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成果発表（2011年以降）

2021

• 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
• 宮崎健太郎（2021）「リボソーム改変による好熱菌の低温適応進化」アグリバイオ 5(10):95-100 （北隆館）
• 宮崎健太郎（2021）「リボソーム改変による好熱菌の低温適応進化」細胞 53(4):49-53 （北隆館）

2020

• 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
• 清水弘樹“マイクロ波酵素反応の作用機序を解き明かす”, 化学と工業, 73(3), 236-237 (2020)

2019

• 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
• 横江孝之、大木裕太、長島生、高橋直之、清水弘樹* “低温マイクロ波利用が切り開いた糖ペプチド合成の汎用化”, 日本電磁波エネルギー応用学会論文誌, Vol3, 32-39 (2019)
• 宮崎健太郎（2019）「進化分子工学：進化によるものづくり」（2018年ノーベル化学賞解説論文）じっきょう理科資料 85:1-5（実教出版）
• 宮崎健太郎（2019）「進化分子工学：分子設計ツールとしての進化」（2018年ノーベル化学賞解説論文）科学2月号 1038:142-147（岩波書店）

2018

• 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
• 長島 生、清水 弘樹（2018）「マイクロ波を利用したペプチド・糖ペプチド固相合成」 化学と生物 56(12):811-818.
• 宮崎健太郎（2018）「進化分子工学：進化によるものづくり」（2018年ノーベル化学賞解説論文）現代化学 12月号 573:21-25（東京化学同人）

2017

• 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

2016

• 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. doi: 10.1128/AEM.02291-16
• 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. doi: 10.1111/febs.13743.
• 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.

2015

• 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):660-5.
• 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):1077-85.

2014

• 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 (www.springerreference.com). 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.
• 宮崎健太郎（2014）「Ribosomal RNAの人工水平伝播による大腸菌宿主デザイン」生物工学会誌 92(11):607-611.
• 宮崎健太郎（2014）「リボソーム改変による大腸菌宿主デザイン」環境バイオテクノロジー学会誌 14(1):3-8.
• 佐藤允治（2014）「水平伝播による腸内細菌目16S rRNAの進化」日本ゲノム微生物学会 ニュースレター 9:9.
• 宮崎健太郎、佃美雪、佐藤允治（2014）「16S rRNA遺伝子の「水平伝播」― 異種16S rRNAによる遺伝的相補」化学と生物 52(2):70-72.

2013

• 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.
• 宮崎健太郎（2013）「生物種を超えた16S rRNA遺伝子の機能相補性の解明」　進化分子工学　～高速分子進化によるタンパク質・核酸の開発～（エヌ・ティー・エス）

2012

• 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.
• 宮崎健太郎（2012）「進化分子工学の事始」生命システム工学 進化分子工学から進化生命工学へ（化学同人）
• 宮崎健太郎（2012）「遺伝子資源の多様化」生命システム工学 進化分子工学から進化生命工学へ（化学同人）
• 宮崎健太郎（2012）「リボソームに翻訳以外の機能がある ― リボヌクレアーゼ作用阻害」生体の科学 63(5):356-357.（医学書院）
• 宮崎健太郎（2012）「リボソームに翻訳以外の機能を発見：16S rRNA ヘリックス41によるリボヌクレアーゼT2の阻害」, 産総研TODAY 12, 20.

2011

• 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.
• 宮崎健太郎（2011）「メタゲノムからの有用酵素の探索」（特集：新規有用酵素を探索せよ）バイオインダストリー 28(9):32-38.（シーエムシー出版）