(1) Nakamura, M., Maruyama, I. N., Soma, M., Kato, J., Suzuki, H., and Hirota, Y. (1983). On the process of cellular division in Escherichia coli: nucleotide sequence of the gene for penicillin-binding protein 3.  Mol. Gen. Genet. 191: 1-9. 

(2) Kato, J., Suzuki, H., and Hirota, Y. (1984). Overlapping of the coding regions for Alpha and Gamma components of penicillin-binding protein 1b in Escherichia coli.  Mol. Gen. Genet. 196: 449-457. 

(3) Kato, J., Suzuki, H., and Hirota, Y. (1985). Dispensability of either penicillin-binding protein-1a or -1b involved in the essential process for cell elongation in Escherichia coli. Mol. Gen. Genet. 200: 272-277. 

(4) Suzuki, H., Kato, J., Sakagami, Y., Mori, M., Suzuki, A., and Hirota, Y. (1987). Conversion of the Alpha component of penicillin-binding protein 1b to the Beta component in Escherichia coli.  J. Bacteriol. 169: 891-893. 

(5) Kato, J., Nishimura, Y., Yamada, M., Suzuki, H., and Hirota, Y. (1988). Gene organization in the region containing a new gene involved in chromosome partition in Escherichia coli. J. Bacteriol. 170: 3967-3977. 

(6) Kato, J., Ito, K., Nakamura, A., and Watanabe, H. (1989). Cloning of regions required for contact hemolysis and entry into LLC-MK2 cells from Shigella sonnei form I plasmid: virF is a positive regulator gene for these phenotypes.  Infect.  Immun. 57: 1391-1398. 

(7) Kato, J., Nishimura, Y., and Suzuki, H. (1989). Escherichia coli parA is an allele of the gyrB gene.  Mol. Gen. Genet. 217: 178-181. 

(8) Hara, H., Nishimura, Y., Kato, J., Suzuki, H., Nagasawa, H., Suzuki, A., and Hirota, Y. (1989). Genetic analyses of processing involving C-terminal cleavage in penicillin-binding protein 3 of Escherichia coli.  J. Bacteriol. 171: 5882-5889. 

(9) Watanabe, H., Arakawa, E., Ito, K., Kato, J., and Nakamura, A. (1990). Genetic analysis of an invasion region by use of a Tn3-lac transposon and identification of a second positive regulator gene, invE, for cell invasion of Shigella sonnei: significant homology of InvE with ParB of plasmid P1.  J. Bacteriol. 172: 619-629. 

(10) Kato, J., Nishimura, Y., Imamura, R., Niki, H., Hiraga, S., and Suzuki, H. (1990). New topoisomerase essential for chromosome segregation in E. coli. Cell 63: 393-404.

(11) Ogawa, A., Kato, J., Watanabe, H., Nair, B. G., Takeda, T. (1990). Cloning and nucleotide sequence of a heat-stable enterotoxin gene from Vibrio cholerae non-O1 isolated from a patient with traveler’s diarrhea. Infect. Immun. 58: 3325-3329.

(12) Yoshida, Y., Okamura, N., Kato, J., and Watanabe, H. (1991). Molecular cloning and characterization of form I antigen genes of Shigella sonnei. J. Gen. Microbiol. 137: 867-874.

(13) Kato, J., Suzuki, H., and Ikeda, H. (1992). Purification and characterization of DNA topoisomerase IV in Escherichia coli. J. Biol. Chem. 267: 25676-25684.

(14) Kato, J. and Ikeda, H. (1993). Purification and characterization of DNA topoisomerase IV in Escherichia coli. In “Molecular Biology of DNA Topoisomerases and its Application to Chemotherapy” (Ed. T. Ando), CRC Press, Inc., Boca Raton, USA. P. 31-37.

(15) Tatebayashi, K., Kato, J., and Ikeda, H. (1994). Structural analyses of DNA fragments integrated by illegitimate recombination in Schizosaccharomyces pombe. Mol. Gen. Genet. 244: 111-119.

(16) Hoshino, K., Kitamura, A., Morrissey, I., Sato, K., Kato, J., and Ikeda, H. (1994). Comparison of inhibition of Escherichia coli topoisomerase IV by quinolones with DNA gyrase inhibition.  Antimicrob. Agents. Chemother. 38: 2623-2627.

(17) Tsukamoto, Y., Kato, J., and Ikeda, H. (1996). Effects of mutations of RAD50, RAD51, RAD52, and related genes on illegitimate recombination in Saccharomyces cerevisiae. Genetics 142: 383-391.

(18) Kumagai, Y., Kato, J., Hoshino, K., Akasaka, T., Sato, K., and Ikeda, H. (1996). Quinolone resistant mutants of Escherichia coli DNA topoisomerase IV parC gene. Antimicrob. Agents Chemother. 40: 710-714.

(19) Kato, J. and Ikeda, H. (1996). Construction of mini-F plasmid vectors for plasmid shuffling in Escherichia coli. Gene 170: 141-142.

(20) Yokochi, T., Kato, J., and Ikeda, H. (1996). Construction of Beta-lactamase-encoding ApR gene cassettes for rapid identification of cloned genes. Gene 170: 143-144.

(21) Tsukamoto, Y., Kato, J., and Ikeda, H. (1996). Hdf1, a yeast Ku-protein homologue, is involved in illegitimate recombination, but not in homologous recombination.  Nucleic Acids Res. 24: 2067-2072.

(22) Yokochi, T., Kato, J., and Ikeda, H. (1996) DNA nicking by Escherichia coli topoisomerase IV with a substitution mutation from tyrosine to histidine at the active site. Genes to Cells 1: 1069-1075.

(23) Shimizu, H., Yamaguchi, H., Ashizawa, Y., Kohno, Y., Asami, M., Kato, J., and Ikeda, H. (1997) Short-homology-independent illegitimate recombination in Escherichia coli: distinct mechanism from short-homology-dependent illegitimate recombination. J. Mol. Biol. 266: 297-305.

(24) Hanada, K., Ukita, T., Kohno, Y., Saito, K., Kato, J., and Ikeda, H. (1997) RecQ DNA helicase is a suppressor of illegitimate recombination in Escherichia coli. Proc. Natl. Acad. Sci. USA 94: 3860-3865.

(25) Tsukamoto, Y., Kato, J., and Ikeda, H. (1997) Budding yeast Rad50, Mre11, Xrs2, and Hdf1, but not Rad52, are involved in formation of deletion mutation on a dicentric plasmid: their possible roles on DNA end-joining. Mol. Gen. Genet. 255: 543-547.

(26) Sato, M., Ishida, R., Narita, T., Kato, J., Ikeda, H., Fukazawa, H., and Andoh, T. (1997) Interaction of DNA topoisomerase II catalytic inhibitor ICRF-193, a bisdioxopiperazine derivative with conserved region(s) of eukaryotes enzyme but not prokaryotic one. Biochem. Pharmacol. 54: 545-550.

(27) Shanadou, Y., Kato, J., and Ikeda, H. (1997) Fis is required for illegitimate recombination during formation of Lambda bio transducing phage.  J. Bacteriol. 179: 4239-4245.

(28) Tsukamoto, Y., Kato, J., and Ikeda, H. (1997) Silencing factors participate in DNA repair and recombination in Saccharomyces cerevisiae.  Nature 388: 900-903.

(29) Heo, S-j., Tatebayashi, K., Kato, J., Ikeda, H. (1998) The RHC21 gene of budding yeast, a homologue of the fission yeast rad21+ gene, is essential for chromosome segregation. Mol. Gen. Genet. 257: 149-156.

(30) Tatebayashi, K., Kato, J., and Ikeda, H. (1998) Isolation of a Schizosaccharomyces pombe rad21ts mutant that is aberrant in chromosome segregation, microtubule function, DNA repair and sensitive to hydroxyurea: possible involvement of Rad21 in ubiquitin-mediated proteolysis. Genetics 148: 49-57.

(31) Yamagata, K., Kato, J., Shimamoto, A., Goto, M., Furuichi, Y., and Ikeda, H. (1998)  Bloom’s and Werner’s syndrome genes suppress hyperrecombination in yeast sgs1 mutant: implication for genomic instability in human diseases. Proc. Natl. Acad. Sci. USA 95: 8733-8738. 

(32) Shanado, Y., Kato, J., and Ikeda, H. (1998) Escherichia coli HU protein suppresses DNA gyrase-mediated illegitimate recombination and SOS induction. Genes to Cells 3: 511-520.

(33) Sato, M., Sato, K., Nishikawa, S., Hirata, A., Kato, J., and Nakano, A. (1999) The yeast RER2 gene, identified by ER protein localization mutations, encodes cis-prenyltransferase, a key enzyme in the dolichol synthesis. Mol. Cell. Biol. 19: 471-483.

(34) Kato, J., Fujisaki, S., Nakajima, K., Nishimura, Y., Sato, M., and Nakano, A. (1999) The E. coli homologue of yeast Rer2, a key enzyme of dolichol synthesis, is essential for carrier lipid formation in bacterial cell wall synthesis. J. Bacteriol.  181: 2733-2738.

(35) Ashizawa, Y., Yokochi, T., Ogata, Y., Shobuike, Y., Kato, J., and Ikeda, H. (1999) Mechanism of DNA gyrase-mediated illegitimate recombination: Characterization of Escherichia coli gyrA mutations that confer hyperrecombination phenotype. J. Mol. Biol. 289: 447-458.

(36) Yamaguchi, H., Hanada, K., Asami, Y., Kato, J., and Ikeda, H. (2000) Control of genetic stability in Escherichia coli: the SbcB 3′-5′ exonuclease suppresses illegitimate recombination promoted by the RecE 5′-3′ exonuclease.  Genes to Cells 5: 101-109.

(37) Inagawa, T., Kato, J., Niki, H., Karata, K., and Ogura, T. (2001) Defective plasmid partition in ftsH mutants of Escherichia coli.  Mol. Gen. Genet. 265: 755-762.

(38) Kato, J. and Katayama, T. (2001) Hda, a novel DnaA-related protein, regulates the replication cycle in Escherichia coli.  EMBO Journal 20: 4253-4262.

(39) Hashimoto, M., and Kato, J. (2003) Indispensability of the Escherichia coli carbonic anhydrases YadF and CynT in cell proliferation at a low CO2 partial pressure.  Biosci. Biotechnol. Biochem. 67: 919-922.

(40) Soma, A., Ikeuchi, Y., Kanemasa, S., Kobayashi, K., Ogasawara, N., Ote, T., Kato, J., Watanabe, K., Sekine, Y., and Suzuki, T. (2003) An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA.  Mol. Cell 12: 689-698.

(41) Hashimoto, M., Ichimura, T., Mizoguchi, H., Tanaka, K., Fujimitsu, K., Keyamura, K., Ote, T., Yamakawa, T., Yamazaki, Y., Mori, H., Katayama, T. and Kato, J. (2005) Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome. Mol. Microbiol. 55: 137-149.

(42) Ikeuchi, Y., Soma, A., Ote, T., Kato, J., Sekine, Y., and Suzuki, T. (2005) Molecular mechanism of lysidine synthesis that determines tRNA identity and codon recognition. Mol. Cell 19: 235-246.

(43) Kato, J. (2005) Regulatory network of the initiation of chromosomal replication in Escherichia coli.  Crit. Rev. Biochem. Mol. Biol. (Critical Reviews in Biochemistry and Molecular Biology) 40: 331-342.

(44) Ote, T., Hashimoto, M., Ikeuchi, Y., Su’etsugu, M., Suzuki, T., Katayama, T., and Kato, J. (2006) Involvement of the Escherichia coli folate-binding protein YgfZ in RNA modification and regulation of chromosomal replication initiation. Mol. Microbiol. 59: 265-275.

(45) Ikeuchi, Y., Shigi, N., Kato, J., Nishimura, A., and Suzuki, T. (2006) Mechanistic insights into sulfur-relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions. Mol Cell 21: 97-108.

(46) Kato, J. and Hashimoto, M. (2007) Construction of consecutive deletions of the Escherichia coli chromosome. Mol. Syst. Biol. 3: Article number 132

(47) Kato, J. and Hashimoto, M. (2008) Construction of long chromosomal deletion mutants of Escherichia coli and minimization of the genome. Methods in Molecular Biology 416: 279-293. Microbial Gene Essentiality: Protocols and Bioinformatics (Edited by : A. L. Osterman and S. Y. Gerdes), Humana Press Inc., Totowa, NJ

(48) Yamazaki, Y., Niki, H., and Kato, J. (2008) Profiling of Escherichia coli chromosome database.  Methods in Molecular Biology 416: 385-389. Microbial Gene Essentiality: Protocols and Bioinformatics (Edited by : A. L. Osterman and S. Y. Gerdes), Humana Press Inc., Totowa, NJ

(49) Mizoguchi, H., Sawano, Y., Kato, J., and Mori, H. (2008) Superpositioning of deletions promotes growth of Escherichia coli with a reduced genome. DNA Research 15: 277-284.

(50) Inoue, A., Murata, Y., Takahashi, H., Tsuji, N., Fujisaki, S., and Kato, J. (2008) Involvement of an essential gene, mviN, in murein synthesis in Escherichia coli. J. Bacteriol. 190: 7298-7301. 

(51) Tachikawa, T., and Kato, J. (2011) Suppression of the temperature-sensitive mutation of the bamD gene required for the assembly of outer membrane proteins by multicopy of the yiaD gene in Escherichia coli.  Biosci. Biotechnol. Biochem. 75: 162-164.

(52) Iwadate, Y., Honda, H., Sato, H., Hashimoto, M. and Kato, J. (2011) Oxidative stress sensitivity of engineered Escherichia coli cells with a reduced genome. FEMS Microbiology Letter. 322: 25-33.

(53) Hashimoto, C., Sakaguchi, K., Taniguchi, Y., Honda, H., Oshima, T., Ogasawara, N., and Kato, J. (2011) Effects on transcription of mutations in ygjD, yeaZ, and yjeE genes involved in a universal tRNA modification in Escherichia coli. J. Bacteriol. 193: 6075-6079.

(54) Iwamoto, A., Osawa, A., Kawai, M., Honda, H., Yoshida, S., Furuya, N., and Kato, J. (2012) Mutations in the essential Escherichia coli gene, yqgF, and their effects on transcription. J. Mol. Microbiol. Biotechnol. 22: 17-23.

(55) Hashimoto, C., Hashimoto, M., Honda, H., and Kato, J. (2013) Effects on IS1 transposition frequency of a mutation in the ygjD gene involved in an essential tRNA Modification in Escherichia coli. FEMS Microbiology Letter. 347: 140-148.

(56) Nishimura, T., Hayashi, K., Suzuki, H., Gyohda, A., Takaoka, C., Sakaguchi, Y., Matsumoto, S., Kasahara, H., Sakai, T., Kato, J., Kamiya, Y., and Koshiba, T. (2014) Yucasin is a potent inhibitor of YUCCA, a key enzyme in auxin biosynthesis. The Plant Journal. 77: 352-366.

(57) Kurata, T., Nakanishi, S., Hashimoto, M., Taoka, M., Yamazaki, Y., Isobe, T., and Kato, J. (2015) Novel essential gene involved in 16S rRNA processing in Escherichia coli. J Mol. Biol. 427: 955-965.

(58) Watanabe, K., Tominaga, K., Kitamura, M., and Kato, J. (2016) Systematic identification of synthetic lethal mutations with reduced-genome Escherichia coli: synthetic genetic interactions among yoaA, xthA and holC related to survival from MMS exposure. Genes Genet. Syst. 91: 183-188.

(59) Iwadate, Y., Funabasama, N. and Kato, J. (2017) Involvement of formate dehydrogenases in stationary phase oxidative stress tolerance in Escherichia coli. FEMS Microbiology Letter. 364(20). doi: 10.1093/femsle/fnx193.

(60) Iwadate, Y. and Kato, J. (2017) Involvement of the ytfK gene from the PhoB regulon in stationary-phase H2O2 stress tolerance in Escherichia coli. Microbiology. 163: 1912-1923.

(61) Kurata, T., Nakanishi, S., Hashimoto, M., Taoka, M., Isobe, T., and Kato, J. (2018) Subunit composition of ribosome in the yqgF mutant deficient in pre-16S rRNA processing of Escherichia coli. J. Mol. Microbiol. Biotechnol. 28:179–182.

(62) Iwadate, Y. and Kato, J. (2019) Identification of a Formate-Dependent Uric Acid Degradation Pathway in Escherichia coli. J. Bacteriol. 201: e00573-18.

(63) Kotaka, Y., Hashimoto, M., Lee, K., and Kato, J. (2023) Mutations identified in engineered Escherichia coli with a reduced genome. Front. Microbiol. 14:1189877. doi: 10.3389/fmicb.2023.1189877

(64) Kotaka, Y., Nagai, T., Tominaga, K., Kurata, T., Iwasaki, W., Nobe, Y., Taoka, M., Asano, T., and Kato, J. (2025) Involvement of Escherichia coli unconventional G protein, YchF, in cell growth at the stationary phase. Genes & Genetic Systems in press