Kishino, R., Saito, T., Muto, S., Tomita, Y., Sekine, Y. Insertion sequence excision is enhanced by a protein that catalyzes branch migration and promotes microhomology-mediated end joining. Genes Cells, 29, 131-149 (2024)
Soma, A., Kubota, A., Tomoe, D., Ikeuchi, Y., Kawamura, F., Arimoto, H., Shiwa, Y., Kanesaki, Y., Nanamiya, H., Yoshikawa, H., Suzuki, T., Sekine, Y. yaaJ, the tRNA-specific adenosine deaminase, is dispensable in Bacillus subtilis. Genes (Basel). 2023 Jul 25;14(8):1515. doi: 10.3390/genes14081515. PMID: 37628567; PMCID: PMC10454642..
Sudo, N., Lee, K., Sekine, Y., Ohnishi, M., Iyoda, S . : RNA-binding protein Hfq downregulates locus of enterocyte effacement-encoded regulators independent of small regulatory RNA in enterohemorrhagic Escherichia coli. Mol Microbiol. 117, 86-101 (2022)
Ogawa, A., Kojima, F., Miyake, Y., Yoshimura, M., Ishijima, N., Iyoda, S., Sekine, Y., Yamanaka, Y., Yamamoto, K. : Regulation of constant cell elongation and Sfm pili synthesis in Escherichia coli via two active forms of FimZ orphan response regulator. Genes to Cells 27, 657-674 (2022)
Deyama T, Matsui Y, Chadani Y, Sekine Y, Doi N, Fujiwara K. (2021) Transcription-translation of the Escherichia coli genome within artificial cells.Chem Commum (Camb) 2021 Oct 7; 57(80):10367-10370
Sudo N, Lee K, Sekine Y, Ohnishi M, Iyoda S. (2021) RNA-binding protein Hfq downregulates locus of enterocyte effacement-encoded regulators independent of small regulatory RNA in enterohemorrhagic Escherichia coli. Mol Microbiol. doi: 10.1111/mmi.14799.
Odahara M, Nakamura K, Sekine Y & Oshima T. (2021) Ultra-deep sequencing reveals dramatic alteration of organellar genomes in Physcomitrella patens due to biased asymmetric recombination. Communication Biology. 2021 4:633 doi.org/10.1038/s42003-021-02141-x
Kobayashi Y, Odahara M, Sekine Y, Hamaji T, Fujiwara S, Nishimura Y, Miyagishima SY. (2020) Holliday junction resolvase MOC1 maintains plastid and mitochondrial genome integrity in algae and bryophytes.Plant Physiol. 2020 Sep 25;pp.00763.2020. doi: 10.1104/pp.20.00763.
Odahara M, Sekine Y. (2018) RECX interacts with mitochondrial RECA to maintain mitochondrial genome stability. Plant Physiol. 2018 Mar 26. doi: 10.1104/pp.18.00218.
Sudo N, Soma A, Iyoda S, Oshima T, Ohto Y, Saito K, Sekine Y. (2018) Small RNA Esr41 inversely regulates expression of LEE and flagellar genes in enterohaemorrhagic Escherichia coli. Microbiology. 2018 Mar 26. doi: 10.1099/mic.0.000652.
Mitsunaka S, Sudo N, Sekine Y. (2017) Lysogenisation of Shiga toxin-encoding bacteriophage represses cell motility.J Gen Appl Microbiol. 2017 Dec 8. doi: 10.2323/jgam.2017.05.001.
Kobayashi Y, Misumi O, Odahara M, Ishibashi K, Hirono M, Hidaka K, Endo M, Sugiyama H, Iwasaki H, Kuroiwa T, Shikanai T, Nishimura Y. (2017) Holliday junction resolvases mediate chloroplast nucleoid segregation. Science. 2017 May 12;356(6338):631-634.
Odahara M, Kishita Y, Sekine Y MSH1 maintains organelle genome stability and genetically interacts with RECA and RECG in the moss Physcomitrella patens. Plant Journal (2017) Aug 91(3):455-465.
Odahara M, Kobayashi Y, Shikanai T, Nishimura Y Dynamic interplay between nucleoid segregation and genome integrity in Chlamydomonas chloroplasts. Plant Physiology (2016) Dec;172(4):2337-2346.
Odahara M, Inouye T, Nishimura Y and Sekine Y. (2016) PCR-based Assay for Genome Integrity after Methyl Methanesulfonate Damage in Physcomitrella patens. Bio-protocol (2016) 6(19): e1954. DOI: 10.21769/BioProtoc.1954
Odahara M, Inouye T, Nishimura Y, Sekine Y. RECA plays a dual role in the maintenance of chloroplast genome stability in Physcomitrella patens. Plant Journal (2015) Nov;84(3):516-26.
Odahara M, Masuda Y, Sato M, Wakazaki, M, Harada C, Toyooka K, and Sekine Y. (2015) RECG maintains plastid and mitochondrial genome stability by suppressing extensive recombination between short dispersed repeats. PLoS Genet 11(3):e1005080. doi:10.1371/journal.pgen.1005080
Ohnuma M, Yokoyama T, Inouye T, Sekine Y, Kuroiwa T, and Tanaka K. (2014) Optimization of polyethylene glycol (PEG)-mediated DNA introduction conditions for transient gene expression in the unicellular red alga Cyanidioschyzon merolae. J Gen Appl Microbiol., 60:156-9.
Suzuki S, Tanigawa O, Akanuma G, Nanamiya H, Kawamura F, Tagami K, Nomura N, Kawabata T, and Sekine Y. (2014) Enhanced expression of Bacillus subtilis yaaA can restore both the growth and sporulation defects caused by mutation of rplB, encoding ribosomal protein L2. Microbiology, 160:1040–1053.
Sudo N, Soma A, Muto A, Iyoda S, Suh M, Kurihara N, Abe H, Tobe T, Ogura Y, Hayashi T, Kurokawa K, Ohnishi M, and Sekine Y. (2014) A novel small regulatory RNA enhances cell motility in enterohemorrhagic Escherichia coli. J Gen Appl Microbiol. 60:44-50.
Soma A, Sugahara J, Onodera A, Yachie N, Kanai A, Watanabe S, Yoshikawa H, Ohnuma M, Kuroiwa H, Kuroiwa T, and Sekine Y. (2013) Identification of highly-disrupted tRNA genes in nuclear genome of the red alga, Cyanidioschyzon merolae 10D. Sci. Rep. 3:2321. doi: 10.1038/srep02321
Akanuma G, Nanamiya H, Natori Y, Yano K, Suzuki S, Omata S, Ishizuka M, Sekine Y, and Kawamura F. (2012) Inactivation of ribosomal protein genes in Bacillus subtilis reveals importance of each ribosomal protein for cell proliferation and cell differentiation. J. Bacteriol. 194:6282-6291.
Imamura, S., Terashita, M., Ohnuma, M., Maruyama, S., Minoda, A., Weber, A. P. M., Inouye, T., Sekine, Y., Fujita, Y., Omata, T., and Tanaka, K. (2010) Nitrate assimilatory genes and their transcriptional regulation in a unicellular red alga Cyanidioschyzon merolae: Genetic evidence for nitrite reduction by a sulfite reductase-like enzyme. Plant & Cell Physiology, 51, 707-717.
Saito, T., Chibazakura, T., Takahashi, K., Yoshikawa, H., and Sekine, Y. (2010) Measurements of transposition frequency of insertion sequence IS1 by GFP hop-on assay. J. Gen. Appl. Microbiol. 56, 187-192.
Imamura, S., Kanesaki, Y., Ohnuma, M., Inouye, T., Sekine, Y., Fujiwara, T., Kuroiwa, T., and Tanaka, K. (2009) R2R3-type MYB transcription factor, CmMYB1, is a central nitrogen assimilation regulator in Cyanidioschyzon merolae. Proc. Natl. Acad. Sci. U S A, 106, 12548 12553.
Odahara M, Kuroiwa H, Kuroiwa T, Sekine Y. (2009) Suppression of repeat-mediated gross mitochondrialgenome rearrangements by RecA in the moss Physcomitrella patens. Plant Cell, 21, 1182 1194
Inouye, T., Odahara, M., Fujita, T., Hasebe, M., and Sekine, Y. (2008) Expression and complementation analyses of a chloroplast-localized homologue of bacterial RecA in the moss, Physcomitrella patens. Biosci. Biotechnol. Biochem., 72, 1340-1347.
Ohnuma, M., Yokoyama, T., Inouye, T., Sekine, Y., and Tanaka, K. (2008) Polyethylene glycol (PEG)-mediated transient gene expression in a red alga, Cyanidioschyzon merolae 10D. Plant & Cell Physiology, 49, 117-120.
Soma, A., Onodera, A., Sugahara, J., Kanai, A., Yachie, N., Tomita, M., Kawamura, F., and Sekine, Y. (2007) Permuted tRNA genes expressed via a circular RNA intermediate in Cyanidioschyzon merolae. Science, 318(5849):450-453.
Takahashi, K., Sekine, Y., Chibazakura, T., and Yoshikawa, H. (2007) Development of an intermolecular transposition assay system in Bacillus subtilis 168 using IS4Bsu1 from Bacillus subtilis (natto). Microbiology, 153, 2553-2559.
Terasawa, K,, Odahara, M., Kabeya, Y., Kikugawa, T., Sekine, Y., Fujiwara, M., and Sato, N.(2007) The Mitochondrial Genome of the Moss Physcomitrella patens Sheds New Light on Mitochondrial Evolution in Land Plants. Mol. Biol. Evol. 24, 699-709.
Takahashi, K., Chibazakura, T., Sekine, Y., Yoshikawa, H. (2007) Development of a new “GFP hop-on assay” system for insertion sequence transposition in Bacillus subtilis 168 using IS4Bsu1 from B. subtilis (natto). Biochem. Biophys. Res. Commun., 355, 426-30.
Odahara, M., Inouye, T., Fujita, T., Hasebe, M., and Sekine, Y. (2007) Involvement of mitochondrial-targeted RecA in the repair of mitochondrial DNA in the moss, Physcomitrella patens. Genes & Genetic Systems, 82, 43-51.
Sugahara, J., Yachie, N. Sekine, Y., Soma, A., Matsui, M., Tomita M., and Kanai, A. (2006) SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level. In Silico Biology, 6, 411-418.
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.
Nakanishi, K., Fukai, S., Ikeuchi, Y., Soma, A. , Sekine, Y., Suzuki, T.,and Nureki, O. (2005) Structural basis for lysidine formation by ATP pyrophosphatase accompanied with a lysine-specific loop and a tRNA-recognition domain. Proc. Natl. Acad.Sci. USA,102, 7487-7492.
Ohtsubo, E., Minematsu, H., Tsuchida, K.,Choi, S., Ohtsubo, H., and Sekine, Y.(2004) Intermediate molecules generated by transposase in the pathway of transposition of bacterial insertion elementIS3. Adv. Biophys. 38,125- 139
Soma, A., Ikeuchi, Y., Kanemasa, S., Kobayashi, K., Ogasawara, N., Ote, T., Kato, J., Watanabe, K., Sekine, Y.,Suzuki,T. (2003) An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA. Mol. Cell. 12, 689-698.
Ohta, S., Tsuchida, K., Choi, S., Sekine, Y., Shiga, Y., Ohtsubo, E. (2002) Presence of a Characteristic D-D-E Motif in IS1 Transposase. J. Bacteriol. 184, 6146-6154
Urasaki, A., Sekine, Y. and Ohtsubo, E. (2002) Transposition of cyanobacterium insertion element ISY100 in Escherichia coli. J. Bacteriol. 184, 5104-5112.
Shiga, Y., Sekine, Y., Kano, Y. and Ohtsubo, E. (2001) Involvement of H-NS in transpositional recombination mediated by IS1.J. Bacteriol.183, 2476-2484
Inokuchi, Y., Hirashima, A., Sekine, Y., Janosi, L. and Kaji, A. (2000) Role of ribosome recycling factor (RRF) in translational coupling. EMBO J., 19, 3788-3798.
Janosi, L., Mori, H., Sekine, Y., Abragan, J., Janosi, R., Hirokawa, G. and Kaji, A. (2000) Mutations influencing the frr gene coding for ribosome recycling factor (RRF). J. Mol. Biol. 295, 815-829
Sekine, Y., Aihara, K., and Ohtsubo, E. (1999) Linearization and transposition of circular molecules of insertion sequence IS3. J. Mol. Biol. 294, 21-34.
Shiga, Y., Sekine, Y. and Ohtsubo, E. (1999) Transposition of IS1 circles. Genes to Cells, 4, 551-561.
Janosi, L., Mottagui-Tabar, S., Isaksson, L. A., Sekine, Y., Ohtsubo, E., Zhang, S., Goon, S., Nelken, S., Shuda, M. and Kaji, A. (1998) Evidence for in vivo ribosome recycling, the fourth step in protein biosynthesis. EMBO J., 17, 1141-1151.
Sekine, Y, Izumi, K., Mizuno, T. and Ohtsubo, E. (1997) Inhibition of transpositional recombination by OrfA and OrfB proteins encoded by insertion sequence IS3. Genes to Cells, 2, 547-557.
Sekine, Y., Eisaki, N., Kobayashi, K. and Ohtsubo, E. (1997) Isolation and characterization of IS1 circles. Gene, 191, 183-190. required for production of thetransposase encoded by insertion sequence 1.Proc. Natl. Acad. Sci. USA, 86, 4609-4613.
Sekine, Y., Eisaki, N. and Ohtsubo, E. (1996)Identification and characterization of the linear IS3 molecules generated by staggered breaks.J. Biol. Chem., 271, 197-202.
Ohtsubo, E. and Sekine, Y. (1996)Bacterial insertion sequences. Cur. Topics Microbiol. Immunol., 204, 1-26.
Sekino, N., Sekine, Y. and Ohtsubo, E. (1995)IS1-encoded proteins, InsA and the InsA-B'-InsB transframe protein (transposase): Functions deduced from their DNA-binding ability. Adv. Biophys., 31, 209-222.
Sekine, Y., Eisaki, N. and Ohtsubo, E. (1994)Translational control in production of transposase and in transposition of insertion sequence IS3. J. Mol. Biol., 235, 1406-1420.
Sekine, Y and Ohtsubo, E. (1992) DNA sequences required for translational frameshifting in production of transposase encoded by IS1.Mol. Gen. Genet., 235, 325-332.
Sekine, Y and Ohtsubo, E. (1992) DNA sequences required for translational frameshifting in production of transposase encoded by IS1.Mol. Gen. Genet., 235, 325-332.
Sekine, Y., Nagasawa, H. and Ohtsubo, E. (1992)Identification of the site of translational frameshifting requierd for production of the transposase encoded by insertion sequence IS1. Mol. Gen. Genet., 235, 317-324.
Sekine, Y. and Ohtsubo, E. (1991) Translational frameshifting in IS elements and other genetic systems. pp. 243-261. In: New Aspects of The Genetics of Molecular Evolution, Edited by Kimura, M. and Takahata,N.,Japan Scientific Societies Press, Tokyo / Springer-Verlag, Berlin.
Sekine, Y and Ohtsubo, E. (1989) Frameshifting is required for production of the transposase encoded by insertion sequence 1. Proc. Natl. Acad. Sci. U S A., 86, 4609-4613..
