apr;36(1):132-40.

総説など

17. 細菌の新奇生存戦略：L-form

塩見大輔、林匡史、大島拓

化学と生物 62 (1) p.14-22 (2024)

16. 大腸菌L-formの増殖における外膜の重要性

塩見大輔、大島拓

生物物理誌 63(1) p. 27-29 (2023)

15. 壁をなくしてみたところ

大島拓、塩見大輔

生物工学会誌第100巻第3号 137. (2022)

14. SanAによる大腸菌の新規バンコマイシン耐性機構の解析

山口穂野香

日本ゲノム微生物学会ニュースレター 2021 (No.23) p.16-17

13. 大腸菌L-formにおける分裂装置の制御メカニズム

林匡史

日本ゲノム微生物学会ニュースレター 2021 (No.23) p.15-16

12. RodZ: a key-player in cell elongation and cell division in Escherichia coli

Ago R, and Shiomi D.

AIMS Microbiology 2019 5(4): 358-367. doi: 10.3934/microbiol.2019.4.358

11. MreBアクチンの細胞内局在と機能の制御機構

栗田恵輔、塩見大輔

生物物理 2019 59 (2), 100-102 DOI: 10.2142/biophys.59.100

10. Can the chloroplast division machinery be evolutionarily dated back to bacteria?

Irieda, H., and Shiomi, D.

ATLAS of Science March 16, 2018

9. Bacterial Heterologous Expression System for Reconstitution of Chloroplast Inner Division Ring and Evaluation of Its Contributors.

Irieda H, and Shiomi D.

Int J Mol Sci. 2018 Feb 11;19(2). pii: E544. doi: 10.3390/ijms19020544. Review.

8. Polar localization of MreB actin is inhibited by anionic phospholipids in the rod-shaped bacterium Escherichia coli.

Daisuke Shiomi

Current Genetics 2017 Oct;63(5):845-848. doi: 10.1007/s00294-017-0696-5.

7. 細菌形態形成制御機構に関する研究（平成26年度黒屋奨学賞受賞論文）

塩見大輔日本細菌学雑誌 2014 69(4), 557-564

6. Escherichia coli and Bacillus subtilis: The Frontiers of Molecular Microbiology Revisited

Sadaie Y and Matsumoto K. Chapter 3-2. Nucleoid organization and chromosome segregation.

Shiomi D, and Niki H. Research Signpost 2012

5. 細胞骨格タンパク質による大腸菌の形態形成機構

塩見大輔、仁木宏典日本微生物生態学会誌 2009 24(2), 51-60

4. Genetic mechanism regulating bacterial cell shape and metabolism.

Shiomi D, Mori H, and Niki H.

Commun Integr Biol. 2009 May;2(3):219-20.

3. 大腸菌におけるタンパク質の細胞内局在とそのメカニズム

塩見大輔日本生化学会誌 2008 80(1), 36-40

2. 細菌の膜貫通型受容体の局在とメカニズム

塩見大輔、川岸郁朗生物物理 2008 48(1), 30-34

1. A sweet sensor for size-conscious bacteria.

Shiomi D, and Margolin W.

Cell. 2007 Jul 27;130(2):216-8.