Synthetic Bioengineering Research Group


  • Miyazaki K, Tomariguchi N, Ueno Y (2021) Complete genome sequences of four halophilic Thermus thermophilus strains isolated from Arima Hot Spring in Japan. Microbiol Resour Announc (in press)
  • Kimura T (2021) Stability and safety of inhibitor cystine knot peptide, GTx1-15, from the Tarantula spider Grammostola rosea. Toxins 13(9):621
  • Miyazaki K, Moriya T, Tokito N, Oshima T, Yura K, Bessho Y (2021) Complete genome sequences of Thermus thermophilus strains HB5002 and HB5008, isolated from Mine Hot Spring in Japan. Microbiology Resource Announcements 10(16):e00272-21
  • Miyazaki K, Moriya T, Nemoto N, Oshima T, Yura K, Bessho Y (2021) Complete genome sequence of Thermus thermophilus strain HB5018, isolated from Mine Hot Spring in Japan. Microbiology Resource Announcements 10(10):e00039-21
  • Miyazaki K, Suenaga H, Oshiki M, Kawano S, Fukushima T (2021) Complete genome sequence of Thiohalobacter sp. strain COW1, isolated from activated sludge treating coke oven wastewater. Microbiol Resour Announc 10(7):e00013-21


  • Umemura M, Kuriiwa K, Tamano K, Kawarabayasi Y (2020) Ustiloxin Biosynthetic Machinery Is Not Compatible between Aspergillus flavus and Ustilaginoidea virens. Fungal Genet Biol 143:103434
  • Umemura M (2020) Peptides derived from Kex2‑processed repeat proteins are widely distributed and highly diverse in the fungi kingdom. Fungal Biol Biotechnol 7:11
  • Miyazaki K, Wiseschart A, Pootanakit K, Kitahara K (2020) Complete genome sequence of Vibrio rotiferianus strain AM7. Microbiol Resour Announc 9(21):e01591-19
  • Miyazaki K, Hase E, Tokito N (2020) Complete genome sequence of Geobacillus sp. strain E55-1, isolated from Mine Geyser in Japan. Microbiol Resour Announc 9:e00339-20
  • Reddy GK, Leferink NGH, Umemura M, Ahmed ST, Breitling R, Scrutton NS, Takano E (2020) Exploring novel bacterial terpene synthases. PLoS One 15(4):e0232220
  • Yoshimura Y, Nagashima I, Yokoe T, Kishimoto T, Shimizu H, Chiba Y (2020) A New Strategy for the Chemoenzymatic Synthesis of Glycopeptides by De-O-acetylation With an Esterase and Glycosylations With Glycosyltransferases. Carbohydr Res 492:108023
  • Miyazaki K, Hase E, Maruya T (2020) Complete genome sequence of Pseudomonas otitidis strain MrB4, isolated from Lake Biwa in Japan. Microbiol Resour Announc 9(16):e00148-20
  • Miyazaki K, Hase E, Maruya T (2020) Complete genome sequence of Bacillus cereus strain PL1, isolated from soil in Japan. Microbiol Resour Announc 9(12):e00195-20
  • Tomariguchi N, Miyazaki K (2020) Complete genome sequences of Rhodothermus marinus strains AA2-13 and AA3-38, isolated from Arima Onsen hot spring in Japan. Microbiol Resour Announc 9(2):e.01475-19
  • Umemura M, Kuriiwa K, Dao LV, Okuda T, Terai G (2020) Promoter tools for further development of Aspergillus oryzae as a platform for fungal secondary metabolite production. Fungal Biol Biotechnol 7:3


  • Miyazaki K, Izumi K (2019) Complete genome sequence of Alteromonas sp. strain I4, isolated from the Japan sea. Microbiol Resour Announc 8(47):e01277-19
  • Yu H, Taniguchi M, Uesaka K., Wiseschart A, Pootanakit K, Nishitani Y, Murakami Y, Ishimori K, Miyazaki K, Kitahara K (2019) Complete genome sequence of Staphylococcus arlettae strain P2 isolated from laboratory environment. Microbiol Resour Announc 8(45):e00696-19
  • Yoshimura Y, Denda-Nagai K, Takahashi Y, Nagashima I, Shimizu H, Kishimoto T, Noji M, Shichino S, Chiba Y, Irimura T (2019) Products of Chemoenzymatic Synthesis Representing MUC1 Tandem Repeat Unit With T-, ST- Or STn-antigen Revealed Distinct Specificities of Anti-MUC1 Antibodies. Sci Rep 9(1):16641
  • Tamano K, Kuninaga M, Kojima N, Umemura M, Machida M, Koike H (2019) Use of the kojA promoter, involved in kojic acid biosynthesis, for polyketide production in Aspergillus oryzae: implications for long-term production. BMC Biotechnol. 19(1):709
  • Miyazaki K (2019) Complete genome sequencing of Thermus thermophilus strain HC11, isolated from Mine geyser in Japan. Microbiol Resour Announc 8(39):e00873-19
  • Zhang Y, Minagawa Y, Kizoe H, Miyazaki K, Iino R, Ueno H, Tabata KV, Shimane Y, Noji H (2019) Accurate high-throughput screening based on digital protein synthesis in a massively parallel femtoliter droplet array. Sci Adv 5(8): eaav8185
  • Miyazaki K, Tomariguchi N (2019) Occurrence of randomly recombined functional 16S rRNA genes in Thermus thermophilus suggests genetic interoperability and promiscuity of bacterial 16S rRNAs. Sci Rep 9:11233.
  • Tomariguchi N, Miyazaki K (2019) Complete genome sequence of Rubrobacter xylanophilus strain AA3-22, isolated from Arima Onsen hot spring in Japan. Microbiol Resour Announc 8(34):e00818-19
  • Miyazaki K, Tomariguchi N (2019) Complete genome sequences of Thermus thermophilus strains AA2-20 and AA2-29, isolated from Arima Onsen in Japan. Microbiol Resour Announc 8(31):e00820-19
  • Falconer, AMD; Chan, CM; Gray, J; Nagashima, I; Holland, RA; Shimizu, H; Pickford, AR; Rowan, AD; Wilkinson, DJ.(2019)Collagenolytic matrix metalloproteinases antagonise proteinase-activated receptor-2 activation, providing insights into extracellular matrix turnover. J Biol Chem 28;294(26):10266-10277
  • Yamasaki K, Kubota T, Yamasaki T, Nagashima I, Shimizu H, Terada RI, Nishigami H, Kang J, Tateno M, Tateno H.(2019)Structural basis for specific recognition of core fucosylation in N-glycans by Pholiota squarrosa lectin (PhoSL). Glycobiology 29(7):576-587


  • Ye Y, Ozaki T, Umemura M, Liu C, Minami A, Oikawa H (2018) Heterologous production of asperipin-2a: proposal for sequential oxidative macrocyclization by a fungi-specific DUF3328 oxidase. Org Biomol Chem. 2018 Dec 19;17(1):39-43. doi: 10.1039/c8ob02824a.
  • Honda Y, Nakano S, Ito S, Dadashipour M, Zhang Z, Kawarabayasi Y (2018) Improvement of ST0452 N-Acetylglucosamine-1-Phosphate Uridyltransferase Activity by the Cooperative Effect of Two Single Mutations Identified through Structure-Based Protein Engineering. Appl Environ Microbiol 84(24). oi: 10.1128/AEM.02213-18
  • Miyazaki K (2018) Molecular engineering of the salicylate-inducible transcription factor Sal7AR for orthogonal and high gene expression in Escherichia coli. PLoS One 13(4):e0194090
  • Kitahara K, Miyazaki K (2018) Constructing mutant ribosomes containing mutant ribosomal RNAs. in Applied RNA Bioscience (eds. Masuda S and Izawa S, Springer) doi:10.1007/978-981-10-8372-3_2
  • Miyazaki K, Kitahara K (2018) Functional metagenomic approach to identify overlooked antibiotic resistance mutations in bacterial rRNA. Sci Rep 8:5179
  • Dadashipour M, Iwamoto M, Hossain MM, Akutsu JI, Zhang Z, Kawarabayasi Y (2018) Identification of direct biosynthetic pathway for UDP-N-acetylgalactosamine from glucosamine-6-phosphate in a thermophilic Crenarchaeon, Sulfolobus tokodaii. J Bacteriol 24;200(10):e00048-18


  • Sato M, Miyazaki K (2017) Phylogenetic network analysis revealed the occurrence of horizontal gene transfer of 16S rRNA in the genus Enterobacter. Front Microbiol 8:2225
  • Tsukuda M, Kitahara K, Miyazaki K (2017) Comparative RNA function analysis reveals high functional similarity between distantly related bacterial 16 S rRNAs. Sci Rep 7: 9993
  • Tamano K, Miura A, Koike H, Kamisaka Y, Umemura M, Machida M (2017) High-efficiency extracellular release of free fatty acids from Aspergillus oryzae using non-ionic surfactants. J Biotechnol 248:9-14
  • Miyazaki K, Sato M, Tsukuda M (2017) PCR primer design for 16S rRNAs for experimental horizontal gene transfer test in Escherichia coli. Front Bioeng Biotechnol 5:14


  • Honda Y, Zang Q, Shimizu Y, Dadashipour M, Zhang Z, Kawarabayasi Y (2016) Increasing the thermostable sugar-1-phosphate nucleotidylyltransferase activities of archaeal ST0452 protein through site-saturation mutagenesis of the 97th amino acid position. Appl Environ Microbiol. 2016 Nov 18. pii: AEM.02291-16. [Epub ahead of print]
  • Kamisaka Y, Kimura K, Uemura H, Ledesma-Amaro R (2016) Modulation of gluconeogenesis and lipid production in an engineered oleaginous Saccharomyces cerevisiae transformant. Appl Microbiol Biotechnol 100(18):8147-8157
  • Baweja M, Nain L, Kawarabayasi Y, Shukla P (2016) Current Technological Improvements in Enzymes toward Their Biotechnological Applications. Front Microbiol 16;7:965.
  • Hirano T, Tanidokoro K, Shimizu Y, Kawarabayasi Y, Ohshima T, Sato M, Tadano S, Ishikawa H, Takio S, Takechi K, Takano H (2016) Moss Chloroplasts Are Surrounded by a Peptidoglycan Wall Containing D-Amino Acids. Plant Cell 28(7):1521-32.
  • Roulling F, Godin A, Cipolla A, Collins T, Miyazaki K, Feller G (2016) Activity-stability relationships revisited in blue oxidases catalyzing electron transfer at extreme temperatures. Extremophiles 20(5):621-629
  • Wherland S, Miyazaki K, Pecht I (2016) Intramolecular Electron Transfer in the Bacterial Two-Domain Multicopper Oxidase mgLAC. Biochemistry 55(21):2960-2966.
  • Matsuzawa T, Jo T, Uchiyama T, Manninen JA, Arakawa T, Miyazaki K, Fushinobu S, Yaoi K (2016) Crystal structure and identification of a key amino acid for glucose tolerance, substrate specificity, and transglycosylation activity of metagenomic β-glucosidase Td2F2. FEBS J 283(12):2340-2353
  • Yamagami T, Matsukawa H, Tsunekawa S, Kawarabayasi Y, Ishino S, Ishino Y (2016) A longer finger-subdomain of family A DNA polymerases found by metagenomic analysis strengthens DNA binding and primer extension abilities. Gene 576:690-695


  • Uchiyama T, Yaoi K and Miyazaki K (2015) Glucose-tolerant β-glucosidase retrieved from a Kusaya gravy metagenome. Front Microbiol 6:548. doi: 10.3389/fmicb.2015.00548.
  • Tsukuda M, Nakashima N, Miyazaki K (2015) Counterselection method based on conditional silencing of antitoxin genes in Escherichia coli. J Biosci Bioeng 120(5):591-595.
  • Miyazaki K (2015) Molecular engineering of a PheS counterselection marker for improved operating efficiency in Escherichia coli. Biotechniques 58(2):86-88.
  • Kamisaka Y, Kimura K, Uemura H, Yamaoka M (2015) Addition of methionine and low cultivation temperatures increase palmitoleic acid production by engineered Saccharomyces cerevisiae. Appl Microbiol Biotechnol 99(1):201-210
  • Ueda T, Ishino S, Suematsu K, Nakashima T, Kakuta Y, Kawarabayasi Y, Ishino Y, Kimura M (2015) Mutation of the gene encoding the ribonuclease P RNA in the hyperthermophilic archaeon Thermococcus kodakarensis causes decreased growth rate and impaired processing of tRNA precursors. Biochem Biophys Res Commun 468(4):660-665
  • Akutsu J, Zhang Z, Morita R, Kawarabayasi Y (2015) Identification and characterization of a thermostable bifunctional enzyme with phosphomannose isomerase and sugar-1-phosphate nucleotidylyltransferase activities from a hyperthermophilic archaeon, Pyrococcus horikoshii OT3. Extremophiles 19(6):1077-1085


  • Kimura K, Kamisaka Y, Uemura H, Yamaoka M (2014) Increase in stearidonic acid by increasing the supply of histidine to oleaginous Saccharomyces cerevisiae. J Biosci Bioeng 117(1):53-56
  • Suenaga H, Mizuta S, Miyazaki K, Yaoi K (2014) Diversity of extradiol dioxygenases in aromatic-degrading microbial community explored using both culture-dependent and culture-independent approaches. FEMS Microbiol Ecol 90(2):367-379
  • Komori H, Sugiyama R, Kataoka K, Miyazaki K, Higuchi Y, Sakurai T (2014) New insights into the catalytic active-site structure of multicopper oxidases. Acta Crystallogr Sect D 70(3):772-779.
  • Nakashima N, Miyazaki K (2014) Bacterial cellular engineering by genome editing and gene silencing. Int J Mol Sci 15(2):2773-2793.
  • Miyazaki K (2014) Extradiol dioxygenases retrieved from the metagenome. in Nelson K. (Ed.) Encyclopedia of Metagenomics: Springer Reference ( Springer-Verlag Berlin Heidelberg, 2013. DOI: 10.1007/SpringerReference_364978 2014-01-07 17:15:16 UTC
  • Miyazaki K (2014) Diversity and evolution of aromatic degradation pathway enzymes in an activated sludge. Biodegradative bacteria-How bacteria degrade, survive, adapt, and evolve (Nojiri, H.; Tsuda, M.; Fukuda, M.; Kamagata, Y. Eds.), Chapter 12 (pp 249-264) (Springer Japan), 10.1007/978-4-431-54520-0_12
  • Hiraguri Y, Aiba S (2014) Synthesis and radical polymerization of bio-based new cyclic ketene acetal, 2-Methylene-4-methyl-1,3-dioxepane. J Macromol Sci Part A, Pure and Applied Chemistry, 51(7):582-588
  • Watanabe N, Masubuchi D, Itoh M, Teradu S, Yazawa H, Uemura H (2014) Oral administration of whole dihomo-g-linolenic acid-producing Saccharomyces cerevisiae suppresses cutaneous inflammatory responses induced by croton oil application in mice. Appl Microbiol Biotechol 98(20):8697-8706.
  • Yazawa H, Ogiso M, Kumagai H, Uemura H (2014) Suppression of ricinoleic acid toxicity by ptl2 overexpression in fission yeast Schizosaccharomyces pombe. Appl Microbiol Biotechol 98(22):9325-9337


  • Tsujimura S, Asahi M, Goda-Tsutsumi M, Shirai O, Kano K, Miyazaki K (2013) Direct electron transfer of a metagenome-derived laccase fused to affinity tags near the electroactive copper site. Phys Chem Chem Phys 15(47):20585-20589
  • Uchiyama T, Miyazaki K (2013) Metagenomic screening for aromatic compound-responsive transcriptional regulators. PLoS One 8(9):e75795
  • Tsukuda M, Miyazaki K (2013) Directed evolution study unveiling key sequence factors that affect translation efficiency in Escherichia coli. J Biosci Bioeng 116(5):540-545
  • Tsukuda M, Miyazaki K (2013) DNA fragmentation caused by an overdose of Zeocin. J Biosci Bioeng 116(5):644-646
  • Uchiyama T, Miyazaki K, Yaoi K (2013) Characterization of a novel β-glucosidase from a compost microbial metagenome with strong transglycosylation activity. J Biol Chem 288(25):18325-18334
  • Engel K, Ashby D, Brady SF, Cowan DA, Doemer J, Edwards EA, Fiebig K, Martens EC, McCormac D, Mead DA, Miyazaki K, Moreno-Hagelsieb G, O’Gara F, Reid A, Rose DR, Simonet P, Sjöling S, Smalla K, Streit WR, Tedman-Jones J, Valla S, Wellington EMH, Wu C-C, Liles MR, Neufeld JD, Sessitsch A, Charles TC (2013) Meeting Report: 1st International Functional Metagenomics Workshop May 7–8, 2012, St. Jacobs, Ontario, Canada. Stand Genomic Sci 8(1):106-111
  • Kitahara K, Miyazaki K (2013) Revisiting bacterial phylogeny: Natural and experimental evidence for horizontal gene transfer of 16S rRNA. Mob Genet Elements 3(1):e24210
  • Verma D, Kawarabayasi Y, Miyazaki K, Satyanarayana T (2013) Cloning, expression and characteristics of a novel alkalistable and thermostable xylanase encoding gene (mxyl) retrieved from compost-soil metagenome. PLoS One 8(1):e52459
  • Yazawa H, Kumagai H, Uemura H (2013) Secretory production of ricinoleic acid in fission yeast Schizosaccharomyces pombe. Appl Microbiol Biotech 97(19):8663-8671
  • Yazawa H, Kumagai H, Uemura H (2013) Toxicity of ricinoleic acid production in fission yeast Schizosaccharomyces pombe< is suppressed by the overexpression of plg7, phospholipase A2 of a platelet-activating factor (PAF) family homolog. Appl Microbiol Biotech 97(18):8193-8203.
  • Kamisaka Y, Kimura K, Uemura H, Yamaoka M (2013) Overexpression of the active diacylglycerol acyltransferase variant transforms Saccharomyces cerevisiae into an oleaginous yeast. Appl Microbiol Biotech 97(16):7345-7355


  • Kitahara K, Yasutake Y, Miyazaki K (2012) Mutational robustness of 16S ribosomal RNA, shown by experimental horizontal gene transfer in Escherichia coli. Proc Natl Acad Sci USA 109(47):19220-19225
  • Yaoi K, Miyazaki K (2012) Cloning and Expression of Isoprimeverose-producing oligoxyloglucan hydrolase from Actinomycetes Species, Oerskovia sp. Y1. J Appl Glycosci 59(2):83-88
  • Im DH, Kimura K, Hayasaka F, Tanaka T, Noguchi M, Kobayashi A, Shoda S, Miyazaki K, Wakagi T, Fushinobu S (2012) Crystal structures of glycoside hydrolase family 51 α-L-arabinofuranosidase from Thermotoga maritima. Biosci Biotechnol Biochem 76(2):423-428
  • Yazawa H, Kumagai H, Uemura H (2012) Characterization of triglyceride lipase genes of fission yeast Schizosaccharomyces pombe. Appl Microbiol Biotech 96(4):981-991
  • Matsuzawa T, Hara F, Tohda H, Uemura H, Takegawa K (2012) Promotion of glycerol utilization using ethanol and 1-propanol in Schizosaccharomyces pombe. Appl Microbiol Biotech 95(2):441-449
  • Holic R, Yazawa H, Kumagai H, Uemura H (2012) Engineered high content of ricinoleic acid in fission yeast Schizosaccharomyces pombe. Appl Microbiol Biotech 95(1):179-187


  • Kitahara K, Miyazaki K (2011) Specific inhibition of bacterial RNase T2 by helix 41 of 16S ribosomal RNA. Nat Commun 2:549
  • Hosokawa-Okamoto R, Miyazaki K (2011) Escherichia coli host engineering for efficient metagenomic enzyme discovery. in “Metagenomics: Current Innovations and Future Trends” (ed. Diana Marco, pp. 241-252, Horizon Scientific Press)
  • Miyazaki K (2011) MEGAWHOP Cloning: A method of creating random mutagenesis libraries via megaprimer PCR of whole plasmids. in “Synthetic Biology: Methods for Building and Programming Life” Part B Volume 498:399-406. (Methods in Enzymology Series, ed. Chris Voigt, Elsevier)
  • Miyazaki K (2011) Novel aromatic degradation pathway genes and their organization as revealed by metagenomic analysis. in “Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats” (ed. Frans J. de Bruijn, pp. 439-450, Wiley-Blackwell)
  • Suenaga H, Miyazaki K (2011) Exploration of a microbial community for novel genetic resources using activity-based screening of a metagenomic library. in Metagenomics and its applications in agriculture, biomedicine and environmental studies (ed. Li RW, Nova Science Publishers, NY)
  • Yazawa H., Kamisaka Y, Kimura K, Yamaoka M, Uemura H (2011) Efficient accumulation of oleic acid in Saccharomyces cerevisiae caused by expression of rat elongase 2 gene (rELO2) and its contribution to tolerance to alcohols. Appl Microbiol Biotech 91(6):1593-1600.
  • Kamisaka Y, Goto R, Shibakami M, Yoshioka K, Sato Y (2011) Surface plasmon resonance analysis of interactions between diacylglycerol acyltransferase and its interacting factors. Biosci Biotech Biochem 75(6):1135-1139.