Nakai, R., Wakana, I., and Niki, H. (2021)
Internal microbial zonation during in the massive growth of marimo, a lake ball of Aegagropila linnaei in Lake Akan.
iScience (in press)

Abe, T., Akazawa, Y., Toyoda, A., Niki, H., and Baba, T. (2020)
Batch-Learning Self-Organizing Map Identifies Horizontal Gene Transfer Candidates and Their Origins in Entire Genomes.
Front Microbiol. 2020 Jul 3;11:1486.
DOI: 10.3389/fmicb.2020.01486
PMID: 32719664

Onaka, A.T., Su, J., Katahira, Y., Tang, C., Zafar, F., Aoki, K., Kagawa, W., Niki, H., Iwasaki, H., and Nakagawa, T. (2020)
DNA replication machinery prevents Rad52-dependent single-strand annealing that leads to gross chromosomal rearrangements at centromeres.
Commun Biol. 2020 Apr 30;3(1):202.
DOI: 10.1038/s42003-020-0934-0
PMID: 32355220

Kagoshima, H., Maslen, R., Kito, K., Imura, S., Niki, H., and Convey, P. (2019)
Integrated taxonomy combining morphological and molecular biological analyses of soil nematodes from maritime Antarctica.
Polar Biology volume 42, pages 877-887 (2019).
DOI: 10.1007/s00300-019-02482-8

Nozaki, S., and Niki, H. (2019)
Exonuclease III (XthA) Enforces In Vivo DNA Cloning of Escherichia coli To Create Cohesive Ends.
J Bacteriol. 2019 Feb 11;201(5):e00660-18.
DOI: 10.1128/JB.00660-18
PMID: 30530516

Seike, T., Shimoda, C., and Niki, H. (2019)
Asymmetric diversification of mating pheromones in fission yeast.
PLoS Biol. 2019 Jan 22;17(1):e3000101.
DOI: 10.1371/journal.pbio.3000101
PMID: 30668560

Yoshii, Y., Niki, H., and Shiomi, D. (2019)
Division-site localization of RodZ is required for efficient Z ring formation in Escherichia coli.
Mol Microbiol. 2019 May;111(5):1229-1244.
DOI: 10.1111/mmi.14217
PMID: 30742332

Nozaki, S., Furuya, K., and Niki, H. (2018)
The Ras1-Cdc42 pathway is involved in hyphal development of Schizosaccharomyces japonicus.
FEMS Yeast Res. 2018 Jun 1;18(4).
DOI: 10.1093/femsyr/foy031
PMID: 29566183

Ikebe, R., Kuwabara, Y., Chikada, T., Niki, H., and Shiomi, D. (2018)
The periplasmic disordered domain of RodZ promotes its self-interaction in Escherichia coli.
Genes Cells . 2018 Apr;23(4):307-317.
DOI: 10.1111/gtc.12572
PMID: 29480545

Yano K, Akiyama K, Niki H.(2018)
In Vivo and In Vitro Assay for Monitoring the Topological Loading of Bacterial Condensins on DNA.
Methods Mol Biol. 2019;2004:181-196.
DOI: 10.1007/978-1-4939-9520-2_14
PMID: 31147918

Arnott ZLP, Nozaki S, Monteiro DCF, Morgan HE, Pearson AR, Niki H, Webb ME.(2017)
The Mechanism of Regulation of Pantothenate Biosynthesis by the PanD-PanZ-AcCoA Complex Reveals an Additional Mode of Action for the Antimetabolite N-Pentyl Pantothenamide (N5-Pan).
Biochemistry. 2017 Sep 19;56(37):4931-4939.
DOI: 10.1021/acs.biochem.7b00509
PMID: 28832133

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, Huang KC.(2017)
Rapid, precise quantification of bacterial cellular dimensions across a genomic-scale knockout library.
BMC Biol. 2017 Feb 21;15(1):17.
DOI: 10.1186/s12915-017-0348-8.
PMID: 28222723

Kawazura T, Matsumoto K, Kojima K, Kato F, Kanai T, Niki H, Shiomi D.(2017)
Exclusion of assembled MreB by anionic phospholipids at cell poles confers cell polarity for bidirectional growth.
Mol Microbiol. 2017 May;104(3):472-486.
DOI: 10.1111/mmi.13639.
PMID: 28164388

Niki H.(2017)
Open and Closed Questions about Open and Closed SMC.
Structure. 2017 Apr 4;25(4):569-570.
ODI: 10.1016/j.str.2017.03.011.
PMID: 28380335

Yano, K., & Niki, H. (2017).
Multiple cis-Acting rDNAs Contribute to Nucleoid Separation and Recruit the Bacterial Condensin Smc-ScpAB. Cell Reports 21(5):1347-1360 DOI:10.1016/j.celrep.2017.10.014

Aoki, K., & Nki, H. (2017).
Release of condensin from mitotic chromosomes requires the Ran-GTP gradient in the reorganized nucleus.
Biology Open November 15; 6(11): 1614-1628
DOI:10.1242/bio.027193

Seike, T., & Niki, H. (2017).
Mating response and construction of heterothallic strains of the fission yeast Schizosaccharomyces octosporus.
FEMS Yeast Res.
Aug 1;17(5). doi: 10.1093/femsyr/fox045.

Aoki, K., Furuya, K., & Niki, H. (2017).
Schizosaccharomyces japonicus: A Distinct Dimorphic Yeast Among the Fission Yeast.
Cold Spring Harb Protoc
DOI: 10.1101/pdb.top082651

Furuya, K., & Niki, H. (2017).
Mating, Spore Dissection, and Selection of Diploid Cells in Schizosaccharomyces japonicus.
Cold Spring Harb Protoc
DOI: 10.1101/pdb.port091843

Aoki, K., & Niki, H. (2017).
Transformation of Schizosaccharomyces japonicus.
Cold Spring Harb Protoc
DOI: 10.1101/pdb.port091850

Hironori Niki (2017).
Induction of Hyphal Growth in Schizosaccharomyces japonicus.
Cold Spring Harb Protoc
DOI: 10.1101/pdb.prot091868

Niki, H. and Yano, K. (2016).
In vitro topological loading of bacterial condensin MukB on DNA, preferentially single-stranded DNA rather than double-stranded DNA.
Sci Rep. 2016 Jul 8;6:29469.
DOI: 10.1038/srep29469.
PMID: 27387439

Niki, H.(2014).
Schizosaccharomyces japonicus: the fission yeast is a fusion with yeast and hyphae.
Yeast.
DOI: 10.1002/yea.2996
PMID:24375690

Keyamura,K., Sakaguchi,C., Kubota,Y., Niki,H.,  Hishida, T.(2013).
RecA Protein Recruits Structural Maintenance of Chromosomes (SMC)-like RecN Protein to DNA Double-strand Breaks.
J Biol Chem 11 0ct 2013,29229-37
10.1074/jbc.M113.485474
PMID:23974212

Yano,K., Wada,T., Suzuki,S., Tagami,K., Matsumoto,T., Shiwa,Y., Ishige,T., Kawaguchi,Y., Masuda,K., Akanuma,G., Nanamiya,H., Niki,H., Yoshikawa,H.,& Kawamura,F.(2013).
Multiple rRNA operons are essential for efficient cell growth and sporulation as well as outgrowth in Bacillus subtilis.
Microbiology 22 Aug 2013
DOI: 10.1099/mic.0.067025-0
PMID:23970567

Okamoto, S., Furuya, K., Nozaki, S., Aoki, K.,& Niki, H.(2013).
Synchronous activation of cell division by light or temperature stimuli in the dimorphic yeast Schizosaccharomyces japonicus.
Eukaryot Cell 12(9), 1235-43.
DOI: 10.1128/EC.00109-13
PMID:23873862

Shiomi, D.,& Niki, H.(2013).
A mutation in the promoter region of zipA, a component of the divisome, suppresses the shape defect of RodZ-deficient cells.
MicrobiologyOpen 6 AUG 2013
DOI: 10.1002/mbo3.116
PMID:

Aoki, K., Shiwa, Y., Takada, H., Yoshikawa, H., & Niki, H.(2013).
Regulation of nuclear envelope dynamics via APC/C is necessary for the progression of semi-open mitosis in Schizosaccharomyces japonicus.
Genes Cells.
DOI: 10.1111/gtc.12072
PMID:23786411

Shiomi, D., Toyoda, A., Aizu, T., Ejima, F., Fujiyama, A., Shini, T., Kohara, Y., & Niki, H.(2013).
Mutations in cell elongation genes mreB, mrdA and mrdB suppress the shape defect of RodZ-deficient cells.
Mol Microbiol.
DOI: 10.1111/mmi.12148
PMID:23301723

Monteiro, D.C.F., Rugen, M.D., Shepherd, D., Nozaki, S., Niki, H., & Webb, M.E.(2012).
Formation of a heterooctameric complex between ADC & its cognate activating factor, PanZ, is CoA-dependent.
Biochem Biophys Res. Commun 426,350-355.
PMID:22940551

Furuya, K., & Niki, H.(2012)
Hyphal differentiation induced via a DNA damage checkpoint-dependent pathway engaged in crosstalk with nutrient stress signaling in Schizosaccharomyces japonicus.
Curr Genet 58,291-303.
PMID:23090706

Nozaki,S., Webb, M.E., & Niki, H.(2012).
An activator for pyruvoyl-dependent l-aspartate α-decarboxylase is conserved in a small group of the γ-proteobacteria including Escherichia coli.
MicrobiologyOpen 1,298-310.
DOI: 10.1002/mbo3.34
PMID:

Xu, J., Yanagisawa, Y., Tsankov, A.M., Hart, C., Aoki, K., Kommajosyula, N., Steinmann, K.E., Bochicchio, J., Russ, C., Regev, A., Rando, O.J., Nusbaum, C., Niki, H., Milos, P., Weng, Z., & Rhind, N.(2012).
Genome-wide identification and characterization of replication origins by deep sequencing.
Genome Biol 13,R27
PMID:22531001

Furuya, K., Aoki, K., & Niki, H.(2012).
Construction of an insertion marker collection of Sz. japonicus (IMACS) for genetic mapping & a fosmid library covering its genome.
Yeast 29,241-249.
PMID:22641476

Gray, A.N., Henderson-Frost, J.M., Boyd, D., Shirafi, S., Niki, H., & Goldberg, M.B.(2011).
Unbalanced charge distribution as a determinant for dependence of a subset of Escherichia coli membrane proteins on the membrane insertase YidC.
mBio 2,e00238-11.
PMID:22108384
DOI: 10.1128/mBio.00238-11

Kagawa, W., Sagawa, T., Niki, H., & Kurumizaka, H.(2011).
Structural basis for the DNA-binding activity of the bacterial Β-propeller protein YncE.
Acta Crystallogra Sect D 67,1045-1053.
PMID:22120742

Shiomi, D.,& Niki, H.(2011).
A mutation of ispA that is involved in isoprenoid biogenesis can improve slow growth of Escherichia coli at low temperature.
Microbiol Immunol 55,885-888
PMID: 22003871

Liu, J., Chen, C.Y., Shiomi, D., Niki, H., & Margolin, W.(2011).
Visualization of bacteriophage P1 infection by cryo-electron tomography of tiny Escherichia coli.
Virology 417,304-311.
PMID: 21745674

Hale, C.A., Shiomi, D., Liu, B., Bernhardt, T.G., Margolin, W., Niki, H., & de Boer, PA.(2011).
Identification of Escherichia coli ZapC (YcbW) as a component of the division apparatus that binds & bundles FtsZ polymers.
J Bacteriol 193,1393-1404.
PMID: 21216997

Yanagihara, K., Niki, H., & Baba, T.(2011).
Direct PCR amplification of the 16S rRNA gene from single microbial cells isolated from an Antarctic iceberg using laser microdissection microscopy.
Polar Science 5, 375-382.

Nakai, R., Abe, T., Baba, T., Imura, S., Kagoshima, H., K&a, H., Kanekiyo, A., Kohara, Y., Koi, A., Nakamura, K., Narita, T., Niki, H., Yanagihara, K., & Naganuma, T.(2011).
Microflorae of aquatic moss pillars in a freshwater lake, East Antarctica, based on fatty acid and 16S rRNA gene analyses.
Polar Biolo. 35, 425-433.

Furuya, K., & Niki, H. (2011).
Construction of diploid zygotes by interallelic complementation of ade6 in Schizosaccharomyces japonicus.
Yeast 28, 747-754.
PMID:21905090

Aoki, K., Hayashi, H., Furuya, K., Sato, M., Takagi, T., Osumi, M., Kimura, A., & Niki, H. (2011).
Breakage of the nuclear envelope by an extending mitotic nucleus occurs during anaphase in Schizosaccharomyces japonicus.
Genes Cells 16, 911-926.
PMID: 21733045

Rhind, N., Chen, Z., Yassour, M., Thompson, D. A., Haas, B. J., Habib, N., Wapinski, I., Roy, S., Lin, M. F., Heiman, D. I., Young, S. K., Furuya, K.,
Guo, Y., Pidoux, A., Chen, H. M., Robbertse, B., Goldberg, J. M., Aoki, K., Bayne, E. H., Berlin, A. M., Desjardins, C. A., Dobbs, E., Dukaj, L.,
Fan, L., FitzGerald, M. G., French, C., Gujja, S., Hansen, K., Keifenheim, D., Levin, J. Z., Mosher, R. A., Muller, C. A., Pfiffner, J., Priest, M.,
Russ, C., Smialowska, A., Swoboda, P., Sykes, S. M., Vaughn, M., Vengrova, S., Yoder, R., Zeng, Q., Allshire, R., Baulcombe, D., Birren, B. W., Brown, W., Ekwall, K., Kellis, M., Leatherwood, J., Levin, H., Margalit, H., Martienssen, R., Nieduszynski, C. A., Spatafora, J. W., Friedman, N., Dalgaard, J. Z., Baumann, P., Niki, H., Regev, A., & Nusbaum, C. (2011).
Comparative functional genomics of the fission yeasts.
Science 332, 930-936.
PMID: 21511999

Hatano, T., & Niki, H. (2010).
Partitioning of P1 Plasmids by Gradual Distribution of the ATPase ParA.
Mol Microbiol 78, 1182-1198.
PMID:21091504

Furuya, K., Miyabe, I., Tsutsui, Y., Paderi, F., Kakusho, N., Masai, H., Niki, H., & Carr, A.M. (2010).
DDK phosphorylates checkpoint clamp component Rad9 and promotes its release from damaged chromatin.
Mol Cell 40, 606-618.
PMID: 21095590

Aoki, K., Nakajima, R., Furuya, K., & Niki, H. (2010).
Novel episomal vectors and a highly efficient transformation procedure for the fission yeast Schizosaccharomyces japonicus.
Yeast 27, 1049-1060.
PMID:20737410

Furuya, K., & Niki, H. (2010).
The DNA damage checkpoint regulates a transition between yeast and hyphal growth in Schizosaccharomyces japonicus.
Mol Cell Biol 30, 2909-2917.
PMID: 20368354

Yamazaki, Y., Akashi, R., Banno, Y., Endo, T., Ezura, H., Fukami-Kobayashi, K., Inaba, K., Isa, T., Kamei, K., Kasai, F., Kobayashi, M., Kurata, N., Kusaba, M., Matuzawa, T., Mitani, S., Nakamura, T., Nakamura, Y., Nakatsuji, N., Naruse, K., Niki, H., Nitasaka, E., Obata, Y., Okamoto, H., Okuma, M., Sato, K., Serikawa, T., Shiroishi, T., Sugawara, H., Urushibara, H., Yamamoto, M., Yaoita, Y., Yoshiki, A., & Kohara, Y. (2009).
NBRP databases: Databases of biological resources in Japan.
Nucleic Acids Res, 38, D26-32.
PMID: 19934255

Janakiraman, A., Fixen, K.R., Gray, A.N., Niki, H., & Goldberg, M.B.(2009).
A genome-scale proteomic screen identifies a role for DnaK in chaperoning of polar autotransporters in Shigella
J Bacteriol 191, 6300-6311.
PMID: 19684128

Nozaki, S., Niki, H., & Ogawa, T.(2009).
Replication initiator DnaA of Escherichia coli changes its assembly form on the replication origin during the cell cycle.
J Bacteriol 191, 4807-4814.
PMID: 19502409

Shiomi, D., Mori, H., & Niki, H. (2009).
Genetic mechanism regulating bacterial cell shape & metabolism.
Commun Integr Biol 2, 219-220.
PMID: 19641734

Furuya, K., & Niki, H. (2009).
Isolation of heterothallic haploid & auxotrophic mutants of Schizosaccharomyces japonicus.
Yeast 26, 221-233.
PMID: 19330769

Shiomi, D., Sakai, M., & Niki, H. (2008).
Determination of bacterial rod shape by a novel cytoskeletal membrane protein.
EMBO J 27, 3081-3091.
PMID: 19008860

Yamazaki, Y., Niki, H., and Kato, J.-I.(2007).
Profiling of Escherichia coli chromosome database.
Mol Biol 416, 385-389.
PMID: 18392982

Kai, M., Furuya, K., Paderi, F., Carr, A.M., & Wang, T.S. (2007).
Rad3-dependent phosphorylation of the checkpoint clamp regulates repair-pathway choice.
Nat Cell Biol 9, 691-697.
PMID: 17515930

Hatano, T., Yamaichi, Y., & Niki, H. (2007).
Oscillating focus of SopA associated with filamentous structure guides partitioning of F plasmid.
Mol Microbiol 64, 1198-1213.
PMID: 17542915

Gerding, M.A., Ogata, Y., Pecora, N.D., Niki, H., & de Boer, P.A. (2007).
The trans-envelope Tol-Pal complex is part of the cell division machinery & required for proper outer-membrane invagination during cell constriction in E. coli.
Mol Microbiol 63, 1008-1025.
PMID: 17233825

Cui, T., Moro-oka, N., Ohsumi, K., Kodama, K., Ohshima, T., Ogasawara, N., Mori, H., Wanner, B., Niki, H., & Horiuchi, T. (2007).
Escherichia coli with a linear genome.
EMBO Rep 8, 181-187.
PMID: 17218953

Yamaichi, Y., & Niki, H. (2004).
migS, a cis-acting site that affects bipolar positioning of oriC on the Escherichia coli chromosome.
EMBO J 23, 221-233.
PMID: 14685268

Kodama, K., Kobayashi, T., Niki, H., Hiraga, S., Oshima, T., Mori, H., & Horiuchi, T. (2002).
Amplification of Hot DNA segments in Escherichia coli.
Mol Microbiol 45, 1575-1588.
PMID: 12354226

Yamaichi, Y., & Niki, H. (2000).
Active segregation by the Bacillus subtilis partitioning system in Escherichia coli.
Proc Natl Acad Sci U S A 97, 14656-14661.
PMID: 11121066

Niki, H., Yamaichi, Y., & Hiraga, S. (2000).
Dynamic organization of chromosomal DNA in Escherichia coli.
Genes Dev 14, 212-223.
PMID: 10652275

Niki, H., & Hiraga, S. (1999).
Subcellular localization of plasmids containing the oriC region of the Escherichia coli chromosome, with or without the sopABC partitioning system.
Mol Microbiol 34, 498-503.
PMID: 10564491

>>Publication before 1999


 

国立遺伝学研究所
遺伝形質研究系 微生物機能研究室(仁木研究室)

〒411-8540 静岡県三島市谷田1111 >連絡先詳細および地図はこちら

Microbial Physiology Laboratory (Niki Laboratory)
Department of Gene Function and Phenomics
National Institute of Genetics

1111 Yata Mishima Shizuoka Japan P.O. 411-8540 > Contact details & Maps